Multiple sequence alignment - TraesCS3B01G461000

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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 TraesCS3B01G461000 chr3B 100.000 2411 0 0 1 2411 704324117 704321707 0.000000e+00 4453
1 TraesCS3B01G461000 chr3B 79.612 309 54 7 1065 1367 147776316 147776621 1.880000e-51 213
2 TraesCS3B01G461000 chr3D 95.210 1002 38 9 1414 2411 532162055 532161060 0.000000e+00 1576
3 TraesCS3B01G461000 chr3D 95.287 488 20 1 1 485 532169857 532169370 0.000000e+00 771
4 TraesCS3B01G461000 chr3D 88.331 617 41 14 794 1410 532168924 532168339 0.000000e+00 712
5 TraesCS3B01G461000 chr3D 83.582 335 48 6 1062 1393 96677240 96677570 8.370000e-80 307
6 TraesCS3B01G461000 chr3A 92.296 636 29 8 915 1536 667351247 667350618 0.000000e+00 885
7 TraesCS3B01G461000 chr3A 93.621 486 24 2 3 485 667353551 667353070 0.000000e+00 719
8 TraesCS3B01G461000 chr3A 83.188 345 48 9 1052 1393 114544703 114545040 8.370000e-80 307
9 TraesCS3B01G461000 chr3A 80.531 226 44 0 1168 1393 112915900 112915675 8.860000e-40 174
10 TraesCS3B01G461000 chr2D 84.918 305 43 2 1075 1379 109076492 109076793 3.010000e-79 305
11 TraesCS3B01G461000 chr2B 84.345 313 46 2 1075 1387 158650536 158650845 1.080000e-78 303
12 TraesCS3B01G461000 chr2A 83.399 253 39 3 1077 1329 104978168 104978417 5.180000e-57 231


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 TraesCS3B01G461000 chr3B 704321707 704324117 2410 True 4453.0 4453 100.0000 1 2411 1 chr3B.!!$R1 2410
1 TraesCS3B01G461000 chr3D 532161060 532162055 995 True 1576.0 1576 95.2100 1414 2411 1 chr3D.!!$R1 997
2 TraesCS3B01G461000 chr3D 532168339 532169857 1518 True 741.5 771 91.8090 1 1410 2 chr3D.!!$R2 1409
3 TraesCS3B01G461000 chr3A 667350618 667353551 2933 True 802.0 885 92.9585 3 1536 2 chr3A.!!$R2 1533

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
346 354 0.533032 CGGGGAGAGAGAGGAACAAC 59.467 60.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 3281 0.038166 TTCTTCCATGGGACTGGCAC 59.962 55.0 13.02 0.0 36.16 5.01 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
121 122 1.227089 CGCGGCTGATGAAGTAGCT 60.227 57.895 0.00 0.00 39.80 3.32
310 311 2.166459 TCGATTCTTCTTGGATGCTCGT 59.834 45.455 0.00 0.00 0.00 4.18
311 312 3.380320 TCGATTCTTCTTGGATGCTCGTA 59.620 43.478 0.00 0.00 0.00 3.43
312 313 3.487574 CGATTCTTCTTGGATGCTCGTAC 59.512 47.826 0.00 0.00 0.00 3.67
313 314 2.561733 TCTTCTTGGATGCTCGTACG 57.438 50.000 9.53 9.53 0.00 3.67
334 342 1.826921 GCTGGTACGATCGGGGAGA 60.827 63.158 20.98 0.00 0.00 3.71
346 354 0.533032 CGGGGAGAGAGAGGAACAAC 59.467 60.000 0.00 0.00 0.00 3.32
469 477 4.076244 GGATACGGGCTCTCGCTA 57.924 61.111 0.00 0.00 36.09 4.26
470 478 2.338381 GGATACGGGCTCTCGCTAA 58.662 57.895 0.00 0.00 36.09 3.09
523 559 0.909610 TTGGTCCCCGCTCTCATCTT 60.910 55.000 0.00 0.00 0.00 2.40
532 568 1.202687 CGCTCTCATCTTGGCCCATTA 60.203 52.381 0.00 0.00 0.00 1.90
533 569 2.551721 CGCTCTCATCTTGGCCCATTAT 60.552 50.000 0.00 0.00 0.00 1.28
534 570 3.306989 CGCTCTCATCTTGGCCCATTATA 60.307 47.826 0.00 0.00 0.00 0.98
535 571 4.006319 GCTCTCATCTTGGCCCATTATAC 58.994 47.826 0.00 0.00 0.00 1.47
536 572 4.263243 GCTCTCATCTTGGCCCATTATACT 60.263 45.833 0.00 0.00 0.00 2.12
537 573 5.486526 CTCTCATCTTGGCCCATTATACTC 58.513 45.833 0.00 0.00 0.00 2.59
538 574 4.907269 TCTCATCTTGGCCCATTATACTCA 59.093 41.667 0.00 0.00 0.00 3.41
539 575 4.973168 TCATCTTGGCCCATTATACTCAC 58.027 43.478 0.00 0.00 0.00 3.51
540 576 4.411869 TCATCTTGGCCCATTATACTCACA 59.588 41.667 0.00 0.00 0.00 3.58
541 577 4.150897 TCTTGGCCCATTATACTCACAC 57.849 45.455 0.00 0.00 0.00 3.82
542 578 3.521531 TCTTGGCCCATTATACTCACACA 59.478 43.478 0.00 0.00 0.00 3.72
543 579 4.165950 TCTTGGCCCATTATACTCACACAT 59.834 41.667 0.00 0.00 0.00 3.21
544 580 5.368230 TCTTGGCCCATTATACTCACACATA 59.632 40.000 0.00 0.00 0.00 2.29
545 581 5.227569 TGGCCCATTATACTCACACATAG 57.772 43.478 0.00 0.00 0.00 2.23
546 582 4.041567 TGGCCCATTATACTCACACATAGG 59.958 45.833 0.00 0.00 0.00 2.57
547 583 4.286032 GGCCCATTATACTCACACATAGGA 59.714 45.833 0.00 0.00 0.00 2.94
548 584 5.482908 GCCCATTATACTCACACATAGGAG 58.517 45.833 0.00 0.00 37.18 3.69
549 585 5.012148 GCCCATTATACTCACACATAGGAGT 59.988 44.000 0.00 0.00 45.72 3.85
551 587 7.603651 CCCATTATACTCACACATAGGAGTAC 58.396 42.308 3.85 0.00 46.17 2.73
552 588 7.451877 CCCATTATACTCACACATAGGAGTACT 59.548 40.741 0.00 0.00 46.17 2.73
553 589 9.516546 CCATTATACTCACACATAGGAGTACTA 57.483 37.037 0.00 0.00 46.17 1.82
699 2094 3.063997 AGCTTTATATGTGCGTGAACAGC 59.936 43.478 0.00 0.00 32.52 4.40
701 2096 4.270084 GCTTTATATGTGCGTGAACAGCTA 59.730 41.667 0.00 0.00 32.52 3.32
704 2099 4.801147 ATATGTGCGTGAACAGCTATTG 57.199 40.909 0.00 0.00 32.52 1.90
717 2112 7.693951 GTGAACAGCTATTGAACATGTGAATAC 59.306 37.037 0.00 1.78 0.00 1.89
863 2452 2.036217 TCCAGAATCGTACACGGTTTGT 59.964 45.455 1.27 0.00 43.48 2.83
907 2534 1.274596 GTAATCCAGCACGTACACGG 58.725 55.000 6.72 0.00 44.95 4.94
909 2536 2.167398 AATCCAGCACGTACACGGCT 62.167 55.000 6.72 8.98 43.15 5.52
912 2539 3.359523 AGCACGTACACGGCTCGA 61.360 61.111 6.72 0.00 44.95 4.04
913 2540 2.202570 GCACGTACACGGCTCGAT 60.203 61.111 6.72 0.00 44.95 3.59
949 2576 3.558505 GATCAACATATACGTACGCGGT 58.441 45.455 16.72 0.39 43.45 5.68
958 2585 2.104859 CGTACGCGGTCTCTCTCCA 61.105 63.158 12.47 0.00 0.00 3.86
1111 2752 1.154580 GAGACAAACGCGCAGAAGC 60.155 57.895 5.73 0.00 37.42 3.86
1317 2958 3.304721 AGCAAGCAAATGGCCGCA 61.305 55.556 0.00 0.00 46.50 5.69
1320 2961 1.289694 CAAGCAAATGGCCGCAGAA 59.710 52.632 0.00 0.00 46.50 3.02
1331 2972 1.017387 GCCGCAGAAATCGAGGAATT 58.983 50.000 0.00 0.00 0.00 2.17
1410 3051 2.711542 GGGCCGGGTGATCAATATTAG 58.288 52.381 2.18 0.00 0.00 1.73
1427 3068 8.308207 TCAATATTAGGGGTTTGTTTTTAGCAC 58.692 33.333 0.00 0.00 0.00 4.40
1478 3119 4.880886 TGTGTATGGAGAATTTGATGCG 57.119 40.909 0.00 0.00 0.00 4.73
1485 3126 5.902613 TGGAGAATTTGATGCGAGATTTT 57.097 34.783 0.00 0.00 0.00 1.82
1486 3127 7.572523 ATGGAGAATTTGATGCGAGATTTTA 57.427 32.000 0.00 0.00 0.00 1.52
1488 3129 7.475015 TGGAGAATTTGATGCGAGATTTTAAG 58.525 34.615 0.00 0.00 0.00 1.85
1569 3211 8.380099 TGTATGTTTATACACTTCCTGTTCCTT 58.620 33.333 0.00 0.00 43.12 3.36
1570 3212 7.687941 ATGTTTATACACTTCCTGTTCCTTG 57.312 36.000 0.00 0.00 37.03 3.61
1628 3270 7.534085 AAAAAGAAGTTTTCCCGAAATGTTC 57.466 32.000 0.00 0.00 34.11 3.18
1639 3281 0.804989 GAAATGTTCCTGGCCACGAG 59.195 55.000 0.00 0.00 0.00 4.18
1657 3299 0.842030 AGTGCCAGTCCCATGGAAGA 60.842 55.000 15.22 0.00 43.57 2.87
1671 3313 5.702209 CCCATGGAAGAAAAATTTGGAGTTG 59.298 40.000 15.22 0.00 0.00 3.16
1940 3583 2.513897 GGCCGCGCCTAAACAGAT 60.514 61.111 0.00 0.00 46.69 2.90
1977 3620 3.461773 GCGAGCTCACCCAGGCTA 61.462 66.667 15.40 0.00 39.05 3.93
1983 3626 0.255890 GCTCACCCAGGCTAATTGGA 59.744 55.000 0.00 0.00 37.96 3.53
2126 3769 2.289890 AACGACGCTTTTAACGCTTC 57.710 45.000 0.00 0.00 0.00 3.86
2279 3923 9.132521 CAAAATCCAGAAAAGATGTTCATGTAC 57.867 33.333 0.00 0.00 0.00 2.90
2325 3969 9.793259 TTTATCAGAATAAATGTCCACCTATCC 57.207 33.333 0.00 0.00 33.41 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 0.037326 CCGCCTCAACAGCTACTTCA 60.037 55.000 0.00 0.00 0.00 3.02
121 122 4.680237 CCAGCGTCCGCCTCAACA 62.680 66.667 8.23 0.00 43.17 3.33
286 287 3.539604 AGCATCCAAGAAGAATCGAAGG 58.460 45.455 0.00 0.00 0.00 3.46
310 311 1.354155 CGATCGTACCAGCTGCGTA 59.646 57.895 8.66 9.51 0.00 4.42
311 312 2.102357 CGATCGTACCAGCTGCGT 59.898 61.111 8.66 10.58 0.00 5.24
312 313 2.655364 CCGATCGTACCAGCTGCG 60.655 66.667 15.09 7.07 0.00 5.18
313 314 2.279517 CCCGATCGTACCAGCTGC 60.280 66.667 15.09 0.00 0.00 5.25
334 342 0.319641 GTTCGCCGTTGTTCCTCTCT 60.320 55.000 0.00 0.00 0.00 3.10
346 354 2.954753 GCAACCAGAGTGTTCGCCG 61.955 63.158 0.00 0.00 0.00 6.46
409 417 1.808411 GGCGACACTTCCAGAAATCA 58.192 50.000 0.00 0.00 0.00 2.57
508 544 2.735772 GCCAAGATGAGAGCGGGGA 61.736 63.158 0.00 0.00 0.00 4.81
523 559 4.041567 CCTATGTGTGAGTATAATGGGCCA 59.958 45.833 9.61 9.61 0.00 5.36
556 592 1.133407 GTGTGAGTTCACCCGCAAAAA 59.867 47.619 9.60 0.00 45.88 1.94
557 593 0.736053 GTGTGAGTTCACCCGCAAAA 59.264 50.000 9.60 0.00 45.88 2.44
558 594 0.393132 TGTGTGAGTTCACCCGCAAA 60.393 50.000 9.60 0.00 45.88 3.68
559 595 0.179032 ATGTGTGAGTTCACCCGCAA 60.179 50.000 9.60 0.00 45.88 4.85
560 596 0.682292 TATGTGTGAGTTCACCCGCA 59.318 50.000 9.60 6.74 45.88 5.69
561 597 1.076332 GTATGTGTGAGTTCACCCGC 58.924 55.000 9.60 1.71 45.88 6.13
562 598 2.743636 AGTATGTGTGAGTTCACCCG 57.256 50.000 9.60 0.00 45.88 5.28
563 599 5.163754 GCATTAAGTATGTGTGAGTTCACCC 60.164 44.000 9.60 0.00 39.10 4.61
564 600 5.411361 TGCATTAAGTATGTGTGAGTTCACC 59.589 40.000 9.60 2.54 39.10 4.02
565 601 6.480524 TGCATTAAGTATGTGTGAGTTCAC 57.519 37.500 5.33 5.33 39.68 3.18
566 602 7.503521 TTTGCATTAAGTATGTGTGAGTTCA 57.496 32.000 0.00 0.00 36.57 3.18
605 1183 8.532977 AGCGTTCAATATTTGCATTAAGTTTT 57.467 26.923 0.00 0.00 0.00 2.43
613 1191 8.931385 ATTTAGAAAGCGTTCAATATTTGCAT 57.069 26.923 14.88 0.00 36.09 3.96
676 2071 4.581493 CTGTTCACGCACATATAAAGCTG 58.419 43.478 0.00 0.00 0.00 4.24
681 2076 6.045955 TCAATAGCTGTTCACGCACATATAA 58.954 36.000 0.00 0.00 0.00 0.98
789 2202 1.982612 CGAGCTTTAAGCCCTTTTGC 58.017 50.000 13.84 0.00 43.77 3.68
790 2203 1.541588 AGCGAGCTTTAAGCCCTTTTG 59.458 47.619 13.84 0.12 43.77 2.44
863 2452 7.493320 ACATCAGCGATTCGGTTTATAACTTAA 59.507 33.333 8.24 0.00 34.62 1.85
907 2534 3.105659 GCCAAAGCCTGATCGAGC 58.894 61.111 0.00 0.00 0.00 5.03
934 2561 2.735663 AGAGAGACCGCGTACGTATATG 59.264 50.000 17.90 3.80 37.70 1.78
958 2585 3.626930 AGGAAGCGTTCTCTACATCTCT 58.373 45.455 0.00 0.00 0.00 3.10
962 2589 6.049790 GGATTTTAGGAAGCGTTCTCTACAT 58.950 40.000 0.00 0.00 0.00 2.29
963 2590 5.187186 AGGATTTTAGGAAGCGTTCTCTACA 59.813 40.000 0.00 0.00 0.00 2.74
1223 2864 1.446272 GGGTCGTAGCAGTGCAGTC 60.446 63.158 19.20 6.03 0.00 3.51
1317 2958 5.941948 AAAACGTGAATTCCTCGATTTCT 57.058 34.783 21.10 5.00 33.58 2.52
1320 2961 5.243207 AGGTAAAACGTGAATTCCTCGATT 58.757 37.500 21.10 14.90 35.87 3.34
1331 2972 3.731652 TTTCCTCGAGGTAAAACGTGA 57.268 42.857 30.17 5.42 36.34 4.35
1410 3051 3.004944 TCATCGTGCTAAAAACAAACCCC 59.995 43.478 0.00 0.00 0.00 4.95
1427 3068 9.698309 AACCACATAGTAATCTTAGATTCATCG 57.302 33.333 11.06 1.00 0.00 3.84
1446 3087 4.724399 TCTCCATACACAAACAACCACAT 58.276 39.130 0.00 0.00 0.00 3.21
1562 3204 4.277476 ACTGTGAATCCAAACAAGGAACA 58.723 39.130 0.00 0.00 41.92 3.18
1569 3211 2.631160 ACGGACTGTGAATCCAAACA 57.369 45.000 0.00 0.00 35.83 2.83
1570 3212 3.432252 CAGTACGGACTGTGAATCCAAAC 59.568 47.826 20.22 0.00 46.88 2.93
1639 3281 0.038166 TTCTTCCATGGGACTGGCAC 59.962 55.000 13.02 0.00 36.16 5.01
1657 3299 3.177997 AGTGCGCAACTCCAAATTTTT 57.822 38.095 14.00 0.00 31.64 1.94
1684 3326 1.012486 CACGTTCCCCTACAGCGAAC 61.012 60.000 0.00 0.00 33.98 3.95
1940 3583 3.303461 CGCCAAACGGATTCGCAAATATA 60.303 43.478 0.00 0.00 40.63 0.86
1977 3620 1.677217 GCTTCAGACGGCTCTCCAATT 60.677 52.381 0.00 0.00 0.00 2.32
1983 3626 3.377759 AGCGCTTCAGACGGCTCT 61.378 61.111 2.64 0.00 0.00 4.09
1989 3632 3.549997 TTTTTGCAGCGCTTCAGAC 57.450 47.368 7.50 0.00 0.00 3.51
2126 3769 7.419204 TGTGGTTTTCCTTTCTTATAAACGTG 58.581 34.615 0.00 0.00 41.38 4.49


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

AutoCloner maintained by Alex Coulton.