<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Are you running a trained gene predictor? Perhaps the predictor does not like something about the area, so even with hints, it cannot make a sensible model. Non-canonical splice sites, runs of NNN, internal stop codons (indicates assembly issue in the region) can be the cause.<br class=""><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 17, 2020, at 9:22 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear Maker developper, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I use a transcipt and a protein file with MAKER, here is the intermediate GFF after the blast :</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">###</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx translated_nucleotide_match<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157392<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>137<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hit:0:3.6.0.0;Name=Tsi_rna</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157186<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157392<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>263<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:0:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 259 465 -;Gap=M69</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157218<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157391<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>284<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:1:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 291 464 -;Gap=M58</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157193<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157390<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>241<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:2:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 266 463 -;Gap=M66</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156985<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157056<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>87<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:3:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 223 294 -;Gap=M24</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156990<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157055<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>96<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:4:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 228 293 -;Gap=M22</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156880<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156993<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>166<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:5:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 117 230 -;Gap=M38</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156879<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156986<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>154<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:6:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 116 223 -;Gap=M36</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156881<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156985<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>141<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:7:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 118 222 -;Gap=M35</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153762<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153845<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>128<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:8:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 3 86 -;Gap=M28</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153761<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153844<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>134<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:9:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 2 85 -;Gap=M28</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>tblastx match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153843<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>137<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>-<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:10:3.6.0.0;Parent=ctg889_racon_pilon3:hit:0:3.6.0.0;Target=Tsi_rna 1 84 -;Gap=M28</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>cdna2genome<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>expressed_sequence_match<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157392<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>2022<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hit:1:3.6.0.0;Name=Tsi_rna</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>cdna2genome<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153845<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>2022<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:11:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 1 86 +;Gap=M86</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>cdna2genome<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>155744<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>155774<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>2022<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:12:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 87 117 +;Gap=M31</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>cdna2genome<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156881<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157055<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>2022<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:13:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 118 293 +;Gap=M105 I1 M70</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>cdna2genome<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157221<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157392<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>2022<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:14:3.6.0.0;Parent=ctg889_racon_pilon3:hit:1:3.6.0.0;Target=Tsi_rna 294 465 +;Gap=M172</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>blastx<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein_match<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157389<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>133<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hit:2:3.10.0.0;Name=TSI_CENPA</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>blastx<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153846<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>133<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:15:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 1 29;Gap=M29</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>blastx<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156881<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156994<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>191<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:16:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 40 77;Gap=M38</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>blastx<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156985<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157389<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>314<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:17:3.10.0.0;Parent=ctg889_racon_pilon3:hit:2:3.10.0.0;Target=TSI_CENPA 75 154;Gap=M19 D35 M4 D20 M57</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein2genome<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein_match<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157389<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>668<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hit:3:3.10.0.0;Name=TSI_CENPA</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein2genome<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153760<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>153845<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>668<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:18:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 1 28;Gap=M28 F2</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein2genome<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>155744<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>155774<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>668<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:19:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 29 39;Gap=R2 M11</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein2genome<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>156881<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157055<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>668<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:20:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 40 97;Gap=M35 I1 M1 F2 M20 F1 F1</span></div><div style="margin: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span class="s1" style="font-variant-ligatures: no-common-ligatures;">ctg889_racon_pilon3<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>protein2genome<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>match_part<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157221<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>157389<span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>668<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>+<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>.<span class="Apple-converted-space"> </span><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>ID=ctg889_racon_pilon3:hsp:21:3.10.0.0;Parent=ctg889_racon_pilon3:hit:3:3.10.0.0;Target=TSI_CENPA 98 154;Gap=R2 M57</span></div><br class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">There is obviously a gene here but at the end I don't have anything annotated by MAKER, why ?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks for your help.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class="">Patrick Tran Van<br class=""><br class="">Bioinformatician: Lab Chapuisat & Schwander<span class="Apple-converted-space"> </span><br class="">Department of Ecology and Evolution<br class="">University of Lausanne<br class="">Lausanne - Switzerland<br class="">Office 3206</div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:maker-devel@yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@yandell-lab.org</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>