Multiple sequence alignment - TraesCS3A01G214200

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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 TraesCS3A01G214200 chr3A 100.000 3982 0 0 1 3982 389123500 389127481 0.000000e+00 7354.0
1 TraesCS3A01G214200 chr3D 95.887 2723 78 11 1287 3982 294344170 294346885 0.000000e+00 4377.0
2 TraesCS3A01G214200 chr3D 94.902 765 21 6 500 1252 294343189 294343947 0.000000e+00 1181.0
3 TraesCS3A01G214200 chr3B 95.206 2712 84 25 500 3179 388100636 388103333 0.000000e+00 4246.0
4 TraesCS3A01G214200 chr3B 94.743 799 27 10 3188 3982 388103521 388104308 0.000000e+00 1229.0
5 TraesCS3A01G214200 chr3B 90.927 507 41 3 1 504 680745066 680744562 0.000000e+00 676.0
6 TraesCS3A01G214200 chr6A 94.048 504 25 4 1 501 30837715 30838216 0.000000e+00 760.0
7 TraesCS3A01G214200 chr2B 82.738 504 83 3 1 501 105417705 105418207 2.820000e-121 446.0
8 TraesCS3A01G214200 chr2B 83.754 357 49 6 153 503 659771377 659771024 2.970000e-86 329.0
9 TraesCS3A01G214200 chr6B 93.220 59 4 0 3425 3483 92070829 92070771 1.970000e-13 87.9
10 TraesCS3A01G214200 chr6B 88.889 72 6 2 3413 3483 267780242 267780172 1.970000e-13 87.9
11 TraesCS3A01G214200 chr5B 88.889 72 6 2 3413 3483 98372697 98372767 1.970000e-13 87.9


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 TraesCS3A01G214200 chr3A 389123500 389127481 3981 False 7354.0 7354 100.0000 1 3982 1 chr3A.!!$F1 3981
1 TraesCS3A01G214200 chr3D 294343189 294346885 3696 False 2779.0 4377 95.3945 500 3982 2 chr3D.!!$F1 3482
2 TraesCS3A01G214200 chr3B 388100636 388104308 3672 False 2737.5 4246 94.9745 500 3982 2 chr3B.!!$F1 3482
3 TraesCS3A01G214200 chr3B 680744562 680745066 504 True 676.0 676 90.9270 1 504 1 chr3B.!!$R1 503
4 TraesCS3A01G214200 chr6A 30837715 30838216 501 False 760.0 760 94.0480 1 501 1 chr6A.!!$F1 500
5 TraesCS3A01G214200 chr2B 105417705 105418207 502 False 446.0 446 82.7380 1 501 1 chr2B.!!$F1 500

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
535 539 0.944386 GTGTCTTCATGCCACACGTT 59.056 50.0 6.06 0.0 31.67 3.99 F
1158 1180 0.247460 TCTCGGTCGTCTTCTCCGTA 59.753 55.0 0.00 0.0 43.94 4.02 F
1311 1544 0.460311 AATCGGTGGATCTGTCGACC 59.540 55.0 14.12 0.0 46.41 4.79 F
1844 2080 0.690744 TGGAGCTACATGGCAGCCTA 60.691 55.0 14.15 0.0 39.99 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2272 0.167470 CGACAAAGTCCTGCAGCATG 59.833 55.000 8.66 4.64 40.87 4.06 R
2683 2925 0.524414 CGTATCATGGCATGGCATGG 59.476 55.000 43.81 31.06 0.00 3.66 R
2685 2927 1.579964 CGCGTATCATGGCATGGCAT 61.580 55.000 27.75 27.75 0.00 4.40 R
3663 4120 1.541588 GCATTGTGGAAGGAGGTTGAC 59.458 52.381 0.00 0.00 0.00 3.18 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
19 20 2.693267 AAGGGTGGATTCTAGCGAAC 57.307 50.000 0.00 0.00 30.67 3.95
87 88 1.725641 GTCTTGCGTGACCATGATGA 58.274 50.000 0.00 0.00 0.00 2.92
129 130 7.078228 GCAACTCAATTCTTTTCGTATGACTT 58.922 34.615 0.00 0.00 0.00 3.01
304 305 7.939039 CCAATTGTTGAGGATATTAAGGCTCTA 59.061 37.037 4.43 0.00 0.00 2.43
305 306 8.997323 CAATTGTTGAGGATATTAAGGCTCTAG 58.003 37.037 0.00 0.00 0.00 2.43
316 317 1.227793 GGCTCTAGTGCAGGGATGC 60.228 63.158 17.89 0.00 34.04 3.91
343 344 5.048013 GGGTTGTAAAGTTTCATGGAGAAGG 60.048 44.000 0.00 0.00 37.57 3.46
381 385 6.037610 GCTGCACATATTCTTGCTAAGTTAGT 59.962 38.462 11.51 0.00 39.62 2.24
412 416 4.701956 ACAAGTATTTCAAGAATGGCGG 57.298 40.909 0.00 0.00 0.00 6.13
434 438 3.412386 GTTGTGCCTCCTGAGTGTATTT 58.588 45.455 0.00 0.00 0.00 1.40
450 454 5.588648 AGTGTATTTTGCATGTAATAGCGGT 59.411 36.000 0.00 0.00 0.00 5.68
478 482 9.925268 GAGATTCCGAACGCTTTTTAATTAATA 57.075 29.630 0.00 0.00 0.00 0.98
524 528 4.422073 ACATCAGGACAAAGTGTCTTCA 57.578 40.909 8.21 0.00 46.19 3.02
535 539 0.944386 GTGTCTTCATGCCACACGTT 59.056 50.000 6.06 0.00 31.67 3.99
538 542 1.601903 GTCTTCATGCCACACGTTTGA 59.398 47.619 2.58 0.00 0.00 2.69
553 557 7.095397 CCACACGTTTGACACTTATCATTTAGA 60.095 37.037 2.58 0.00 0.00 2.10
556 560 9.901724 CACGTTTGACACTTATCATTTAGATAC 57.098 33.333 0.00 0.00 38.90 2.24
571 575 9.023962 TCATTTAGATACAAAATTGACTTGCCT 57.976 29.630 0.00 0.00 0.00 4.75
649 671 2.552093 TCTGTAAAGAGAGGGGGAGG 57.448 55.000 0.00 0.00 0.00 4.30
881 903 1.805945 GCTGAGGGCGACAACGTAG 60.806 63.158 0.00 0.00 41.98 3.51
962 984 3.325870 GACTCGTCAATTGGTGATCACA 58.674 45.455 26.47 8.28 38.90 3.58
1158 1180 0.247460 TCTCGGTCGTCTTCTCCGTA 59.753 55.000 0.00 0.00 43.94 4.02
1277 1312 1.128724 CTCGTCGTCATGTCTGCGTC 61.129 60.000 0.00 0.00 0.00 5.19
1278 1313 1.154207 CGTCGTCATGTCTGCGTCT 60.154 57.895 0.00 0.00 0.00 4.18
1279 1314 1.398762 CGTCGTCATGTCTGCGTCTG 61.399 60.000 0.00 0.00 0.00 3.51
1280 1315 1.444383 TCGTCATGTCTGCGTCTGC 60.444 57.895 0.00 0.00 43.20 4.26
1304 1537 3.054434 TGGTTGAATGAATCGGTGGATCT 60.054 43.478 0.00 0.00 30.81 2.75
1309 1542 1.470051 TGAATCGGTGGATCTGTCGA 58.530 50.000 7.12 7.12 36.07 4.20
1311 1544 0.460311 AATCGGTGGATCTGTCGACC 59.540 55.000 14.12 0.00 46.41 4.79
1384 1617 3.454375 CATACATATTCCCGGCCGATAC 58.546 50.000 30.73 0.00 0.00 2.24
1844 2080 0.690744 TGGAGCTACATGGCAGCCTA 60.691 55.000 14.15 0.00 39.99 3.93
2009 2245 0.747255 GCATCCTCAGCTACCTCGAA 59.253 55.000 0.00 0.00 0.00 3.71
2051 2287 2.986306 GCGCATGCTGCAGGACTTT 61.986 57.895 19.50 0.00 45.36 2.66
2541 2781 1.079612 GCATGCAACTGAAAGGGCC 60.080 57.895 14.21 0.00 39.30 5.80
2682 2924 0.816825 CGATGAGGCAAGGACCCATG 60.817 60.000 0.00 0.00 0.00 3.66
2683 2925 1.076485 ATGAGGCAAGGACCCATGC 60.076 57.895 10.68 10.68 39.58 4.06
2687 2929 3.213264 GCAAGGACCCATGCCATG 58.787 61.111 8.37 0.00 34.96 3.66
2807 3065 2.548067 GGAGACGCTTCAGAACAAGGAA 60.548 50.000 0.00 0.00 0.00 3.36
2903 3161 1.743252 CTTCGCCAGCAAGGAGGAC 60.743 63.158 0.00 0.00 41.22 3.85
3056 3331 6.176183 ACCTTCTTTCAGGTCATGTTATGAG 58.824 40.000 0.00 0.00 44.63 2.90
3089 3364 4.724279 TTAGGCAATCTAATTCTCCCCC 57.276 45.455 0.00 0.00 33.34 5.40
3167 3442 1.359848 ACTGTGCAGTATGTTAGCGC 58.640 50.000 0.00 0.00 40.43 5.92
3180 3455 1.573829 TTAGCGCGGCTTTCAACCTG 61.574 55.000 8.83 0.00 40.44 4.00
3183 3458 2.964978 GCGGCTTTCAACCTGCAT 59.035 55.556 0.00 0.00 0.00 3.96
3189 3464 3.670627 CGGCTTTCAACCTGCATTACTTC 60.671 47.826 0.00 0.00 0.00 3.01
3235 3691 3.570912 ACGAGGAACCAAAGAAAAGGA 57.429 42.857 0.00 0.00 0.00 3.36
3248 3704 9.547279 ACCAAAGAAAAGGATATCCAATAAGTT 57.453 29.630 23.81 5.21 38.89 2.66
3265 3721 8.081633 CCAATAAGTTTACTTTCATCTGCAACA 58.918 33.333 0.00 0.00 37.40 3.33
3450 3907 9.877137 AAACTTTTCAGAAACAAAATTGTGAAC 57.123 25.926 1.62 0.00 40.83 3.18
3663 4120 1.165907 TCCAAAGCTGCTTGACACCG 61.166 55.000 16.73 0.94 0.00 4.94
3719 4176 5.189928 TGGTAGACTGAAGAAAACAGCAAA 58.810 37.500 0.00 0.00 38.74 3.68
3720 4177 5.827797 TGGTAGACTGAAGAAAACAGCAAAT 59.172 36.000 0.00 0.00 38.74 2.32
3836 4293 2.767960 TCCTTGCACTGATCAGCATAGA 59.232 45.455 22.83 12.68 40.94 1.98
3881 4338 6.512415 GCTCATGAAAGATATAGTGTTGCACC 60.512 42.308 0.00 0.00 34.49 5.01
3894 4351 2.299582 TGTTGCACCCCATTTGAAGATG 59.700 45.455 0.00 0.00 0.00 2.90
3913 4370 7.334671 TGAAGATGGCAAACACGTAAATATACA 59.665 33.333 0.00 0.00 32.02 2.29
3926 4383 8.670135 CACGTAAATATACAAAATGGAGAACCA 58.330 33.333 0.00 0.00 40.01 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.948623 TTGACACCGCTCCATCAACG 60.949 55.000 0.00 0.00 0.00 4.10
129 130 8.783833 TTTCAATTCAACAAATTCTGGTTTCA 57.216 26.923 0.00 0.00 35.32 2.69
316 317 4.148838 TCCATGAAACTTTACAACCCTGG 58.851 43.478 0.00 0.00 0.00 4.45
399 403 0.958091 CACAACCCGCCATTCTTGAA 59.042 50.000 0.00 0.00 0.00 2.69
412 416 0.685097 TACACTCAGGAGGCACAACC 59.315 55.000 0.83 0.00 39.61 3.77
434 438 2.169561 TCTCCACCGCTATTACATGCAA 59.830 45.455 0.00 0.00 0.00 4.08
450 454 2.178912 AAAAGCGTTCGGAATCTCCA 57.821 45.000 0.00 0.00 35.91 3.86
524 528 1.388547 AAGTGTCAAACGTGTGGCAT 58.611 45.000 17.47 0.00 35.16 4.40
649 671 0.799534 GCATGGTGTCTGCAAATCGC 60.800 55.000 0.00 0.00 39.46 4.58
881 903 2.098233 CACATGTACGGTGGGACGC 61.098 63.158 0.00 0.00 37.37 5.19
1158 1180 2.307098 CAGGAGGAAAAGGAGACACCAT 59.693 50.000 0.00 0.00 42.04 3.55
1227 1249 4.241681 GCATCGAAGGAGATGGAAGATAC 58.758 47.826 8.74 0.00 45.94 2.24
1228 1250 3.259374 GGCATCGAAGGAGATGGAAGATA 59.741 47.826 8.74 0.00 45.94 1.98
1229 1251 2.038295 GGCATCGAAGGAGATGGAAGAT 59.962 50.000 8.74 0.00 45.94 2.40
1277 1312 1.202065 CCGATTCATTCAACCACGCAG 60.202 52.381 0.00 0.00 0.00 5.18
1278 1313 0.801872 CCGATTCATTCAACCACGCA 59.198 50.000 0.00 0.00 0.00 5.24
1279 1314 0.802494 ACCGATTCATTCAACCACGC 59.198 50.000 0.00 0.00 0.00 5.34
1280 1315 1.130373 CCACCGATTCATTCAACCACG 59.870 52.381 0.00 0.00 0.00 4.94
1282 1317 2.869101 TCCACCGATTCATTCAACCA 57.131 45.000 0.00 0.00 0.00 3.67
1283 1318 3.313526 CAGATCCACCGATTCATTCAACC 59.686 47.826 0.00 0.00 0.00 3.77
1284 1319 3.941483 ACAGATCCACCGATTCATTCAAC 59.059 43.478 0.00 0.00 0.00 3.18
1285 1320 4.191544 GACAGATCCACCGATTCATTCAA 58.808 43.478 0.00 0.00 0.00 2.69
1304 1537 1.475280 CCGTAGAAATCTGGGTCGACA 59.525 52.381 18.91 0.00 0.00 4.35
1309 1542 0.460311 CTCGCCGTAGAAATCTGGGT 59.540 55.000 0.00 0.00 0.00 4.51
1311 1544 1.209275 CGCTCGCCGTAGAAATCTGG 61.209 60.000 0.00 0.00 0.00 3.86
1426 1659 1.299976 GGTGGTAGTGCTTCTGGGG 59.700 63.158 0.00 0.00 0.00 4.96
1436 1672 2.030490 TTGCGTTGGACGGTGGTAGT 62.030 55.000 2.48 0.00 42.82 2.73
2009 2245 2.202570 GCGTCGATGCCGTACACT 60.203 61.111 19.11 0.00 37.05 3.55
2036 2272 0.167470 CGACAAAGTCCTGCAGCATG 59.833 55.000 8.66 4.64 40.87 4.06
2111 2347 3.712881 GTGTCGTTGTGGCCGCTC 61.713 66.667 18.96 9.76 0.00 5.03
2541 2781 6.423604 ACAACAAAAGAAACTCAAACCACTTG 59.576 34.615 0.00 0.00 36.25 3.16
2683 2925 0.524414 CGTATCATGGCATGGCATGG 59.476 55.000 43.81 31.06 0.00 3.66
2685 2927 1.579964 CGCGTATCATGGCATGGCAT 61.580 55.000 27.75 27.75 0.00 4.40
2686 2928 2.253051 CGCGTATCATGGCATGGCA 61.253 57.895 25.52 25.52 0.00 4.92
2687 2929 1.960763 TCGCGTATCATGGCATGGC 60.961 57.895 26.15 19.60 0.00 4.40
2807 3065 1.675641 GATGGAAAGCACCGCCAGT 60.676 57.895 0.00 0.00 34.74 4.00
3056 3331 7.553881 TTAGATTGCCTAATGACTTGCTAAC 57.446 36.000 0.00 0.00 32.67 2.34
3089 3364 2.656560 AGACTAGCTGTGCTAAACGG 57.343 50.000 0.00 0.00 40.82 4.44
3167 3442 1.812571 AGTAATGCAGGTTGAAAGCCG 59.187 47.619 0.00 0.00 0.00 5.52
3180 3455 4.389077 AGCGTCTTGTAGTTGAAGTAATGC 59.611 41.667 0.00 0.00 0.00 3.56
3183 3458 6.071784 TCCATAGCGTCTTGTAGTTGAAGTAA 60.072 38.462 0.00 0.00 0.00 2.24
3189 3464 4.504461 GTCATCCATAGCGTCTTGTAGTTG 59.496 45.833 0.00 0.00 0.00 3.16
3248 3704 7.147312 CCATTTCTTGTTGCAGATGAAAGTAA 58.853 34.615 11.83 4.05 31.50 2.24
3318 3774 4.196971 GTGGTCTGTAACTTGTTCCACTT 58.803 43.478 11.60 0.00 40.14 3.16
3354 3811 4.799949 TCAATAATTTGCTCGCTCAATTGC 59.200 37.500 0.00 0.00 32.61 3.56
3422 3879 8.716909 TCACAATTTTGTTTCTGAAAAGTTTCC 58.283 29.630 4.09 0.00 39.91 3.13
3450 3907 4.378459 GCTTGTCGAAATTACCTGTCTTGG 60.378 45.833 0.00 0.00 0.00 3.61
3663 4120 1.541588 GCATTGTGGAAGGAGGTTGAC 59.458 52.381 0.00 0.00 0.00 3.18
3719 4176 9.486123 AGTCTGATCAGTGGCTTGTATATATAT 57.514 33.333 21.92 0.00 0.00 0.86
3720 4177 8.885693 AGTCTGATCAGTGGCTTGTATATATA 57.114 34.615 21.92 0.00 0.00 0.86
3836 4293 5.299028 TGAGCCGTAATTTGATTATGCACAT 59.701 36.000 0.00 0.00 31.82 3.21
3881 4338 3.328505 GTGTTTGCCATCTTCAAATGGG 58.671 45.455 5.15 0.00 45.40 4.00
3894 4351 7.755822 TCCATTTTGTATATTTACGTGTTTGCC 59.244 33.333 0.00 0.00 0.00 4.52
3913 4370 3.564352 CCTTAGGCCTGGTTCTCCATTTT 60.564 47.826 17.99 0.00 43.43 1.82
3926 4383 0.694783 GGCTAGTTCCCCTTAGGCCT 60.695 60.000 11.78 11.78 35.73 5.19
3933 4390 1.281925 CCACATGGGCTAGTTCCCCT 61.282 60.000 0.00 0.00 45.97 4.79


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

AutoCloner maintained by Alex Coulton.