Multiple sequence alignment - TraesCS2A01G551900

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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 TraesCS2A01G551900 chr2A 100.000 3578 0 0 1 3578 758393680 758397257 0.000000e+00 6608
1 TraesCS2A01G551900 chr2B 93.706 1859 56 22 847 2658 770677632 770679476 0.000000e+00 2728
2 TraesCS2A01G551900 chr2B 95.387 802 34 3 2779 3578 770679795 770680595 0.000000e+00 1273
3 TraesCS2A01G551900 chr2B 88.905 676 38 17 1 644 770676761 770677431 0.000000e+00 798
4 TraesCS2A01G551900 chr2B 86.934 574 37 16 2 556 748356508 748355954 8.490000e-171 610
5 TraesCS2A01G551900 chr2B 88.060 469 36 10 107 556 748203008 748202541 4.060000e-149 538
6 TraesCS2A01G551900 chr2B 96.032 126 4 1 2656 2780 770679508 770679633 1.680000e-48 204
7 TraesCS2A01G551900 chr2B 75.843 356 44 25 1383 1705 770678537 770678883 3.720000e-30 143
8 TraesCS2A01G551900 chr2B 97.468 79 2 0 3 81 748203081 748203003 6.230000e-28 135
9 TraesCS2A01G551900 chr2D 86.990 1691 85 51 2 1594 627917308 627918961 0.000000e+00 1779
10 TraesCS2A01G551900 chr2D 95.887 924 34 4 2656 3578 627919902 627920822 0.000000e+00 1493
11 TraesCS2A01G551900 chr2D 96.154 702 27 0 1957 2658 627919169 627919870 0.000000e+00 1147
12 TraesCS2A01G551900 chr2D 84.259 108 13 2 1602 1705 627919169 627919276 6.320000e-18 102


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 TraesCS2A01G551900 chr2A 758393680 758397257 3577 False 6608.00 6608 100.0000 1 3578 1 chr2A.!!$F1 3577
1 TraesCS2A01G551900 chr2B 770676761 770680595 3834 False 1029.20 2728 89.9746 1 3578 5 chr2B.!!$F1 3577
2 TraesCS2A01G551900 chr2B 748355954 748356508 554 True 610.00 610 86.9340 2 556 1 chr2B.!!$R1 554
3 TraesCS2A01G551900 chr2B 748202541 748203081 540 True 336.50 538 92.7640 3 556 2 chr2B.!!$R2 553
4 TraesCS2A01G551900 chr2D 627917308 627920822 3514 False 1130.25 1779 90.8225 2 3578 4 chr2D.!!$F1 3576

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
448 488 0.106894 GTGGGCGAGGCTAGCTTAAT 59.893 55.0 19.05 0.0 34.52 1.40 F
772 867 0.109086 CTGTGATCGGTTCGACTGCT 60.109 55.0 0.00 0.0 39.18 4.24 F
773 868 0.317160 TGTGATCGGTTCGACTGCTT 59.683 50.0 0.00 0.0 39.18 3.91 F
2238 2386 0.464916 AAACCGACGACCTTGCCTTT 60.465 50.0 0.00 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2347 0.321564 CCATGAAGCGAACTGGTGGA 60.322 55.000 0.00 0.00 0.00 4.02 R
2220 2368 1.147600 AAAGGCAAGGTCGTCGGTT 59.852 52.632 0.00 0.00 0.00 4.44 R
2561 2709 1.248486 AGTCTAAGCACTGCTCGTCA 58.752 50.000 3.40 0.00 38.25 4.35 R
3056 3404 0.878416 TTCTGTAAATTTGGCGCGCT 59.122 45.000 32.29 12.78 0.00 5.92 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
402 436 2.027605 ATCGCCGTCGCCATGTAG 59.972 61.111 0.00 0.00 35.26 2.74
404 438 4.201679 CGCCGTCGCCATGTAGGA 62.202 66.667 0.00 0.00 41.22 2.94
405 439 2.279517 GCCGTCGCCATGTAGGAG 60.280 66.667 0.00 0.00 41.22 3.69
415 455 3.594134 GCCATGTAGGAGTAGATGATGC 58.406 50.000 0.00 0.00 41.22 3.91
433 473 2.113139 AACGGCTTGGACAGTGGG 59.887 61.111 0.00 0.00 0.00 4.61
441 481 3.075005 GGACAGTGGGCGAGGCTA 61.075 66.667 0.00 0.00 0.00 3.93
444 484 3.465403 CAGTGGGCGAGGCTAGCT 61.465 66.667 19.05 0.00 34.52 3.32
445 485 2.685380 AGTGGGCGAGGCTAGCTT 60.685 61.111 19.05 6.94 34.52 3.74
447 487 0.976073 AGTGGGCGAGGCTAGCTTAA 60.976 55.000 19.05 2.70 34.52 1.85
448 488 0.106894 GTGGGCGAGGCTAGCTTAAT 59.893 55.000 19.05 0.00 34.52 1.40
451 491 2.436542 TGGGCGAGGCTAGCTTAATAAA 59.563 45.455 19.05 0.00 34.52 1.40
452 492 2.806818 GGGCGAGGCTAGCTTAATAAAC 59.193 50.000 19.05 0.00 34.52 2.01
455 507 5.295152 GGCGAGGCTAGCTTAATAAACTAA 58.705 41.667 19.05 0.00 34.52 2.24
458 510 5.927115 CGAGGCTAGCTTAATAAACTAAGGG 59.073 44.000 15.72 0.00 30.79 3.95
460 512 7.209340 AGGCTAGCTTAATAAACTAAGGGTT 57.791 36.000 15.72 0.00 40.28 4.11
464 516 9.784680 GCTAGCTTAATAAACTAAGGGTTTTTC 57.215 33.333 7.70 0.00 44.77 2.29
473 525 4.878439 ACTAAGGGTTTTTCCGCAATTTC 58.122 39.130 0.00 0.00 37.00 2.17
576 634 5.913137 CCATCCAGGCATAAACAAGTAAA 57.087 39.130 0.00 0.00 0.00 2.01
582 640 5.920273 CCAGGCATAAACAAGTAAACAACTG 59.080 40.000 0.00 0.00 38.88 3.16
586 644 5.778862 CATAAACAAGTAAACAACTGGGGG 58.221 41.667 0.00 0.00 38.88 5.40
594 652 0.474660 AACAACTGGGGGCTCTCTCT 60.475 55.000 0.00 0.00 0.00 3.10
692 785 1.306141 ACATTCCTCTCGGCTCCCA 60.306 57.895 0.00 0.00 0.00 4.37
731 826 1.359459 GGTTTCGTGGGATGTCGAGC 61.359 60.000 0.00 0.00 37.38 5.03
772 867 0.109086 CTGTGATCGGTTCGACTGCT 60.109 55.000 0.00 0.00 39.18 4.24
773 868 0.317160 TGTGATCGGTTCGACTGCTT 59.683 50.000 0.00 0.00 39.18 3.91
774 869 0.716108 GTGATCGGTTCGACTGCTTG 59.284 55.000 0.00 0.00 39.18 4.01
778 873 2.383527 CGGTTCGACTGCTTGCTCC 61.384 63.158 0.00 0.00 0.00 4.70
779 874 2.383527 GGTTCGACTGCTTGCTCCG 61.384 63.158 0.00 0.00 0.00 4.63
780 875 2.738521 TTCGACTGCTTGCTCCGC 60.739 61.111 0.00 0.00 0.00 5.54
799 894 3.188786 GCGATGCGGCGTCTTCTT 61.189 61.111 19.14 0.00 0.00 2.52
801 896 1.517257 CGATGCGGCGTCTTCTTCT 60.517 57.895 19.14 0.00 0.00 2.85
940 1048 0.529337 CCTCTCACTATGTGGCTGCG 60.529 60.000 0.00 0.00 33.87 5.18
1062 1190 1.723608 CTGTTGCAGTTGGTTCGGCA 61.724 55.000 0.00 0.00 36.82 5.69
1083 1211 2.360191 GGGGCCTTGCTTGATCCA 59.640 61.111 0.84 0.00 0.00 3.41
1211 1353 5.243954 CACACTCTCCCTTATCATAATCGGA 59.756 44.000 0.00 0.00 0.00 4.55
1231 1373 3.758554 GGATGTGCTGTTATGTTTGGACT 59.241 43.478 0.00 0.00 0.00 3.85
1233 1375 4.829064 TGTGCTGTTATGTTTGGACTTC 57.171 40.909 0.00 0.00 0.00 3.01
1313 1459 7.724305 TTTTATAGGTATGGTTGCTCGATTC 57.276 36.000 0.00 0.00 0.00 2.52
1396 1542 9.453572 ACCCATGCTATTGTTGTAGAATATATG 57.546 33.333 0.00 0.00 0.00 1.78
1430 1576 6.537301 TGTTTATGTCGTTTGTTTCAGAGAGT 59.463 34.615 0.00 0.00 0.00 3.24
1434 1580 3.869246 GTCGTTTGTTTCAGAGAGTGGAA 59.131 43.478 0.00 0.00 0.00 3.53
1594 1741 5.295292 CCATTGTTATTACTGTCTGAGGCAG 59.705 44.000 13.32 13.32 39.67 4.85
1867 2015 9.679661 TTTTATGGCTATACTGTTCATTCTTCA 57.320 29.630 0.00 0.00 0.00 3.02
1992 2140 7.009440 CCAGTTCGATGCAATTTGTATATACG 58.991 38.462 8.33 1.09 0.00 3.06
2062 2210 7.553881 TTCCAGTCTAACTAAAATAGCATGC 57.446 36.000 10.51 10.51 0.00 4.06
2082 2230 6.558909 CATGCTCCTACAGGAAATTCTTTTC 58.441 40.000 0.00 0.00 44.91 2.29
2220 2368 1.522668 CACCAGTTCGCTTCATGGAA 58.477 50.000 0.00 0.00 36.62 3.53
2232 2380 0.682852 TCATGGAAACCGACGACCTT 59.317 50.000 0.00 0.00 0.00 3.50
2238 2386 0.464916 AAACCGACGACCTTGCCTTT 60.465 50.000 0.00 0.00 0.00 3.11
2561 2709 2.696125 ATGCCCGGATCCCAAGGT 60.696 61.111 0.73 0.00 0.00 3.50
2626 2774 9.113876 CATAAAAACGTCTGTATCTTTGGTTTC 57.886 33.333 0.00 0.00 0.00 2.78
2734 2916 4.739716 GCAATGTTGACCACAAACTACTTG 59.260 41.667 0.00 0.00 39.50 3.16
2739 2921 5.529430 TGTTGACCACAAACTACTTGTATGG 59.471 40.000 0.00 0.00 46.91 2.74
2772 2955 3.609373 CGGTTTGCTCGAACGACTTATAA 59.391 43.478 0.00 0.00 0.00 0.98
2819 3165 4.677683 GTGTATTACACTTCTGATCGCG 57.322 45.455 17.77 0.00 45.27 5.87
2894 3241 5.067023 ACTTCAGCTTGAAACAAGGAGAAAG 59.933 40.000 12.36 1.91 35.73 2.62
2904 3251 7.035004 TGAAACAAGGAGAAAGATGTTGTTTG 58.965 34.615 14.36 0.00 46.24 2.93
3056 3404 3.857157 AACCTTGCTCAAACTCAGGTA 57.143 42.857 0.00 0.00 0.00 3.08
3085 3433 4.388469 CCAAATTTACAGAAAACCCATGCG 59.612 41.667 0.00 0.00 0.00 4.73
3227 3575 3.784511 ATATGGACAGCTCAATGAGGG 57.215 47.619 12.66 0.00 0.00 4.30
3229 3577 0.907486 TGGACAGCTCAATGAGGGAG 59.093 55.000 12.66 0.00 35.47 4.30
3359 3707 4.641396 TGTTTGATTTCATCGAGTCCAGT 58.359 39.130 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 4.308458 CCCAACGTCGGAGCCACA 62.308 66.667 0.00 0.00 0.00 4.17
402 436 1.202580 AGCCGTTGCATCATCTACTCC 60.203 52.381 0.00 0.00 41.13 3.85
404 438 2.283298 CAAGCCGTTGCATCATCTACT 58.717 47.619 0.00 0.00 41.13 2.57
405 439 1.331756 CCAAGCCGTTGCATCATCTAC 59.668 52.381 0.00 0.00 41.13 2.59
415 455 2.260869 CCCACTGTCCAAGCCGTTG 61.261 63.158 0.00 0.00 0.00 4.10
433 473 5.405873 CCTTAGTTTATTAAGCTAGCCTCGC 59.594 44.000 12.13 0.00 30.84 5.03
451 491 4.557895 CGAAATTGCGGAAAAACCCTTAGT 60.558 41.667 0.00 0.00 34.64 2.24
452 492 3.917985 CGAAATTGCGGAAAAACCCTTAG 59.082 43.478 0.00 0.00 34.64 2.18
455 507 1.604438 GCGAAATTGCGGAAAAACCCT 60.604 47.619 8.18 0.00 34.64 4.34
458 510 2.721495 GCATGCGAAATTGCGGAAAAAC 60.721 45.455 3.39 0.00 37.81 2.43
460 512 1.066914 GCATGCGAAATTGCGGAAAA 58.933 45.000 3.39 0.00 37.81 2.29
534 592 1.003718 CTGGACGGGAGGGTGTTTC 60.004 63.158 0.00 0.00 0.00 2.78
572 630 1.351350 AGAGAGCCCCCAGTTGTTTAC 59.649 52.381 0.00 0.00 0.00 2.01
573 631 1.628846 GAGAGAGCCCCCAGTTGTTTA 59.371 52.381 0.00 0.00 0.00 2.01
574 632 0.402121 GAGAGAGCCCCCAGTTGTTT 59.598 55.000 0.00 0.00 0.00 2.83
575 633 0.474660 AGAGAGAGCCCCCAGTTGTT 60.475 55.000 0.00 0.00 0.00 2.83
576 634 0.413832 TAGAGAGAGCCCCCAGTTGT 59.586 55.000 0.00 0.00 0.00 3.32
582 640 3.228017 GGCGTAGAGAGAGCCCCC 61.228 72.222 0.00 0.00 44.80 5.40
586 644 4.615834 CGGCGGCGTAGAGAGAGC 62.616 72.222 24.74 0.00 0.00 4.09
644 719 1.614850 GGTGGATACCTTGCGGGAAAA 60.615 52.381 2.42 0.00 43.97 2.29
692 785 0.175989 GCGGAGAGAAAAGTCCCGAT 59.824 55.000 0.00 0.00 42.49 4.18
782 877 3.144120 GAAGAAGACGCCGCATCGC 62.144 63.158 0.00 0.00 0.00 4.58
783 878 1.078759 AAGAAGAAGACGCCGCATCG 61.079 55.000 0.00 0.00 0.00 3.84
784 879 0.647925 GAAGAAGAAGACGCCGCATC 59.352 55.000 0.00 0.00 0.00 3.91
785 880 0.247736 AGAAGAAGAAGACGCCGCAT 59.752 50.000 0.00 0.00 0.00 4.73
786 881 0.033504 AAGAAGAAGAAGACGCCGCA 59.966 50.000 0.00 0.00 0.00 5.69
790 885 2.091432 GCGAAGAAGAAGAAGAAGACGC 59.909 50.000 0.00 0.00 36.06 5.19
791 886 2.339988 CGCGAAGAAGAAGAAGAAGACG 59.660 50.000 0.00 0.00 0.00 4.18
792 887 2.091432 GCGCGAAGAAGAAGAAGAAGAC 59.909 50.000 12.10 0.00 0.00 3.01
793 888 2.329379 GCGCGAAGAAGAAGAAGAAGA 58.671 47.619 12.10 0.00 0.00 2.87
794 889 1.058412 CGCGCGAAGAAGAAGAAGAAG 59.942 52.381 28.94 0.00 0.00 2.85
795 890 1.060713 CGCGCGAAGAAGAAGAAGAA 58.939 50.000 28.94 0.00 0.00 2.52
797 892 1.057976 GCGCGCGAAGAAGAAGAAG 59.942 57.895 37.18 0.00 0.00 2.85
798 893 3.156334 GCGCGCGAAGAAGAAGAA 58.844 55.556 37.18 0.00 0.00 2.52
880 975 2.474266 CGTGATCACAAACGCCGG 59.526 61.111 24.93 0.00 32.40 6.13
890 985 0.684479 ACAGCTAGAGGGCGTGATCA 60.684 55.000 0.00 0.00 37.29 2.92
940 1048 3.782046 ACAACAGCATCATACGAGTACC 58.218 45.455 0.00 0.00 0.00 3.34
1062 1190 0.753111 GATCAAGCAAGGCCCCGAAT 60.753 55.000 0.00 0.00 0.00 3.34
1083 1211 4.501915 GCAGCTATCAGATCAGCTCTCTTT 60.502 45.833 2.42 0.00 44.83 2.52
1211 1353 5.048504 CAGAAGTCCAAACATAACAGCACAT 60.049 40.000 0.00 0.00 0.00 3.21
1231 1373 4.040339 TGATGGTCTAAGACAGCAACAGAA 59.960 41.667 0.00 0.00 33.68 3.02
1233 1375 3.930336 TGATGGTCTAAGACAGCAACAG 58.070 45.455 0.00 0.00 33.68 3.16
1298 1444 5.000591 TGTTTCAAGAATCGAGCAACCATA 58.999 37.500 0.00 0.00 0.00 2.74
1313 1459 6.205784 ACATGACAAATTACGGTGTTTCAAG 58.794 36.000 0.00 0.00 0.00 3.02
1396 1542 6.037726 ACAAACGACATAAACAGGGAAAAAC 58.962 36.000 0.00 0.00 0.00 2.43
1594 1741 1.946768 TGGTAAAAGACAGTGTGCAGC 59.053 47.619 0.00 0.00 0.00 5.25
1657 1804 5.671463 AGTCCATAGACAGAGGGATAGAA 57.329 43.478 0.00 0.00 46.15 2.10
1847 1995 6.767902 TCCAATGAAGAATGAACAGTATAGCC 59.232 38.462 0.00 0.00 0.00 3.93
1879 2027 8.912988 CCAGCTAAATAGGAACATAATTTGGAA 58.087 33.333 0.00 0.00 0.00 3.53
2062 2210 5.064071 GCTCGAAAAGAATTTCCTGTAGGAG 59.936 44.000 0.26 0.00 46.36 3.69
2082 2230 0.879765 ATATAACCCGAGGACGCTCG 59.120 55.000 5.58 5.58 45.43 5.03
2199 2347 0.321564 CCATGAAGCGAACTGGTGGA 60.322 55.000 0.00 0.00 0.00 4.02
2220 2368 1.147600 AAAGGCAAGGTCGTCGGTT 59.852 52.632 0.00 0.00 0.00 4.44
2265 2413 1.595109 CAGCACGTGCCAGAAGTCA 60.595 57.895 35.51 0.00 43.38 3.41
2431 2579 2.124570 CTTGGTCGCCCATGGGAG 60.125 66.667 36.00 31.62 41.49 4.30
2561 2709 1.248486 AGTCTAAGCACTGCTCGTCA 58.752 50.000 3.40 0.00 38.25 4.35
2626 2774 1.266175 CTGACAACAAGCAAGGCTGAG 59.734 52.381 0.00 0.00 39.62 3.35
2734 2916 6.456501 AGCAAACCGAGAAGATATACCATAC 58.543 40.000 0.00 0.00 0.00 2.39
2739 2921 4.856664 TCGAGCAAACCGAGAAGATATAC 58.143 43.478 0.00 0.00 0.00 1.47
2816 3162 0.806102 ATTGACACCGAGATTCCGCG 60.806 55.000 0.00 0.00 35.33 6.46
2819 3165 6.265577 CCATTTTAATTGACACCGAGATTCC 58.734 40.000 0.00 0.00 0.00 3.01
2894 3241 7.475771 TGTTTTCCTATTTGCAAACAACATC 57.524 32.000 15.41 2.51 36.44 3.06
2928 3275 7.821846 GGGATGAGCAATTTTATTTTTGGTGTA 59.178 33.333 0.00 0.00 33.99 2.90
3035 3383 3.018423 ACCTGAGTTTGAGCAAGGTTT 57.982 42.857 0.00 0.00 0.00 3.27
3056 3404 0.878416 TTCTGTAAATTTGGCGCGCT 59.122 45.000 32.29 12.78 0.00 5.92
3141 3489 1.372087 GCGCTCTTCTGGGGTTGATG 61.372 60.000 0.00 0.00 0.00 3.07
3227 3575 1.725164 GCCGCCGCATAAGTTATACTC 59.275 52.381 0.00 0.00 34.03 2.59
3229 3577 1.459592 CAGCCGCCGCATAAGTTATAC 59.540 52.381 0.00 0.00 37.52 1.47
3461 3809 3.007940 TGAAATCCAGAACGAGATGTGGT 59.992 43.478 0.00 0.00 35.34 4.16


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

AutoCloner maintained by Alex Coulton.