Multiple sequence alignment - TraesCS5B01G269700

Loading Multiple Alignment...

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 TraesCS5B01G269700 chr5B 100.000 2255 0 0 1 2255 455626972 455629226 0 4165
1 TraesCS5B01G269700 chr1D 97.857 1680 34 2 577 2255 141314376 141312698 0 2902
2 TraesCS5B01G269700 chr2B 97.798 1680 35 2 577 2255 799246731 799248409 0 2896
3 TraesCS5B01G269700 chr7B 97.739 1681 36 1 577 2255 644466202 644467882 0 2892
4 TraesCS5B01G269700 chr7B 97.909 526 10 1 1 525 644460630 644460105 0 909
5 TraesCS5B01G269700 chrUn 97.679 1680 38 1 577 2255 225927012 225928691 0 2885
6 TraesCS5B01G269700 chrUn 98.286 525 9 0 1 525 395660661 395660137 0 920
7 TraesCS5B01G269700 chrUn 98.289 526 8 1 1 525 454076046 454075521 0 920
8 TraesCS5B01G269700 chrUn 97.909 526 10 1 1 525 384428970 384428445 0 909
9 TraesCS5B01G269700 chrUn 97.714 525 12 0 1 525 189404269 189403745 0 904
10 TraesCS5B01G269700 chr7A 97.619 1680 39 1 577 2255 60149528 60147849 0 2880
11 TraesCS5B01G269700 chr3A 97.619 1680 39 1 577 2255 633110013 633111692 0 2880
12 TraesCS5B01G269700 chr6B 97.381 1680 43 1 577 2255 306997231 306995552 0 2857
13 TraesCS5B01G269700 chr6B 97.917 528 10 1 1 527 307002793 307003320 0 913
14 TraesCS5B01G269700 chr1B 97.378 1678 43 1 579 2255 672477922 672479599 0 2854
15 TraesCS5B01G269700 chr1B 97.323 1681 42 3 577 2255 638701907 638700228 0 2852
16 TraesCS5B01G269700 chr1B 98.289 526 8 1 1 525 668811976 668812501 0 920
17 TraesCS5B01G269700 chr7D 97.909 526 10 1 1 525 382061865 382061340 0 909
18 TraesCS5B01G269700 chr6D 97.905 525 11 0 1 525 458909965 458909441 0 909


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 TraesCS5B01G269700 chr5B 455626972 455629226 2254 False 4165 4165 100.000 1 2255 1 chr5B.!!$F1 2254
1 TraesCS5B01G269700 chr1D 141312698 141314376 1678 True 2902 2902 97.857 577 2255 1 chr1D.!!$R1 1678
2 TraesCS5B01G269700 chr2B 799246731 799248409 1678 False 2896 2896 97.798 577 2255 1 chr2B.!!$F1 1678
3 TraesCS5B01G269700 chr7B 644466202 644467882 1680 False 2892 2892 97.739 577 2255 1 chr7B.!!$F1 1678
4 TraesCS5B01G269700 chr7B 644460105 644460630 525 True 909 909 97.909 1 525 1 chr7B.!!$R1 524
5 TraesCS5B01G269700 chrUn 225927012 225928691 1679 False 2885 2885 97.679 577 2255 1 chrUn.!!$F1 1678
6 TraesCS5B01G269700 chrUn 395660137 395660661 524 True 920 920 98.286 1 525 1 chrUn.!!$R3 524
7 TraesCS5B01G269700 chrUn 454075521 454076046 525 True 920 920 98.289 1 525 1 chrUn.!!$R4 524
8 TraesCS5B01G269700 chrUn 384428445 384428970 525 True 909 909 97.909 1 525 1 chrUn.!!$R2 524
9 TraesCS5B01G269700 chrUn 189403745 189404269 524 True 904 904 97.714 1 525 1 chrUn.!!$R1 524
10 TraesCS5B01G269700 chr7A 60147849 60149528 1679 True 2880 2880 97.619 577 2255 1 chr7A.!!$R1 1678
11 TraesCS5B01G269700 chr3A 633110013 633111692 1679 False 2880 2880 97.619 577 2255 1 chr3A.!!$F1 1678
12 TraesCS5B01G269700 chr6B 306995552 306997231 1679 True 2857 2857 97.381 577 2255 1 chr6B.!!$R1 1678
13 TraesCS5B01G269700 chr6B 307002793 307003320 527 False 913 913 97.917 1 527 1 chr6B.!!$F1 526
14 TraesCS5B01G269700 chr1B 672477922 672479599 1677 False 2854 2854 97.378 579 2255 1 chr1B.!!$F2 1676
15 TraesCS5B01G269700 chr1B 638700228 638701907 1679 True 2852 2852 97.323 577 2255 1 chr1B.!!$R1 1678
16 TraesCS5B01G269700 chr1B 668811976 668812501 525 False 920 920 98.289 1 525 1 chr1B.!!$F1 524
17 TraesCS5B01G269700 chr7D 382061340 382061865 525 True 909 909 97.909 1 525 1 chr7D.!!$R1 524
18 TraesCS5B01G269700 chr6D 458909441 458909965 524 True 909 909 97.905 1 525 1 chr6D.!!$R1 524

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
570 573 0.108585 AGTCCCGCAAGCTTTCTGAA 59.891 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1833 0.03563 CAGTGAAGGAAGGGAGCCTG 60.036 60.0 0.0 0.0 35.5 4.85 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
88 89 3.102204 TCAGCTGAATCTGATCAGTGGA 58.898 45.455 21.92 4.02 46.85 4.02
225 226 4.853007 CAGTCTGGGATCCTTTCTTGATT 58.147 43.478 12.58 0.00 0.00 2.57
287 290 0.541863 ATACAGCCAAGACTTCCGGG 59.458 55.000 0.00 0.00 0.00 5.73
324 327 5.300411 TCTCCCTTTTCTACGAAGGTTTT 57.700 39.130 0.00 0.00 41.70 2.43
503 506 5.324409 AGAGAGTGAGAGAAAGAGTGTGAT 58.676 41.667 0.00 0.00 0.00 3.06
509 512 6.491745 AGTGAGAGAAAGAGTGTGATACTTGA 59.508 38.462 0.00 0.00 40.53 3.02
518 521 1.550524 TGTGATACTTGAGCCGCTCTT 59.449 47.619 20.87 8.22 0.00 2.85
527 530 2.503331 TGAGCCGCTCTTCATTTCAAA 58.497 42.857 20.87 0.00 0.00 2.69
528 531 2.485426 TGAGCCGCTCTTCATTTCAAAG 59.515 45.455 20.87 0.00 0.00 2.77
529 532 1.815003 AGCCGCTCTTCATTTCAAAGG 59.185 47.619 0.00 0.00 0.00 3.11
530 533 1.541588 GCCGCTCTTCATTTCAAAGGT 59.458 47.619 0.00 0.00 0.00 3.50
531 534 2.029918 GCCGCTCTTCATTTCAAAGGTT 60.030 45.455 0.00 0.00 0.00 3.50
532 535 3.568538 CCGCTCTTCATTTCAAAGGTTG 58.431 45.455 0.00 0.00 0.00 3.77
533 536 3.004734 CCGCTCTTCATTTCAAAGGTTGT 59.995 43.478 0.00 0.00 0.00 3.32
534 537 3.976942 CGCTCTTCATTTCAAAGGTTGTG 59.023 43.478 0.00 0.00 0.00 3.33
535 538 3.737774 GCTCTTCATTTCAAAGGTTGTGC 59.262 43.478 0.00 0.00 0.00 4.57
536 539 3.963665 TCTTCATTTCAAAGGTTGTGCG 58.036 40.909 0.00 0.00 0.00 5.34
537 540 2.791383 TCATTTCAAAGGTTGTGCGG 57.209 45.000 0.00 0.00 0.00 5.69
538 541 1.339610 TCATTTCAAAGGTTGTGCGGG 59.660 47.619 0.00 0.00 0.00 6.13
539 542 1.339610 CATTTCAAAGGTTGTGCGGGA 59.660 47.619 0.00 0.00 0.00 5.14
540 543 1.028905 TTTCAAAGGTTGTGCGGGAG 58.971 50.000 0.00 0.00 0.00 4.30
555 558 2.156098 CGGGAGCTGATCTAGTAGTCC 58.844 57.143 0.00 0.00 0.00 3.85
556 559 2.521126 GGGAGCTGATCTAGTAGTCCC 58.479 57.143 5.72 5.72 36.51 4.46
557 560 2.156098 GGAGCTGATCTAGTAGTCCCG 58.844 57.143 0.00 0.00 0.00 5.14
558 561 1.538075 GAGCTGATCTAGTAGTCCCGC 59.462 57.143 0.00 0.00 0.00 6.13
559 562 1.133761 AGCTGATCTAGTAGTCCCGCA 60.134 52.381 0.00 0.00 0.00 5.69
560 563 1.681793 GCTGATCTAGTAGTCCCGCAA 59.318 52.381 0.00 0.00 0.00 4.85
561 564 2.287909 GCTGATCTAGTAGTCCCGCAAG 60.288 54.545 0.00 0.00 0.00 4.01
562 565 1.681793 TGATCTAGTAGTCCCGCAAGC 59.318 52.381 0.00 0.00 0.00 4.01
563 566 1.957877 GATCTAGTAGTCCCGCAAGCT 59.042 52.381 0.00 0.00 0.00 3.74
564 567 1.848652 TCTAGTAGTCCCGCAAGCTT 58.151 50.000 0.00 0.00 0.00 3.74
565 568 2.176889 TCTAGTAGTCCCGCAAGCTTT 58.823 47.619 0.00 0.00 0.00 3.51
566 569 2.165845 TCTAGTAGTCCCGCAAGCTTTC 59.834 50.000 0.00 0.00 0.00 2.62
567 570 0.977395 AGTAGTCCCGCAAGCTTTCT 59.023 50.000 0.00 0.00 0.00 2.52
568 571 1.079503 GTAGTCCCGCAAGCTTTCTG 58.920 55.000 0.00 0.00 0.00 3.02
569 572 0.973632 TAGTCCCGCAAGCTTTCTGA 59.026 50.000 0.00 0.00 0.00 3.27
570 573 0.108585 AGTCCCGCAAGCTTTCTGAA 59.891 50.000 0.00 0.00 0.00 3.02
571 574 0.951558 GTCCCGCAAGCTTTCTGAAA 59.048 50.000 0.00 2.44 0.00 2.69
572 575 1.068954 GTCCCGCAAGCTTTCTGAAAG 60.069 52.381 22.62 22.62 41.46 2.62
573 576 0.954452 CCCGCAAGCTTTCTGAAAGT 59.046 50.000 26.02 13.52 40.64 2.66
574 577 1.338020 CCCGCAAGCTTTCTGAAAGTT 59.662 47.619 26.02 19.96 40.64 2.66
575 578 2.552315 CCCGCAAGCTTTCTGAAAGTTA 59.448 45.455 26.02 0.00 40.64 2.24
633 636 8.566260 GCTCTAAATACAGATTCAAAGCATCAT 58.434 33.333 0.00 0.00 0.00 2.45
838 841 1.541588 GCCAAAGGCTTTCTCATTCGT 59.458 47.619 10.08 0.00 46.69 3.85
1005 1010 3.202906 GCTGGTTATCGAGTTTATGGCA 58.797 45.455 0.00 0.00 0.00 4.92
1160 1165 5.329399 TGGCCTATCTTCTTTAAAAAGCCA 58.671 37.500 3.32 0.00 43.97 4.75
1209 1214 5.715070 TGCGTTCCTTTTTCTTTGAAAAGA 58.285 33.333 10.70 1.31 45.20 2.52
1400 1406 8.682936 AAATCATTAAAGATATGCTCGACCTT 57.317 30.769 0.00 0.00 0.00 3.50
1622 1628 2.315720 AGCAAAGGGAGGCTGAAAAT 57.684 45.000 0.00 0.00 39.30 1.82
1625 1631 2.528564 CAAAGGGAGGCTGAAAATCCA 58.471 47.619 0.00 0.00 34.62 3.41
1636 1642 4.640201 GGCTGAAAATCCATAGTGCTAACA 59.360 41.667 0.00 0.00 0.00 2.41
1668 1674 8.352942 CCTGTAGTTTTGAAGCTAAAAAGACAT 58.647 33.333 15.53 5.47 31.53 3.06
1732 1738 3.738281 GCGCTACTCTTCCTTTATGAGCA 60.738 47.826 0.00 0.00 33.62 4.26
1750 1756 4.583907 TGAGCAAGACTCTATCCAGATCTG 59.416 45.833 16.24 16.24 46.41 2.90
1753 1759 4.522405 GCAAGACTCTATCCAGATCTGCTA 59.478 45.833 17.76 7.80 0.00 3.49
1859 1865 3.648067 TCCTTCACTGAACTGATTCACCT 59.352 43.478 0.00 0.00 40.01 4.00
1949 1955 2.598787 CCCCGCCTCCACTTGGTTA 61.599 63.158 0.00 0.00 36.34 2.85
1995 2001 6.239396 GGACTACTTCCTTAAAGAGCCTTTT 58.761 40.000 5.65 0.00 41.95 2.27
2176 2183 4.141665 TGGTACCCGAATCCATTTACGATT 60.142 41.667 10.07 0.00 32.62 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 2.481441 TGGTGGATTAGGCAGAGACAT 58.519 47.619 0.00 0.00 0.00 3.06
225 226 2.677836 GCTGCGTATTCAGATCCAAACA 59.322 45.455 0.00 0.00 36.19 2.83
503 506 3.262420 GAAATGAAGAGCGGCTCAAGTA 58.738 45.455 29.88 14.38 32.06 2.24
509 512 1.815003 CCTTTGAAATGAAGAGCGGCT 59.185 47.619 0.00 0.00 0.00 5.52
518 521 1.339610 CCCGCACAACCTTTGAAATGA 59.660 47.619 0.00 0.00 0.00 2.57
527 530 2.527951 GATCAGCTCCCGCACAACCT 62.528 60.000 0.00 0.00 39.10 3.50
528 531 2.045926 ATCAGCTCCCGCACAACC 60.046 61.111 0.00 0.00 39.10 3.77
529 532 0.175760 TAGATCAGCTCCCGCACAAC 59.824 55.000 0.00 0.00 39.10 3.32
530 533 0.461548 CTAGATCAGCTCCCGCACAA 59.538 55.000 0.00 0.00 39.10 3.33
531 534 0.684479 ACTAGATCAGCTCCCGCACA 60.684 55.000 0.00 0.00 39.10 4.57
532 535 1.268352 CTACTAGATCAGCTCCCGCAC 59.732 57.143 0.00 0.00 39.10 5.34
533 536 1.133761 ACTACTAGATCAGCTCCCGCA 60.134 52.381 0.00 0.00 39.10 5.69
534 537 1.538075 GACTACTAGATCAGCTCCCGC 59.462 57.143 0.00 0.00 0.00 6.13
535 538 2.156098 GGACTACTAGATCAGCTCCCG 58.844 57.143 0.00 0.00 0.00 5.14
536 539 2.521126 GGGACTACTAGATCAGCTCCC 58.479 57.143 0.00 6.28 0.00 4.30
537 540 2.156098 CGGGACTACTAGATCAGCTCC 58.844 57.143 0.00 1.33 0.00 4.70
538 541 1.538075 GCGGGACTACTAGATCAGCTC 59.462 57.143 0.00 0.00 0.00 4.09
539 542 1.133761 TGCGGGACTACTAGATCAGCT 60.134 52.381 0.00 0.00 0.00 4.24
540 543 1.319541 TGCGGGACTACTAGATCAGC 58.680 55.000 0.00 2.06 0.00 4.26
541 544 2.287909 GCTTGCGGGACTACTAGATCAG 60.288 54.545 0.00 0.00 0.00 2.90
542 545 1.681793 GCTTGCGGGACTACTAGATCA 59.318 52.381 0.00 0.00 0.00 2.92
543 546 1.957877 AGCTTGCGGGACTACTAGATC 59.042 52.381 0.00 0.00 0.00 2.75
544 547 2.074729 AGCTTGCGGGACTACTAGAT 57.925 50.000 0.00 0.00 0.00 1.98
545 548 1.848652 AAGCTTGCGGGACTACTAGA 58.151 50.000 0.00 0.00 0.00 2.43
546 549 2.166664 AGAAAGCTTGCGGGACTACTAG 59.833 50.000 0.00 0.00 0.00 2.57
547 550 2.094182 CAGAAAGCTTGCGGGACTACTA 60.094 50.000 0.00 0.00 0.00 1.82
548 551 0.977395 AGAAAGCTTGCGGGACTACT 59.023 50.000 0.00 0.00 0.00 2.57
549 552 1.079503 CAGAAAGCTTGCGGGACTAC 58.920 55.000 0.00 0.00 0.00 2.73
550 553 0.973632 TCAGAAAGCTTGCGGGACTA 59.026 50.000 0.00 0.00 0.00 2.59
551 554 0.108585 TTCAGAAAGCTTGCGGGACT 59.891 50.000 0.00 0.00 0.00 3.85
552 555 0.951558 TTTCAGAAAGCTTGCGGGAC 59.048 50.000 0.00 0.00 0.00 4.46
553 556 1.238439 CTTTCAGAAAGCTTGCGGGA 58.762 50.000 10.03 0.00 0.00 5.14
554 557 0.954452 ACTTTCAGAAAGCTTGCGGG 59.046 50.000 21.00 0.00 42.27 6.13
555 558 2.781945 AACTTTCAGAAAGCTTGCGG 57.218 45.000 21.00 0.00 42.27 5.69
556 559 5.034554 TCATAACTTTCAGAAAGCTTGCG 57.965 39.130 21.00 7.91 42.27 4.85
557 560 7.880059 ATTTCATAACTTTCAGAAAGCTTGC 57.120 32.000 21.00 0.00 42.27 4.01
565 568 9.886132 GGGACTACTAATTTCATAACTTTCAGA 57.114 33.333 0.00 0.00 0.00 3.27
566 569 8.818057 CGGGACTACTAATTTCATAACTTTCAG 58.182 37.037 0.00 0.00 0.00 3.02
567 570 7.767198 CCGGGACTACTAATTTCATAACTTTCA 59.233 37.037 0.00 0.00 0.00 2.69
568 571 7.767659 ACCGGGACTACTAATTTCATAACTTTC 59.232 37.037 6.32 0.00 0.00 2.62
569 572 7.627311 ACCGGGACTACTAATTTCATAACTTT 58.373 34.615 6.32 0.00 0.00 2.66
570 573 7.191593 ACCGGGACTACTAATTTCATAACTT 57.808 36.000 6.32 0.00 0.00 2.66
571 574 6.803366 ACCGGGACTACTAATTTCATAACT 57.197 37.500 6.32 0.00 0.00 2.24
572 575 7.720442 ACTACCGGGACTACTAATTTCATAAC 58.280 38.462 6.32 0.00 0.00 1.89
573 576 7.902920 ACTACCGGGACTACTAATTTCATAA 57.097 36.000 6.32 0.00 0.00 1.90
574 577 7.201938 CCAACTACCGGGACTACTAATTTCATA 60.202 40.741 6.32 0.00 0.00 2.15
575 578 6.407752 CCAACTACCGGGACTACTAATTTCAT 60.408 42.308 6.32 0.00 0.00 2.57
659 662 8.669243 GCTTTCTACTTAAATTGCTATGACTGT 58.331 33.333 0.00 0.00 0.00 3.55
1005 1010 1.228306 TTTTTGGATGGTCGGCGGT 60.228 52.632 7.21 0.00 0.00 5.68
1160 1165 8.887036 AAAGTTTTGCGAAATCCTTATCTTTT 57.113 26.923 1.61 0.00 0.00 2.27
1209 1214 3.495276 CGGCCCAAAAATGGTAAGGTTTT 60.495 43.478 0.00 0.00 0.00 2.43
1213 1218 0.108377 GCGGCCCAAAAATGGTAAGG 60.108 55.000 0.00 0.00 0.00 2.69
1400 1406 5.924356 ACGATGATACCATGGACATAAACA 58.076 37.500 21.47 8.65 33.43 2.83
1622 1628 1.404986 GGCGTGTGTTAGCACTATGGA 60.405 52.381 11.22 0.00 45.44 3.41
1625 1631 0.902531 AGGGCGTGTGTTAGCACTAT 59.097 50.000 11.22 0.00 46.53 2.12
1636 1642 2.218603 CTTCAAAACTACAGGGCGTGT 58.781 47.619 17.69 17.69 43.86 4.49
1703 1709 1.064296 GAAGAGTAGCGCGCTAGCA 59.936 57.895 39.08 20.25 45.49 3.49
1732 1738 7.240897 AGATTAGCAGATCTGGATAGAGTCTT 58.759 38.462 23.89 0.00 36.14 3.01
1750 1756 3.301706 CTCGCGGAGTTCTTAGATTAGC 58.698 50.000 6.13 0.00 0.00 3.09
1753 1759 1.534175 CGCTCGCGGAGTTCTTAGATT 60.534 52.381 6.13 0.00 35.56 2.40
1827 1833 0.035630 CAGTGAAGGAAGGGAGCCTG 60.036 60.000 0.00 0.00 35.50 4.85
1941 1947 1.373812 GGCCCGACACTAACCAAGT 59.626 57.895 0.00 0.00 39.81 3.16
1949 1955 4.680537 ACTCTCGGGCCCGACACT 62.681 66.667 42.66 23.65 44.01 3.55
1953 1959 3.147595 CATCACTCTCGGGCCCGA 61.148 66.667 42.62 42.62 46.87 5.14
2176 2183 1.067846 CGATGTGTCTGGAAACTCGGA 60.068 52.381 5.49 0.00 0.00 4.55
2234 2241 3.059352 CCCACTCTTCTTTGATCCGTT 57.941 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.