Multiple sequence alignment - TraesCS2A01G320300

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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 TraesCS2A01G320300 chr2A 100.000 3896 0 0 1 3896 549684702 549680807 0.000000e+00 7195
1 TraesCS2A01G320300 chr2D 94.710 3743 116 18 1 3712 439436068 439439759 0.000000e+00 5740
2 TraesCS2A01G320300 chr2D 80.193 207 23 5 3707 3896 439439845 439440050 5.250000e-29 139
3 TraesCS2A01G320300 chr2B 91.379 3770 170 61 1 3707 517377558 517381235 0.000000e+00 5018
4 TraesCS2A01G320300 chr2B 82.759 203 16 9 3713 3896 517381330 517381532 3.110000e-36 163
5 TraesCS2A01G320300 chr4D 100.000 76 0 0 1199 1274 482965416 482965491 1.460000e-29 141
6 TraesCS2A01G320300 chr4D 87.500 104 9 4 3186 3288 4680233 4680133 2.460000e-22 117
7 TraesCS2A01G320300 chrUn 88.679 106 10 2 3186 3290 100775675 100775571 1.140000e-25 128


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 TraesCS2A01G320300 chr2A 549680807 549684702 3895 True 7195.0 7195 100.0000 1 3896 1 chr2A.!!$R1 3895
1 TraesCS2A01G320300 chr2D 439436068 439440050 3982 False 2939.5 5740 87.4515 1 3896 2 chr2D.!!$F1 3895
2 TraesCS2A01G320300 chr2B 517377558 517381532 3974 False 2590.5 5018 87.0690 1 3896 2 chr2B.!!$F1 3895

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
934 973 2.125912 CGTCCCCACTCTTCGCTG 60.126 66.667 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2896 2941 0.470766 AACCACCGCCAGAACTACAA 59.529 50.0 0.0 0.0 0.0 2.41 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
73 74 3.309682 CAGTAATAGAACCGGCACACATG 59.690 47.826 0.00 0.00 0.00 3.21
326 339 7.036220 GCATATCAGACCGCTATTTATGTACT 58.964 38.462 0.00 0.00 0.00 2.73
356 369 6.521151 ACTTCTTCAACATCATGGAATTCC 57.479 37.500 18.17 18.17 0.00 3.01
467 486 3.725740 CACACGAGCTCAACAAAATTCAC 59.274 43.478 15.40 0.00 0.00 3.18
482 501 4.566545 AATTCACACACAATCGCAAAGA 57.433 36.364 0.00 0.00 0.00 2.52
486 506 5.281693 TCACACACAATCGCAAAGAATAG 57.718 39.130 0.00 0.00 0.00 1.73
795 816 3.342627 CGGCGGCGAAACACAGAA 61.343 61.111 29.19 0.00 0.00 3.02
934 973 2.125912 CGTCCCCACTCTTCGCTG 60.126 66.667 0.00 0.00 0.00 5.18
1279 1318 4.640690 AGTGAGCGACCCACCCCT 62.641 66.667 0.00 0.00 35.23 4.79
1334 1373 0.605319 TCAGTGTCAATCGCAACCCC 60.605 55.000 0.00 0.00 0.00 4.95
1345 1384 4.760047 CAACCCCCACGCTCCTCG 62.760 72.222 0.00 0.00 45.38 4.63
1387 1426 2.262211 CGACGACATGAATGCTTCTCA 58.738 47.619 0.00 0.00 0.00 3.27
1396 1435 3.149196 TGAATGCTTCTCACTCCCAAAC 58.851 45.455 0.00 0.00 0.00 2.93
1431 1470 1.152383 GAAATGCTCGCGGTAGTCCC 61.152 60.000 6.13 0.00 0.00 4.46
1448 1487 3.118149 AGTCCCGTTTAGTTTCAGGTTGT 60.118 43.478 0.00 0.00 0.00 3.32
1478 1517 9.461312 TTGGATTATTGTAGCTTACTGATTGTT 57.539 29.630 0.00 0.00 0.00 2.83
1484 1525 5.616270 TGTAGCTTACTGATTGTTGTTCCA 58.384 37.500 0.00 0.00 0.00 3.53
1491 1532 7.437862 GCTTACTGATTGTTGTTCCAAATTTGA 59.562 33.333 19.86 3.14 0.00 2.69
1495 1536 6.511416 TGATTGTTGTTCCAAATTTGATCGT 58.489 32.000 19.86 0.00 0.00 3.73
1608 1649 3.250744 CAAGATTGCAGGCTGTCATTTG 58.749 45.455 17.16 13.83 0.00 2.32
1626 1667 6.204882 GTCATTTGCAGTTACCTAGAGTTTGT 59.795 38.462 0.00 0.00 0.00 2.83
1670 1711 2.669364 CTTTGCACCTGTCAGAAATGC 58.331 47.619 13.70 13.70 36.81 3.56
1737 1778 2.132996 CCCTTGGTGGTTGCTTGCA 61.133 57.895 0.00 0.00 0.00 4.08
1744 1785 2.170187 TGGTGGTTGCTTGCAAAATTCT 59.830 40.909 9.75 0.00 0.00 2.40
1746 1787 3.627123 GGTGGTTGCTTGCAAAATTCTTT 59.373 39.130 9.75 0.00 0.00 2.52
1761 1802 8.173130 GCAAAATTCTTTCATGCTTTATCCAAG 58.827 33.333 0.00 0.00 34.29 3.61
1765 1806 6.199937 TCTTTCATGCTTTATCCAAGAAGC 57.800 37.500 1.38 1.38 46.42 3.86
1985 2030 2.801679 CAACGGCATTTTGCTCAACATT 59.198 40.909 0.00 0.00 44.28 2.71
2313 2358 2.158769 AGATATCAAGTTGGCGGATGCA 60.159 45.455 5.32 0.00 45.35 3.96
2602 2647 0.109913 GCTGATGGAGATCATGGGCA 59.890 55.000 0.00 0.00 37.97 5.36
2896 2941 5.075493 GCCATGTAGAATTCTTCCCATGAT 58.925 41.667 27.24 8.97 39.77 2.45
2918 2963 0.250124 TAGTTCTGGCGGTGGTTGTG 60.250 55.000 0.00 0.00 0.00 3.33
3068 3114 7.439157 TCCACATGTTCTTCAGATTTACTTG 57.561 36.000 0.00 0.00 0.00 3.16
3096 3143 5.265407 GTGAAACTAGAAAACAGGTAGCG 57.735 43.478 0.00 0.00 0.00 4.26
3109 3156 0.462047 GGTAGCGGTGAATCAGGTGG 60.462 60.000 0.00 0.00 0.00 4.61
3268 3334 5.175859 GTGTCTTAAATGGAATCCGAGTGA 58.824 41.667 0.00 0.00 0.00 3.41
3281 3347 5.657826 ATCCGAGTGATCCATATCAGAAG 57.342 43.478 0.00 0.00 42.80 2.85
3312 3382 8.706322 AAGTAAATAACAGACACCAAAAGGAT 57.294 30.769 0.00 0.00 0.00 3.24
3336 3406 0.320374 TCTGGCCAAAGTGGTCTACG 59.680 55.000 7.01 0.00 44.07 3.51
3350 3420 2.479275 GGTCTACGAGAAACAAACAGGC 59.521 50.000 0.00 0.00 0.00 4.85
3356 3426 2.599848 CGAGAAACAAACAGGCTTCACG 60.600 50.000 0.00 0.00 0.00 4.35
3392 3462 4.342665 GGTTAGAGGGATCACTCAAGGTAG 59.657 50.000 26.55 0.00 39.97 3.18
3472 3542 1.821332 GCTTGATCCTTCTGGCCGG 60.821 63.158 4.71 4.71 0.00 6.13
3482 3552 2.203070 CTGGCCGGTGCTATGGTC 60.203 66.667 2.29 0.00 37.74 4.02
3483 3553 3.006133 TGGCCGGTGCTATGGTCA 61.006 61.111 1.90 0.00 37.57 4.02
3507 3577 3.411351 CCAACACGTTCCCTCGCG 61.411 66.667 0.00 0.00 0.00 5.87
3526 3597 0.668401 GCGCAAGGCAAGAAAAGCAT 60.668 50.000 0.30 0.00 42.87 3.79
3568 3639 0.819666 GCTTCCGGGACATGGATTCC 60.820 60.000 0.00 0.00 34.91 3.01
3629 3700 4.410400 AACCTACTGCTGGCCGCC 62.410 66.667 15.40 1.04 38.05 6.13
3708 3779 0.036388 GGAGTCGACATGCTTCCCAA 60.036 55.000 19.50 0.00 0.00 4.12
3742 3903 0.473755 TTGGGAGCAGAACAAGCAGA 59.526 50.000 0.00 0.00 0.00 4.26
3745 3906 0.604780 GGAGCAGAACAAGCAGAGCA 60.605 55.000 0.00 0.00 0.00 4.26
3767 3928 5.008019 GCAAGCTTTGGATGAATCGATCTAA 59.992 40.000 0.00 0.00 0.00 2.10
3773 3934 8.939929 GCTTTGGATGAATCGATCTAATATCAA 58.060 33.333 0.00 0.00 0.00 2.57
3790 3951 9.342308 CTAATATCAAGCAATCTTAACAAGGGA 57.658 33.333 0.00 0.00 0.00 4.20
3816 3979 7.814693 TCCCCAAATACCCAAAATTTCATAA 57.185 32.000 0.00 0.00 0.00 1.90
3818 3981 6.536941 CCCCAAATACCCAAAATTTCATAACG 59.463 38.462 0.00 0.00 0.00 3.18
3872 4052 1.093159 GACAGCCAAGGAGCAGATTG 58.907 55.000 0.00 0.00 34.23 2.67
3875 4055 2.012673 CAGCCAAGGAGCAGATTGTAC 58.987 52.381 0.00 0.00 34.23 2.90
3882 4062 5.185454 CAAGGAGCAGATTGTACCATAACA 58.815 41.667 0.00 0.00 0.00 2.41
3889 4069 7.164122 AGCAGATTGTACCATAACAGGATATG 58.836 38.462 0.00 0.00 33.85 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 6.947258 TGATTCTCATACATGTACGCAAATG 58.053 36.000 7.96 2.57 0.00 2.32
326 339 9.958180 TTCCATGATGTTGAAGAAGTTAAGATA 57.042 29.630 0.00 0.00 0.00 1.98
356 369 9.214957 TGTGTACAAAGTTATTTATCTGACCAG 57.785 33.333 0.00 0.00 0.00 4.00
467 486 5.082059 GTGACTATTCTTTGCGATTGTGTG 58.918 41.667 0.00 0.00 0.00 3.82
482 501 3.181455 TGGTCTGCACTTGTGTGACTATT 60.181 43.478 19.36 0.00 46.55 1.73
486 506 1.597742 ATGGTCTGCACTTGTGTGAC 58.402 50.000 15.14 15.14 46.55 3.67
795 816 8.290325 GGTTTTAGACTCGTTTCTGATGAATTT 58.710 33.333 0.00 0.00 31.56 1.82
1030 1069 0.535102 CGAACACAACCAGCCTTCCT 60.535 55.000 0.00 0.00 0.00 3.36
1031 1070 0.534203 TCGAACACAACCAGCCTTCC 60.534 55.000 0.00 0.00 0.00 3.46
1032 1071 0.586802 GTCGAACACAACCAGCCTTC 59.413 55.000 0.00 0.00 0.00 3.46
1033 1072 0.818040 GGTCGAACACAACCAGCCTT 60.818 55.000 0.00 0.00 35.53 4.35
1034 1073 1.227853 GGTCGAACACAACCAGCCT 60.228 57.895 0.00 0.00 35.53 4.58
1345 1384 0.796491 CACGACGCTCTGAAGCTCTC 60.796 60.000 0.00 0.00 46.91 3.20
1387 1426 2.188062 TAATTTCCGCGTTTGGGAGT 57.812 45.000 4.92 0.00 34.45 3.85
1396 1435 3.245048 GCATTTCCCAAATAATTTCCGCG 59.755 43.478 0.00 0.00 0.00 6.46
1476 1515 7.018826 TCGATTACGATCAAATTTGGAACAAC 58.981 34.615 17.90 0.00 43.94 3.32
1478 1517 6.729391 TCGATTACGATCAAATTTGGAACA 57.271 33.333 17.90 0.00 43.81 3.18
1495 1536 8.771920 ACAGACATTACAAAGTGAATCGATTA 57.228 30.769 11.38 0.00 0.00 1.75
1506 1547 7.433708 TCCAACATGTACAGACATTACAAAG 57.566 36.000 0.00 0.00 44.18 2.77
1508 1549 7.882791 AGATTCCAACATGTACAGACATTACAA 59.117 33.333 0.00 0.00 44.18 2.41
1626 1667 5.291128 GCTTATGCTGCTACTAGAACGAAAA 59.709 40.000 0.00 0.00 36.03 2.29
1744 1785 4.699735 TCGCTTCTTGGATAAAGCATGAAA 59.300 37.500 0.00 0.00 46.49 2.69
1746 1787 3.872696 TCGCTTCTTGGATAAAGCATGA 58.127 40.909 0.00 0.00 46.49 3.07
1765 1806 6.918626 TCTCTTATATGAAGAGATTGCCTCG 58.081 40.000 14.69 0.00 45.52 4.63
1883 1928 5.462398 GTGATGCGGTTTGGATAAGTAGTAG 59.538 44.000 0.00 0.00 0.00 2.57
1985 2030 1.957186 GGAGTTAACCGCACACGCA 60.957 57.895 0.88 0.00 38.40 5.24
2259 2304 2.301583 GACCTTCTCACTCCAAAGCTCT 59.698 50.000 0.00 0.00 0.00 4.09
2478 2523 1.216064 CTTCCAGGATCCCACCATCA 58.784 55.000 8.55 0.00 0.00 3.07
2602 2647 1.065272 GTAGAGGTCGACCCAGTCTCT 60.065 57.143 30.82 25.97 38.26 3.10
2742 2787 2.853542 TCCTTCCCCAGCAGCACA 60.854 61.111 0.00 0.00 0.00 4.57
2896 2941 0.470766 AACCACCGCCAGAACTACAA 59.529 50.000 0.00 0.00 0.00 2.41
2918 2963 9.769093 ATTTAACGAATAAACAGAATACAGTGC 57.231 29.630 0.00 0.00 36.35 4.40
3068 3114 9.194271 CTACCTGTTTTCTAGTTTCACTAGTTC 57.806 37.037 10.12 2.38 46.31 3.01
3109 3156 2.497273 CACATTTCTTTGGATGACCCCC 59.503 50.000 0.00 0.00 34.81 5.40
3312 3382 2.158475 AGACCACTTTGGCCAGAAATGA 60.158 45.455 5.11 0.00 42.67 2.57
3336 3406 2.354821 ACGTGAAGCCTGTTTGTTTCTC 59.645 45.455 0.00 0.00 0.00 2.87
3350 3420 3.408634 ACCCCTTGTTTCATACGTGAAG 58.591 45.455 0.00 0.00 44.62 3.02
3356 3426 4.226620 TCCCTCTAACCCCTTGTTTCATAC 59.773 45.833 0.00 0.00 38.42 2.39
3392 3462 3.668447 TGAGAAGACTGAAATCTGGTGC 58.332 45.455 0.00 0.00 0.00 5.01
3472 3542 0.811281 GGCCAACTTGACCATAGCAC 59.189 55.000 0.00 0.00 0.00 4.40
3482 3552 0.248866 GGAACGTGTTGGCCAACTTG 60.249 55.000 40.40 33.76 41.67 3.16
3483 3553 1.388837 GGGAACGTGTTGGCCAACTT 61.389 55.000 40.40 29.77 41.67 2.66
3507 3577 0.668401 ATGCTTTTCTTGCCTTGCGC 60.668 50.000 0.00 0.00 38.31 6.09
3526 3597 2.736995 GCACCTGTCGCGTTGCTA 60.737 61.111 5.77 0.00 0.00 3.49
3568 3639 0.178767 TCCACATTCTCATCCGGCAG 59.821 55.000 0.00 0.00 0.00 4.85
3629 3700 2.955660 AGGGATTCGTTAGAGCTGAGAG 59.044 50.000 0.00 0.00 0.00 3.20
3708 3779 3.551846 CTCCCAATAATGTAAGCGGGTT 58.448 45.455 0.00 0.00 35.08 4.11
3742 3903 2.715046 TCGATTCATCCAAAGCTTGCT 58.285 42.857 0.00 0.00 0.00 3.91
3745 3906 9.160496 GATATTAGATCGATTCATCCAAAGCTT 57.840 33.333 0.00 0.00 0.00 3.74
3767 3928 8.773033 AATCCCTTGTTAAGATTGCTTGATAT 57.227 30.769 0.00 0.00 35.56 1.63
3773 3934 4.281657 GGGAATCCCTTGTTAAGATTGCT 58.718 43.478 11.95 0.00 41.34 3.91
3790 3951 6.710499 TGAAATTTTGGGTATTTGGGGAAT 57.290 33.333 0.00 0.00 0.00 3.01
3797 3958 9.418045 CAGTTCGTTATGAAATTTTGGGTATTT 57.582 29.630 0.00 0.00 38.60 1.40
3816 3979 2.158871 TGGTAAAACCTGAGCAGTTCGT 60.159 45.455 0.00 0.00 39.58 3.85
3818 3981 4.911514 TTTGGTAAAACCTGAGCAGTTC 57.088 40.909 0.00 0.00 39.58 3.01
3852 4032 0.392193 AATCTGCTCCTTGGCTGTCG 60.392 55.000 0.00 0.00 33.78 4.35
3856 4036 1.065126 GGTACAATCTGCTCCTTGGCT 60.065 52.381 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.