Multiple sequence alignment - TraesCS6B01G275400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G275400 chr6B 100.000 2359 0 0 1 2359 497880391 497882749 0.000000e+00 4357
1 TraesCS6B01G275400 chr6B 85.052 194 24 5 1587 1780 125173026 125173214 2.390000e-45 193
2 TraesCS6B01G275400 chr6A 91.785 2398 151 21 1 2359 463541563 463539173 0.000000e+00 3295
3 TraesCS6B01G275400 chr6D 95.009 1643 60 13 732 2359 325403830 325402195 0.000000e+00 2560
4 TraesCS6B01G275400 chr6D 87.208 727 69 9 13 719 325404537 325403815 0.000000e+00 806
5 TraesCS6B01G275400 chr4D 85.714 301 37 2 1032 1332 397686403 397686109 1.760000e-81 313
6 TraesCS6B01G275400 chr2B 86.207 116 13 3 1648 1763 594271446 594271334 3.180000e-24 122
7 TraesCS6B01G275400 chr7A 85.217 115 14 3 1649 1763 691597125 691597236 5.330000e-22 115


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G275400 chr6B 497880391 497882749 2358 False 4357 4357 100.0000 1 2359 1 chr6B.!!$F2 2358
1 TraesCS6B01G275400 chr6A 463539173 463541563 2390 True 3295 3295 91.7850 1 2359 1 chr6A.!!$R1 2358
2 TraesCS6B01G275400 chr6D 325402195 325404537 2342 True 1683 2560 91.1085 13 2359 2 chr6D.!!$R1 2346

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
430 441 0.11358 AAAGGCCCACCCATAACGTT 59.886 50.0 5.88 5.88 36.11 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1556 0.236711 CACGGAGCAAACAAGCAGAG 59.763 55.0 0.0 0.0 36.85 3.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.179192 CCATGCATTGTCGTGTTCCG 60.179 55.000 0.00 0.00 38.13 4.30
24 25 0.795698 CATGCATTGTCGTGTTCCGA 59.204 50.000 0.00 0.00 45.00 4.55
38 39 2.224523 TGTTCCGATCTCCAAAGCACTT 60.225 45.455 0.00 0.00 0.00 3.16
97 98 0.662619 CTTCACCTCTTGCGCACAAA 59.337 50.000 11.12 0.00 34.74 2.83
128 129 0.537143 TGCATGGCCGTGAAGAAAGT 60.537 50.000 29.54 0.00 0.00 2.66
130 131 0.443869 CATGGCCGTGAAGAAAGTCG 59.556 55.000 21.08 0.00 0.00 4.18
152 153 2.270434 TGACTAGAGGGGGCTTTCAT 57.730 50.000 0.00 0.00 0.00 2.57
158 159 1.785208 AGAGGGGGCTTTCATGCATAT 59.215 47.619 0.00 0.00 34.04 1.78
171 172 7.255381 GCTTTCATGCATATCCTTATCAACACT 60.255 37.037 0.00 0.00 0.00 3.55
190 191 2.350895 CCCAACATGTCTCCCGCA 59.649 61.111 0.00 0.00 0.00 5.69
208 209 1.992277 AGAGGCTTGCTGACCCGAT 60.992 57.895 0.00 0.00 0.00 4.18
254 255 7.841956 TCTTCCTTCAATTATCTCGAGTCTTT 58.158 34.615 13.13 0.00 0.00 2.52
255 256 7.761704 TCTTCCTTCAATTATCTCGAGTCTTTG 59.238 37.037 13.13 11.98 0.00 2.77
267 268 7.397892 TCTCGAGTCTTTGAAGTAGATCATT 57.602 36.000 13.13 0.00 0.00 2.57
282 283 6.995091 AGTAGATCATTAACTTCTCCATTGGC 59.005 38.462 0.00 0.00 0.00 4.52
284 285 6.060788 AGATCATTAACTTCTCCATTGGCTC 58.939 40.000 0.00 0.00 0.00 4.70
296 306 1.783250 ATTGGCTCCGGATCCATCCC 61.783 60.000 26.95 10.54 44.24 3.85
335 346 2.007049 GCCATCACCACCACTACTTCG 61.007 57.143 0.00 0.00 0.00 3.79
365 376 3.484407 GATGTGAAGGATTAGGCATGCT 58.516 45.455 18.92 6.26 34.29 3.79
369 380 2.773661 TGAAGGATTAGGCATGCTCTCA 59.226 45.455 18.92 5.12 30.78 3.27
371 382 2.121948 AGGATTAGGCATGCTCTCACA 58.878 47.619 18.92 1.91 0.00 3.58
378 389 1.495878 GCATGCTCTCACACGATAGG 58.504 55.000 11.37 0.00 43.77 2.57
392 403 0.255033 GATAGGGCCCAAGGACGTTT 59.745 55.000 27.56 1.16 28.84 3.60
395 406 1.228459 GGGCCCAAGGACGTTTTCT 60.228 57.895 19.95 0.00 0.00 2.52
401 412 1.128692 CCAAGGACGTTTTCTCGATGC 59.871 52.381 0.00 0.00 34.70 3.91
430 441 0.113580 AAAGGCCCACCCATAACGTT 59.886 50.000 5.88 5.88 36.11 3.99
432 443 1.001887 GGCCCACCCATAACGTTGA 60.002 57.895 11.99 0.00 0.00 3.18
440 451 5.163693 CCCACCCATAACGTTGATAAAAGAC 60.164 44.000 11.99 0.00 0.00 3.01
441 452 5.413213 CCACCCATAACGTTGATAAAAGACA 59.587 40.000 11.99 0.00 0.00 3.41
450 461 7.090953 ACGTTGATAAAAGACAAGTTCCAAA 57.909 32.000 0.00 0.00 0.00 3.28
454 465 8.626526 GTTGATAAAAGACAAGTTCCAAAGGTA 58.373 33.333 0.00 0.00 0.00 3.08
459 470 5.304686 AGACAAGTTCCAAAGGTATCACA 57.695 39.130 0.00 0.00 0.00 3.58
466 477 0.392998 CAAAGGTATCACAGCCGCCT 60.393 55.000 0.00 0.00 0.00 5.52
468 479 1.264749 AAGGTATCACAGCCGCCTGA 61.265 55.000 0.00 0.00 41.77 3.86
539 550 3.369787 CCTGTTGTATCATGCACCTCTCA 60.370 47.826 0.00 0.00 0.00 3.27
553 564 3.941483 CACCTCTCAATGATGGTTGGTAC 59.059 47.826 5.53 0.00 0.00 3.34
554 565 3.846588 ACCTCTCAATGATGGTTGGTACT 59.153 43.478 2.87 0.00 0.00 2.73
555 566 5.030147 ACCTCTCAATGATGGTTGGTACTA 58.970 41.667 2.87 0.00 0.00 1.82
556 567 5.487488 ACCTCTCAATGATGGTTGGTACTAA 59.513 40.000 2.87 0.00 0.00 2.24
557 568 6.012858 ACCTCTCAATGATGGTTGGTACTAAA 60.013 38.462 0.00 0.00 0.00 1.85
573 592 5.468072 GGTACTAAATCGAGGTGATAGACGA 59.532 44.000 0.00 0.00 35.84 4.20
586 605 5.266242 GTGATAGACGATGAATTTGCCAAC 58.734 41.667 0.00 0.00 0.00 3.77
588 607 2.795329 AGACGATGAATTTGCCAACCT 58.205 42.857 0.00 0.00 0.00 3.50
637 656 6.906157 AATCATCAGATTGGTTTTGACACT 57.094 33.333 0.00 0.00 42.72 3.55
787 835 1.829523 TTGCCCAAGAAATGCAGCCC 61.830 55.000 0.00 0.00 36.21 5.19
843 903 2.224159 AGGATCCTGTTGGGCGTGT 61.224 57.895 15.29 0.00 34.39 4.49
857 917 1.900981 CGTGTGGCCCAACATGGAA 60.901 57.895 0.00 0.00 40.96 3.53
859 919 1.900981 TGTGGCCCAACATGGAACG 60.901 57.895 0.00 0.00 40.96 3.95
867 927 1.404047 CCAACATGGAACGGGAAATGC 60.404 52.381 0.00 0.00 40.96 3.56
934 994 2.657143 CCCTAAACGCTCCTACTCTCT 58.343 52.381 0.00 0.00 0.00 3.10
935 995 2.619646 CCCTAAACGCTCCTACTCTCTC 59.380 54.545 0.00 0.00 0.00 3.20
946 1006 1.766496 CTACTCTCTCCTCGGTCCTCT 59.234 57.143 0.00 0.00 0.00 3.69
1159 1219 4.283467 ACGCAGTTGATAGCCTTATCCATA 59.717 41.667 0.00 0.00 37.78 2.74
1250 1310 2.291457 TAATGTCGCTGCTGCCGCTA 62.291 55.000 14.02 0.00 36.97 4.26
1454 1515 1.338769 ACCTTCCTTTATCTTGCGCGT 60.339 47.619 8.43 0.00 0.00 6.01
1495 1556 4.034975 GCTTAGCATGGTGAAGAATCTGAC 59.965 45.833 7.89 0.00 0.00 3.51
1496 1557 3.996921 AGCATGGTGAAGAATCTGACT 57.003 42.857 0.00 0.00 0.00 3.41
1511 1572 1.534595 CTGACTCTGCTTGTTTGCTCC 59.465 52.381 0.00 0.00 0.00 4.70
1591 1652 0.674581 TGGTCGTCGTCGTATCACCT 60.675 55.000 10.83 0.00 38.33 4.00
1601 1662 3.490249 CGTCGTATCACCTAAATGCCAGA 60.490 47.826 0.00 0.00 0.00 3.86
1602 1663 4.439057 GTCGTATCACCTAAATGCCAGAA 58.561 43.478 0.00 0.00 0.00 3.02
1813 1874 1.522806 TGCTGTTCCACGGTGACAC 60.523 57.895 10.28 6.23 0.00 3.67
1833 1894 2.036733 ACCACTGTGCGTAGTAACATGT 59.963 45.455 1.29 0.00 0.00 3.21
1917 1978 2.106511 ACATGTCAGTGCTACCTTTGGT 59.893 45.455 0.00 0.00 40.16 3.67
1930 1991 3.243724 ACCTTTGGTTCTCTCTAGCTGT 58.756 45.455 0.00 0.00 27.29 4.40
1960 2021 6.210984 CACTCCATACTATACCTCCTTTACCC 59.789 46.154 0.00 0.00 0.00 3.69
1962 2023 6.882155 TCCATACTATACCTCCTTTACCCAT 58.118 40.000 0.00 0.00 0.00 4.00
2017 2078 8.668353 CATACTATAAGCCAATAACGATTGCAT 58.332 33.333 0.00 0.00 41.09 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.438434 GGAGTTCAAGTGCTTTGGAGATC 59.562 47.826 2.44 0.00 37.39 2.75
24 25 3.181440 TGGAGTTCAAGTGCTTTGGAGAT 60.181 43.478 2.44 0.00 37.39 2.75
38 39 3.627395 ACTTGTTCACAGTGGAGTTCA 57.373 42.857 0.00 0.00 0.00 3.18
128 129 0.851469 AGCCCCCTCTAGTCATACGA 59.149 55.000 0.00 0.00 0.00 3.43
130 131 3.039011 TGAAAGCCCCCTCTAGTCATAC 58.961 50.000 0.00 0.00 0.00 2.39
152 153 4.136796 GGCAGTGTTGATAAGGATATGCA 58.863 43.478 0.00 0.00 32.92 3.96
158 159 2.107378 TGTTGGGCAGTGTTGATAAGGA 59.893 45.455 0.00 0.00 0.00 3.36
171 172 2.350895 CGGGAGACATGTTGGGCA 59.649 61.111 0.00 0.00 0.00 5.36
190 191 1.965754 GATCGGGTCAGCAAGCCTCT 61.966 60.000 5.89 0.00 43.82 3.69
197 198 0.690192 TCTTTTGGATCGGGTCAGCA 59.310 50.000 0.00 0.00 0.00 4.41
208 209 7.554118 GGAAGATGATGTAGTTGATCTTTTGGA 59.446 37.037 0.00 0.00 35.71 3.53
222 223 8.860088 TCGAGATAATTGAAGGAAGATGATGTA 58.140 33.333 0.00 0.00 0.00 2.29
254 255 9.605275 CAATGGAGAAGTTAATGATCTACTTCA 57.395 33.333 21.40 10.41 46.37 3.02
255 256 9.050601 CCAATGGAGAAGTTAATGATCTACTTC 57.949 37.037 16.12 16.12 45.04 3.01
267 268 1.209504 CCGGAGCCAATGGAGAAGTTA 59.790 52.381 2.05 0.00 0.00 2.24
273 274 1.072159 GGATCCGGAGCCAATGGAG 59.928 63.158 33.57 0.00 36.74 3.86
316 326 1.275291 ACGAAGTAGTGGTGGTGATGG 59.725 52.381 0.00 0.00 41.94 3.51
365 376 0.616395 TTGGGCCCTATCGTGTGAGA 60.616 55.000 25.70 0.00 0.00 3.27
369 380 1.306654 TCCTTGGGCCCTATCGTGT 60.307 57.895 25.70 0.00 0.00 4.49
371 382 2.432300 CGTCCTTGGGCCCTATCGT 61.432 63.158 25.70 0.00 0.00 3.73
378 389 1.574702 CGAGAAAACGTCCTTGGGCC 61.575 60.000 0.00 0.00 0.00 5.80
395 406 0.391130 CTTTCCCTCGTTGGCATCGA 60.391 55.000 18.55 18.55 35.96 3.59
419 430 6.713450 ACTTGTCTTTTATCAACGTTATGGGT 59.287 34.615 0.00 0.00 0.00 4.51
424 435 7.789273 TGGAACTTGTCTTTTATCAACGTTA 57.211 32.000 0.00 0.00 0.00 3.18
430 441 8.934023 ATACCTTTGGAACTTGTCTTTTATCA 57.066 30.769 0.00 0.00 0.00 2.15
432 443 8.793592 GTGATACCTTTGGAACTTGTCTTTTAT 58.206 33.333 0.00 0.00 0.00 1.40
440 451 3.191371 GGCTGTGATACCTTTGGAACTTG 59.809 47.826 0.00 0.00 0.00 3.16
441 452 3.421844 GGCTGTGATACCTTTGGAACTT 58.578 45.455 0.00 0.00 0.00 2.66
450 461 1.680522 CTCAGGCGGCTGTGATACCT 61.681 60.000 34.57 2.47 0.00 3.08
454 465 1.260538 TTCTCTCAGGCGGCTGTGAT 61.261 55.000 34.46 2.83 0.00 3.06
459 470 2.665603 GGTTTCTCTCAGGCGGCT 59.334 61.111 5.25 5.25 0.00 5.52
492 503 7.309012 GGGTGTAAGGGTTTTACAGAAGATTTC 60.309 40.741 0.33 0.00 35.77 2.17
505 516 4.105057 TGATACAACAGGGTGTAAGGGTTT 59.895 41.667 0.70 0.00 37.52 3.27
539 550 6.055588 CCTCGATTTAGTACCAACCATCATT 58.944 40.000 0.00 0.00 0.00 2.57
553 564 6.242508 TCATCGTCTATCACCTCGATTTAG 57.757 41.667 0.00 0.00 40.29 1.85
554 565 6.628919 TTCATCGTCTATCACCTCGATTTA 57.371 37.500 0.00 0.00 40.29 1.40
555 566 5.515797 TTCATCGTCTATCACCTCGATTT 57.484 39.130 0.00 0.00 40.29 2.17
556 567 5.713792 ATTCATCGTCTATCACCTCGATT 57.286 39.130 0.00 0.00 40.29 3.34
557 568 5.713792 AATTCATCGTCTATCACCTCGAT 57.286 39.130 0.00 0.00 42.44 3.59
573 592 4.686191 TTTGTGAGGTTGGCAAATTCAT 57.314 36.364 15.30 0.00 0.00 2.57
586 605 8.755941 CATATTCACTACTAACGATTTGTGAGG 58.244 37.037 0.00 0.00 36.12 3.86
588 607 9.863845 TTCATATTCACTACTAACGATTTGTGA 57.136 29.630 0.00 0.00 33.41 3.58
622 641 4.035017 CGTGTTCAGTGTCAAAACCAATC 58.965 43.478 0.00 0.00 0.00 2.67
687 706 7.385752 AGAATAGTTCGTTCGGTTACAAAATGA 59.614 33.333 0.00 0.00 34.02 2.57
688 707 7.477422 CAGAATAGTTCGTTCGGTTACAAAATG 59.523 37.037 0.00 0.00 34.02 2.32
689 708 7.172019 ACAGAATAGTTCGTTCGGTTACAAAAT 59.828 33.333 0.00 0.00 31.48 1.82
723 744 8.644619 CGAATAACAAAATAGTTCGAGTTCTCA 58.355 33.333 0.00 0.00 42.94 3.27
724 745 8.645487 ACGAATAACAAAATAGTTCGAGTTCTC 58.355 33.333 12.03 0.00 42.94 2.87
725 746 8.530269 ACGAATAACAAAATAGTTCGAGTTCT 57.470 30.769 12.03 0.00 42.94 3.01
727 748 8.225777 GGAACGAATAACAAAATAGTTCGAGTT 58.774 33.333 12.03 0.00 42.94 3.01
728 749 7.736447 GGAACGAATAACAAAATAGTTCGAGT 58.264 34.615 12.03 0.79 42.94 4.18
843 903 2.282816 CCGTTCCATGTTGGGCCA 60.283 61.111 0.00 0.00 38.32 5.36
857 917 1.376812 GGAAGGACGCATTTCCCGT 60.377 57.895 1.98 0.00 42.31 5.28
859 919 1.095600 GAAGGAAGGACGCATTTCCC 58.904 55.000 8.34 0.00 43.12 3.97
867 927 2.269241 GGCTGGGAAGGAAGGACG 59.731 66.667 0.00 0.00 0.00 4.79
925 985 0.841289 AGGACCGAGGAGAGAGTAGG 59.159 60.000 0.00 0.00 0.00 3.18
934 994 2.359404 GTGGGAGAGGACCGAGGA 59.641 66.667 0.00 0.00 0.00 3.71
935 995 2.760385 GGTGGGAGAGGACCGAGG 60.760 72.222 0.00 0.00 0.00 4.63
988 1048 0.179936 GAGGCCATCTCTGAGGGTTG 59.820 60.000 5.01 1.03 39.38 3.77
1159 1219 1.995066 TCACAGATCCGGCACCCAT 60.995 57.895 0.00 0.00 0.00 4.00
1231 1291 3.195002 GCGGCAGCAGCGACATTA 61.195 61.111 3.18 0.00 44.35 1.90
1495 1556 0.236711 CACGGAGCAAACAAGCAGAG 59.763 55.000 0.00 0.00 36.85 3.35
1496 1557 0.463654 ACACGGAGCAAACAAGCAGA 60.464 50.000 0.00 0.00 36.85 4.26
1591 1652 7.888021 TGGAACTTCTTAGAATTCTGGCATTTA 59.112 33.333 18.47 0.00 0.00 1.40
1601 1662 7.839680 ACACCAAATGGAACTTCTTAGAATT 57.160 32.000 6.42 0.00 38.94 2.17
1602 1663 7.839680 AACACCAAATGGAACTTCTTAGAAT 57.160 32.000 6.42 0.00 38.94 2.40
1664 1725 3.003480 GTCAAACCATCTACAGTGAGCC 58.997 50.000 0.00 0.00 0.00 4.70
1813 1874 2.666508 GACATGTTACTACGCACAGTGG 59.333 50.000 0.00 0.00 37.35 4.00
1930 1991 4.833380 GGAGGTATAGTATGGAGTGCTGAA 59.167 45.833 0.00 0.00 0.00 3.02
1960 2021 7.602517 AAAATGTTTTCTCTCTCGGAGTATG 57.397 36.000 4.69 0.00 42.40 2.39
1989 2050 8.717821 GCAATCGTTATTGGCTTATAGTATGAA 58.282 33.333 0.00 0.00 42.39 2.57
1990 2051 7.875554 TGCAATCGTTATTGGCTTATAGTATGA 59.124 33.333 0.00 0.00 42.39 2.15
2073 2134 2.036346 GCCTGCAGAAACCAAATGTCTT 59.964 45.455 17.39 0.00 0.00 3.01
2268 2329 5.957774 ACTGCATAAAACATAGGGAAATGGT 59.042 36.000 0.00 0.00 0.00 3.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.