Multiple sequence alignment - TraesCS4B01G170400

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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 TraesCS4B01G170400 chr4B 100.000 7529 0 0 1 7529 372909609 372902081 0.000000e+00 13904
1 TraesCS4B01G170400 chr4D 98.039 7546 105 22 1 7528 299778750 299771230 0.000000e+00 13075
2 TraesCS4B01G170400 chr4A 97.134 7468 129 28 1 7452 183969609 183977007 0.000000e+00 12526
3 TraesCS4B01G170400 chr4A 78.763 970 140 26 5133 6060 94765911 94766856 2.340000e-164 590
4 TraesCS4B01G170400 chr6D 78.931 992 144 29 5133 6084 161151665 161152631 1.390000e-171 614
5 TraesCS4B01G170400 chr5D 78.815 996 144 27 5130 6084 435152511 435153480 6.460000e-170 608
6 TraesCS4B01G170400 chr5D 77.007 735 103 29 5389 6084 159613325 159612618 2.000000e-95 361
7 TraesCS4B01G170400 chr7A 78.485 990 143 31 5133 6082 8739568 8740527 1.090000e-162 584
8 TraesCS4B01G170400 chr6A 78.189 972 142 30 5133 6060 77892857 77893802 2.370000e-154 556
9 TraesCS4B01G170400 chr5A 77.856 989 154 27 5133 6082 154491835 154490873 3.070000e-153 553
10 TraesCS4B01G170400 chr3A 83.108 444 46 13 5515 5937 725058453 725058888 1.980000e-100 377
11 TraesCS4B01G170400 chrUn 82.883 444 47 13 5515 5937 45785436 45785871 9.230000e-99 372
12 TraesCS4B01G170400 chr3D 82.883 444 47 13 5515 5937 594480526 594480961 9.230000e-99 372


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 TraesCS4B01G170400 chr4B 372902081 372909609 7528 True 13904 13904 100.000 1 7529 1 chr4B.!!$R1 7528
1 TraesCS4B01G170400 chr4D 299771230 299778750 7520 True 13075 13075 98.039 1 7528 1 chr4D.!!$R1 7527
2 TraesCS4B01G170400 chr4A 183969609 183977007 7398 False 12526 12526 97.134 1 7452 1 chr4A.!!$F2 7451
3 TraesCS4B01G170400 chr4A 94765911 94766856 945 False 590 590 78.763 5133 6060 1 chr4A.!!$F1 927
4 TraesCS4B01G170400 chr6D 161151665 161152631 966 False 614 614 78.931 5133 6084 1 chr6D.!!$F1 951
5 TraesCS4B01G170400 chr5D 435152511 435153480 969 False 608 608 78.815 5130 6084 1 chr5D.!!$F1 954
6 TraesCS4B01G170400 chr5D 159612618 159613325 707 True 361 361 77.007 5389 6084 1 chr5D.!!$R1 695
7 TraesCS4B01G170400 chr7A 8739568 8740527 959 False 584 584 78.485 5133 6082 1 chr7A.!!$F1 949
8 TraesCS4B01G170400 chr6A 77892857 77893802 945 False 556 556 78.189 5133 6060 1 chr6A.!!$F1 927
9 TraesCS4B01G170400 chr5A 154490873 154491835 962 True 553 553 77.856 5133 6082 1 chr5A.!!$R1 949

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
413 428 1.059913 CCTGTTTCTGTCTGGTCCCT 58.940 55.000 0.00 0.00 0.00 4.20 F
1060 1079 0.106708 TGCAGACTCGCCTTCAAAGT 59.893 50.000 0.00 0.00 0.00 2.66 F
1341 1360 0.940126 GTGTAATGGAGATGCAGCGG 59.060 55.000 0.00 0.00 0.00 5.52 F
2133 2152 3.052082 CGTGGGTGCCAGCTCAAG 61.052 66.667 0.00 0.00 32.34 3.02 F
2622 2641 3.101437 TGAAGACCTAGGCCAAATACGA 58.899 45.455 9.30 0.00 0.00 3.43 F
2917 2937 3.133362 CCAGGCTGAATTACTACCCGTTA 59.867 47.826 17.94 0.00 0.00 3.18 F
3613 3633 4.988540 TGTTGTAAGATTTCCAGACGACAG 59.011 41.667 0.00 0.00 32.09 3.51 F
4569 4589 6.091169 ACGTACAAAAATACCGGTCATACTTG 59.909 38.462 12.40 12.34 0.00 3.16 F
5174 5197 2.125269 CCCAGTCGCTTAACCCGG 60.125 66.667 0.00 0.00 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1255 1.065926 TGCGAATCAGCAGACTGGAAT 60.066 47.619 4.26 0.00 44.59 3.01 R
2151 2170 1.379443 AGCATAGACGACGACCCCA 60.379 57.895 0.00 0.00 0.00 4.96 R
3236 3256 6.430925 CCTCACTTACTTCATTGGTCAAATCA 59.569 38.462 0.00 0.00 0.00 2.57 R
3452 3472 2.083774 GCATTTCATGGTCAACTCGGA 58.916 47.619 0.00 0.00 0.00 4.55 R
4509 4529 0.038021 ACATGTGCAGCCATGGTGTA 59.962 50.000 21.16 7.28 45.21 2.90 R
4855 4875 6.434028 TGGCATTCTAGTTCAAGCAAGTTATT 59.566 34.615 0.00 0.00 0.00 1.40 R
5054 5075 2.024414 GATGGCCAGGATACAACAACC 58.976 52.381 13.05 0.00 41.41 3.77 R
5720 5780 0.843309 CCAAAAAGGCCAAAAGGGGT 59.157 50.000 5.01 0.00 37.04 4.95 R
6950 7037 1.202313 GGTCAGCACTAGTCCACGATC 60.202 57.143 0.00 0.00 0.00 3.69 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
89 90 1.602323 CCTCTCCTCCCCGATCTCG 60.602 68.421 0.00 0.00 39.44 4.04
90 91 2.203365 TCTCCTCCCCGATCTCGC 60.203 66.667 0.00 0.00 38.18 5.03
91 92 3.299190 CTCCTCCCCGATCTCGCC 61.299 72.222 0.00 0.00 38.18 5.54
182 185 2.158340 TCTCCTCCATCTCATCCTCCTG 60.158 54.545 0.00 0.00 0.00 3.86
413 428 1.059913 CCTGTTTCTGTCTGGTCCCT 58.940 55.000 0.00 0.00 0.00 4.20
522 537 1.342819 GATCCAGCTTCGAGGCATAGT 59.657 52.381 22.42 4.77 34.17 2.12
535 550 5.828328 TCGAGGCATAGTTCAGAGATTAAGA 59.172 40.000 0.00 0.00 0.00 2.10
570 585 1.108776 TTTACTAGCTCCGCGACCAT 58.891 50.000 8.23 0.00 0.00 3.55
702 717 2.590821 ACCTGCATTCAAGTCAAGCTT 58.409 42.857 0.00 0.00 38.08 3.74
726 741 5.814705 TGTTGAAATGTTTAACCCAGCTTTG 59.185 36.000 0.00 0.00 0.00 2.77
743 758 7.067494 CCCAGCTTTGAGTAATATTAGCTTGTT 59.933 37.037 5.59 0.00 36.88 2.83
744 759 8.462016 CCAGCTTTGAGTAATATTAGCTTGTTT 58.538 33.333 5.59 0.00 36.88 2.83
745 760 9.846248 CAGCTTTGAGTAATATTAGCTTGTTTT 57.154 29.630 5.59 0.00 36.88 2.43
810 825 9.582431 CACAATAATCATGAGCTGAGAAAAATT 57.418 29.630 0.09 0.00 37.28 1.82
832 847 5.878406 TCAACTCCAACTCTCTCTTTTCT 57.122 39.130 0.00 0.00 0.00 2.52
943 962 1.966451 CCGGTGTGAACTTGCCCTC 60.966 63.158 0.00 0.00 0.00 4.30
1060 1079 0.106708 TGCAGACTCGCCTTCAAAGT 59.893 50.000 0.00 0.00 0.00 2.66
1065 1084 4.678309 GCAGACTCGCCTTCAAAGTATACT 60.678 45.833 0.00 0.00 0.00 2.12
1069 1088 4.184629 CTCGCCTTCAAAGTATACTGCTT 58.815 43.478 6.06 0.00 0.00 3.91
1074 1093 4.333926 CCTTCAAAGTATACTGCTTCTGCC 59.666 45.833 6.06 0.00 38.71 4.85
1341 1360 0.940126 GTGTAATGGAGATGCAGCGG 59.060 55.000 0.00 0.00 0.00 5.52
1491 1510 7.232127 CCAAGGCTAATTTACATCAATGATCCT 59.768 37.037 0.00 0.00 0.00 3.24
1493 1512 7.520798 AGGCTAATTTACATCAATGATCCTGA 58.479 34.615 0.00 0.00 0.00 3.86
1536 1555 8.737168 ATGAATTTACAGGAAATGAGATTCGA 57.263 30.769 0.00 0.00 37.82 3.71
2025 2044 5.916318 TCATATTTGGGGTTGATCAAATGC 58.084 37.500 10.35 0.00 41.77 3.56
2133 2152 3.052082 CGTGGGTGCCAGCTCAAG 61.052 66.667 0.00 0.00 32.34 3.02
2151 2170 6.888632 AGCTCAAGAACACAGAATGGATTATT 59.111 34.615 0.00 0.00 43.62 1.40
2415 2434 7.234355 ACAGAAAGGATTTTGAGTTCTATGGT 58.766 34.615 0.00 0.00 39.27 3.55
2622 2641 3.101437 TGAAGACCTAGGCCAAATACGA 58.899 45.455 9.30 0.00 0.00 3.43
2917 2937 3.133362 CCAGGCTGAATTACTACCCGTTA 59.867 47.826 17.94 0.00 0.00 3.18
3613 3633 4.988540 TGTTGTAAGATTTCCAGACGACAG 59.011 41.667 0.00 0.00 32.09 3.51
3788 3808 6.755607 CCTTAGTAATTGGTTCGAAGTACCTC 59.244 42.308 0.00 0.00 36.60 3.85
4285 4305 6.428385 AGTTATTGCTAATGACAAGTCAGC 57.572 37.500 8.99 7.40 43.61 4.26
4403 4423 7.862274 ATCAGAGGTTTGTGATCATATCCTA 57.138 36.000 13.69 3.48 32.22 2.94
4569 4589 6.091169 ACGTACAAAAATACCGGTCATACTTG 59.909 38.462 12.40 12.34 0.00 3.16
5116 5138 5.814188 TCTGTAAGAGTGCAATTCAGCTATG 59.186 40.000 0.00 0.00 38.67 2.23
5174 5197 2.125269 CCCAGTCGCTTAACCCGG 60.125 66.667 0.00 0.00 0.00 5.73
5283 5306 3.723260 TCGCTGTACATCAAACTTGTCA 58.277 40.909 0.00 0.00 0.00 3.58
5284 5307 4.123506 TCGCTGTACATCAAACTTGTCAA 58.876 39.130 0.00 0.00 0.00 3.18
5335 5368 6.653740 GCTAACTGTTTCCTACACTATTTGGT 59.346 38.462 0.00 0.00 32.10 3.67
5363 5396 4.627467 GCTCACGTTCATATTGACAGTCTT 59.373 41.667 1.31 0.00 0.00 3.01
5364 5397 5.120830 GCTCACGTTCATATTGACAGTCTTT 59.879 40.000 1.31 0.00 0.00 2.52
5640 5675 6.915786 ACATATTCCCTCCTCTATGCTTTTT 58.084 36.000 0.00 0.00 0.00 1.94
5720 5780 1.588239 ACAGAAGCATCATCCTCCCA 58.412 50.000 0.00 0.00 0.00 4.37
5921 6003 5.652994 AGGACTTGAGTCACAATACTCTC 57.347 43.478 12.76 0.00 46.47 3.20
6535 6617 6.543465 TGAAAGTGATATCAGCTAACAATGGG 59.457 38.462 5.42 0.00 0.00 4.00
6816 6902 8.786898 TGTTTCTGTAGGATGAAGATTGAAAAG 58.213 33.333 0.00 0.00 0.00 2.27
6822 6908 7.884877 TGTAGGATGAAGATTGAAAAGTCACAT 59.115 33.333 0.00 0.00 31.90 3.21
6941 7028 3.056107 TGTTCTTCCTGTAGCATAGCGTT 60.056 43.478 0.00 0.00 0.00 4.84
6950 7037 6.021596 CCTGTAGCATAGCGTTTAAGTTTTG 58.978 40.000 0.00 0.00 0.00 2.44
7350 7437 4.562963 CCTCGTTGAGGTTTTAGGTAGCTT 60.563 45.833 0.00 0.00 44.25 3.74
7351 7438 5.337009 CCTCGTTGAGGTTTTAGGTAGCTTA 60.337 44.000 0.00 0.00 44.25 3.09
7364 7451 3.705072 AGGTAGCTTATAGTGGTGTGTCC 59.295 47.826 0.00 0.00 0.00 4.02
7437 7524 7.720957 TGAGATCCAGAACTTCAGAAATTTGAA 59.279 33.333 0.00 0.00 35.83 2.69
7479 7566 2.781174 ACAAGTCCTACAAAGGGTGGAA 59.219 45.455 0.00 0.00 43.84 3.53
7493 7580 9.492730 ACAAAGGGTGGAAATTTCATTATATCT 57.507 29.630 19.49 5.00 0.00 1.98
7525 7612 2.611224 GGTTTCTTGCTGAATTGCCCTG 60.611 50.000 0.00 0.00 34.24 4.45
7528 7615 1.202915 TCTTGCTGAATTGCCCTGACA 60.203 47.619 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.586357 GGTGGAGGAGCGCGAATC 60.586 66.667 12.10 6.78 0.00 2.52
413 428 3.068881 CCAAAGGGAGACAGCCGA 58.931 61.111 0.00 0.00 35.59 5.54
522 537 7.875041 CCTCACTCAAACTTCTTAATCTCTGAA 59.125 37.037 0.00 0.00 0.00 3.02
535 550 6.013293 AGCTAGTAAATCCCTCACTCAAACTT 60.013 38.462 0.00 0.00 0.00 2.66
570 585 7.040201 ACAACTAATACGAAACAGACCAGACTA 60.040 37.037 0.00 0.00 0.00 2.59
702 717 5.606348 AAGCTGGGTTAAACATTTCAACA 57.394 34.783 0.00 0.00 0.00 3.33
782 797 7.926674 TTTCTCAGCTCATGATTATTGTGAA 57.073 32.000 0.00 3.13 37.28 3.18
810 825 5.878406 AGAAAAGAGAGAGTTGGAGTTGA 57.122 39.130 0.00 0.00 0.00 3.18
943 962 3.502211 CAGTAAGCAACCAAGTTACCAGG 59.498 47.826 0.00 0.00 0.00 4.45
1060 1079 1.445942 GCCGGGCAGAAGCAGTATA 59.554 57.895 15.62 0.00 44.61 1.47
1065 1084 4.802051 GATGGCCGGGCAGAAGCA 62.802 66.667 35.19 11.78 44.61 3.91
1236 1255 1.065926 TGCGAATCAGCAGACTGGAAT 60.066 47.619 4.26 0.00 44.59 3.01
1341 1360 3.161866 GACCTCTAGGGATGATGGAGAC 58.838 54.545 0.20 0.00 40.27 3.36
1491 1510 2.519377 ATCGGTCGTTTGTTCTGTCA 57.481 45.000 0.00 0.00 0.00 3.58
1493 1512 4.182693 TCATATCGGTCGTTTGTTCTGT 57.817 40.909 0.00 0.00 0.00 3.41
2025 2044 4.626042 AGATATTTCTGTTAGGCTGCTCG 58.374 43.478 0.00 0.00 0.00 5.03
2133 2152 4.956075 ACCCCAATAATCCATTCTGTGTTC 59.044 41.667 0.00 0.00 0.00 3.18
2151 2170 1.379443 AGCATAGACGACGACCCCA 60.379 57.895 0.00 0.00 0.00 4.96
2805 2825 7.602517 AGGAATGAAAGAGTGATCTAAAACG 57.397 36.000 0.00 0.00 0.00 3.60
3236 3256 6.430925 CCTCACTTACTTCATTGGTCAAATCA 59.569 38.462 0.00 0.00 0.00 2.57
3452 3472 2.083774 GCATTTCATGGTCAACTCGGA 58.916 47.619 0.00 0.00 0.00 4.55
3613 3633 3.694566 ACCCTTGACAAGAACTTTCACAC 59.305 43.478 16.99 0.00 0.00 3.82
3788 3808 5.805486 CCATTCACTGAATTCTTCATTGCTG 59.195 40.000 7.05 3.82 39.40 4.41
4285 4305 7.733402 AAATTTGGTGATTCCTCAATGTTTG 57.267 32.000 0.00 0.00 37.07 2.93
4426 4446 6.486253 TTGAAACAGAACACAGAGATATGC 57.514 37.500 0.00 0.00 0.00 3.14
4434 4454 5.247507 TGACCAATTGAAACAGAACACAG 57.752 39.130 7.12 0.00 0.00 3.66
4509 4529 0.038021 ACATGTGCAGCCATGGTGTA 59.962 50.000 21.16 7.28 45.21 2.90
4569 4589 9.101655 AGTTGGCAAATATGAAATTATTGCTTC 57.898 29.630 0.00 1.22 42.62 3.86
4855 4875 6.434028 TGGCATTCTAGTTCAAGCAAGTTATT 59.566 34.615 0.00 0.00 0.00 1.40
5054 5075 2.024414 GATGGCCAGGATACAACAACC 58.976 52.381 13.05 0.00 41.41 3.77
5116 5138 4.117685 CCCGTATAAACTCTTACCAGTGC 58.882 47.826 0.00 0.00 0.00 4.40
5174 5197 5.123820 TGATTTGTGGCTCTGTACTAATTGC 59.876 40.000 0.00 0.00 0.00 3.56
5234 5257 5.238868 CAGAAATTGGCATCATCCTAGAGTG 59.761 44.000 0.00 0.00 0.00 3.51
5307 5340 3.665190 AGTGTAGGAAACAGTTAGCTGC 58.335 45.455 6.48 0.00 46.30 5.25
5335 5368 4.082245 TGTCAATATGAACGTGAGCAGAGA 60.082 41.667 0.00 0.00 0.00 3.10
5640 5675 7.728981 AGGTATACTTAGCTTACAGCATAGGAA 59.271 37.037 2.25 0.00 45.56 3.36
5720 5780 0.843309 CCAAAAAGGCCAAAAGGGGT 59.157 50.000 5.01 0.00 37.04 4.95
5921 6003 8.138712 GCCTCATATAGTCTCGGATAATAAAGG 58.861 40.741 0.00 0.00 0.00 3.11
6535 6617 2.412089 GGTGACGAACTAACTGCATGAC 59.588 50.000 0.00 0.00 0.00 3.06
6816 6902 1.875514 TGAAACTGCAGCTCATGTGAC 59.124 47.619 15.27 0.00 0.00 3.67
6941 7028 5.407387 GCACTAGTCCACGATCAAAACTTAA 59.593 40.000 0.00 0.00 0.00 1.85
6950 7037 1.202313 GGTCAGCACTAGTCCACGATC 60.202 57.143 0.00 0.00 0.00 3.69
7109 7196 2.334946 GCTGTTTGATGCCTCGCCA 61.335 57.895 0.00 0.00 0.00 5.69
7350 7437 1.551430 CCAACCGGACACACCACTATA 59.449 52.381 9.46 0.00 38.90 1.31
7351 7438 0.323629 CCAACCGGACACACCACTAT 59.676 55.000 9.46 0.00 38.90 2.12
7364 7451 6.129035 CCTTTTAAAGCGTAAAATTCCAACCG 60.129 38.462 0.00 0.00 0.00 4.44
7500 7587 2.867647 GCAATTCAGCAAGAAACCCCAC 60.868 50.000 0.00 0.00 40.22 4.61
7503 7590 1.338105 GGGCAATTCAGCAAGAAACCC 60.338 52.381 10.27 10.27 40.22 4.11
7509 7596 1.250328 TGTCAGGGCAATTCAGCAAG 58.750 50.000 0.00 0.00 35.83 4.01


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

AutoCloner maintained by Alex Coulton.