Multiple sequence alignment - TraesCS7B01G207600

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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 TraesCS7B01G207600 chr7B 100.000 2821 0 0 1 2821 380078683 380081503 0.000000e+00 5210.0
1 TraesCS7B01G207600 chr7B 91.497 541 41 5 2281 2818 152799436 152799974 0.000000e+00 739.0
2 TraesCS7B01G207600 chr7D 93.975 1776 66 14 515 2254 385717474 385719244 0.000000e+00 2649.0
3 TraesCS7B01G207600 chr7D 93.705 556 31 4 2265 2818 385721380 385721933 0.000000e+00 830.0
4 TraesCS7B01G207600 chr7A 93.754 1537 51 21 515 2036 433742726 433744232 0.000000e+00 2265.0
5 TraesCS7B01G207600 chr7A 90.964 664 45 10 2158 2818 433744972 433745623 0.000000e+00 880.0
6 TraesCS7B01G207600 chr5B 96.117 515 19 1 1 515 684443216 684443729 0.000000e+00 839.0
7 TraesCS7B01G207600 chr5B 95.127 513 23 2 1 513 611696635 611696125 0.000000e+00 808.0
8 TraesCS7B01G207600 chr5B 94.208 518 28 2 1 518 534586709 534586194 0.000000e+00 789.0
9 TraesCS7B01G207600 chr2B 95.127 513 23 2 1 513 91497192 91496682 0.000000e+00 808.0
10 TraesCS7B01G207600 chr2B 94.336 512 27 2 1 512 398049201 398048692 0.000000e+00 784.0
11 TraesCS7B01G207600 chr2B 94.325 511 26 3 1 511 673092004 673092511 0.000000e+00 780.0
12 TraesCS7B01G207600 chr2B 88.929 560 56 5 2267 2821 476026691 476026133 0.000000e+00 686.0
13 TraesCS7B01G207600 chr3B 95.108 511 20 3 1 511 679507257 679507762 0.000000e+00 800.0
14 TraesCS7B01G207600 chr3B 100.000 28 0 0 658 685 17405639 17405666 5.000000e-03 52.8
15 TraesCS7B01G207600 chr1D 94.369 515 27 2 1 515 12417577 12417065 0.000000e+00 789.0
16 TraesCS7B01G207600 chr1D 91.176 544 44 4 2278 2818 452115461 452116003 0.000000e+00 736.0
17 TraesCS7B01G207600 chr4B 94.325 511 27 2 1 511 2409066 2408558 0.000000e+00 782.0
18 TraesCS7B01G207600 chr6A 90.758 541 46 3 2282 2821 182506066 182505529 0.000000e+00 719.0
19 TraesCS7B01G207600 chr6A 87.454 542 58 9 2279 2816 15505978 15505443 1.440000e-172 616.0
20 TraesCS7B01G207600 chr3D 89.444 540 52 4 2286 2821 14380019 14379481 0.000000e+00 676.0
21 TraesCS7B01G207600 chr6D 88.707 549 55 4 2280 2821 27661722 27661174 0.000000e+00 664.0


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 TraesCS7B01G207600 chr7B 380078683 380081503 2820 False 5210.0 5210 100.000 1 2821 1 chr7B.!!$F2 2820
1 TraesCS7B01G207600 chr7B 152799436 152799974 538 False 739.0 739 91.497 2281 2818 1 chr7B.!!$F1 537
2 TraesCS7B01G207600 chr7D 385717474 385721933 4459 False 1739.5 2649 93.840 515 2818 2 chr7D.!!$F1 2303
3 TraesCS7B01G207600 chr7A 433742726 433745623 2897 False 1572.5 2265 92.359 515 2818 2 chr7A.!!$F1 2303
4 TraesCS7B01G207600 chr5B 684443216 684443729 513 False 839.0 839 96.117 1 515 1 chr5B.!!$F1 514
5 TraesCS7B01G207600 chr5B 611696125 611696635 510 True 808.0 808 95.127 1 513 1 chr5B.!!$R2 512
6 TraesCS7B01G207600 chr5B 534586194 534586709 515 True 789.0 789 94.208 1 518 1 chr5B.!!$R1 517
7 TraesCS7B01G207600 chr2B 91496682 91497192 510 True 808.0 808 95.127 1 513 1 chr2B.!!$R1 512
8 TraesCS7B01G207600 chr2B 398048692 398049201 509 True 784.0 784 94.336 1 512 1 chr2B.!!$R2 511
9 TraesCS7B01G207600 chr2B 673092004 673092511 507 False 780.0 780 94.325 1 511 1 chr2B.!!$F1 510
10 TraesCS7B01G207600 chr2B 476026133 476026691 558 True 686.0 686 88.929 2267 2821 1 chr2B.!!$R3 554
11 TraesCS7B01G207600 chr3B 679507257 679507762 505 False 800.0 800 95.108 1 511 1 chr3B.!!$F2 510
12 TraesCS7B01G207600 chr1D 12417065 12417577 512 True 789.0 789 94.369 1 515 1 chr1D.!!$R1 514
13 TraesCS7B01G207600 chr1D 452115461 452116003 542 False 736.0 736 91.176 2278 2818 1 chr1D.!!$F1 540
14 TraesCS7B01G207600 chr4B 2408558 2409066 508 True 782.0 782 94.325 1 511 1 chr4B.!!$R1 510
15 TraesCS7B01G207600 chr6A 182505529 182506066 537 True 719.0 719 90.758 2282 2821 1 chr6A.!!$R2 539
16 TraesCS7B01G207600 chr6A 15505443 15505978 535 True 616.0 616 87.454 2279 2816 1 chr6A.!!$R1 537
17 TraesCS7B01G207600 chr3D 14379481 14380019 538 True 676.0 676 89.444 2286 2821 1 chr3D.!!$R1 535
18 TraesCS7B01G207600 chr6D 27661174 27661722 548 True 664.0 664 88.707 2280 2821 1 chr6D.!!$R1 541

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
977 993 1.139455 CCCTCCGCGAACCCTATAAAA 59.861 52.381 8.23 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 5092 0.677731 CCGAAGCTTGCTCCAATCCA 60.678 55.0 2.1 0.0 0.0 3.41 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
269 271 2.202866 CCATCGACTAGGCTGGTGT 58.797 57.895 8.74 0.00 0.00 4.16
342 344 2.296471 CTCTGTTGTAGGGTGTCGTCTT 59.704 50.000 0.00 0.00 0.00 3.01
354 356 1.483004 TGTCGTCTTTGGTCACTTGGA 59.517 47.619 0.00 0.00 0.00 3.53
368 370 1.686587 ACTTGGATGACAGTGTCGTCA 59.313 47.619 35.05 23.12 46.76 4.35
505 507 2.680913 CCTGCCGGTTGCTCGAAAG 61.681 63.158 1.90 0.00 42.00 2.62
583 589 2.627933 TCTGCTACTTGGTTTACCCCT 58.372 47.619 0.00 0.00 34.29 4.79
612 622 7.530426 AAAAAGTTCATTCTGCTATTCCACT 57.470 32.000 0.00 0.00 0.00 4.00
619 634 2.923121 TCTGCTATTCCACTGGCATTC 58.077 47.619 0.00 0.00 31.81 2.67
625 640 3.967332 ATTCCACTGGCATTCTTTTGG 57.033 42.857 0.00 0.00 0.00 3.28
626 641 1.631405 TCCACTGGCATTCTTTTGGG 58.369 50.000 0.00 0.00 0.00 4.12
832 848 3.673338 TCGACTGAACTTTTGCGATAGTG 59.327 43.478 0.00 0.00 39.35 2.74
833 849 3.428870 CGACTGAACTTTTGCGATAGTGT 59.571 43.478 0.00 0.00 39.35 3.55
866 882 1.263356 CCACCGAAACTCCCTCTACA 58.737 55.000 0.00 0.00 0.00 2.74
944 960 2.809601 CGGAGCGGAGGTGTTTCG 60.810 66.667 0.00 0.00 39.88 3.46
977 993 1.139455 CCCTCCGCGAACCCTATAAAA 59.861 52.381 8.23 0.00 0.00 1.52
1145 1161 7.982919 TGTAGAGTAGACTGTACAGAGAGAATC 59.017 40.741 29.30 17.46 44.50 2.52
1161 1177 6.095580 AGAGAGAATCGTTAGCTGTGTATCAA 59.904 38.462 0.00 0.00 42.67 2.57
1170 1186 4.981806 AGCTGTGTATCAAGAGAGAGAC 57.018 45.455 0.00 0.00 30.60 3.36
1176 1192 6.353323 TGTGTATCAAGAGAGAGACTAGAGG 58.647 44.000 0.00 0.00 31.20 3.69
1187 1203 1.941820 ACTAGAGGCAGGGGAGGGA 60.942 63.158 0.00 0.00 0.00 4.20
1188 1204 1.152355 CTAGAGGCAGGGGAGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
1204 1220 2.089059 AGGGAGGATCTAGAGAGAGGGA 60.089 54.545 0.00 0.00 34.35 4.20
1555 1571 2.871633 TGACGAATACAGGTACGCGATA 59.128 45.455 15.93 0.00 0.00 2.92
1754 1770 0.962356 AACCAAGCAGCAGAATCGGG 60.962 55.000 0.00 0.00 0.00 5.14
1762 1778 3.072184 AGCAGCAGAATCGGGAATCTATT 59.928 43.478 0.00 0.00 0.00 1.73
1798 1814 2.165845 ACTGTCTACGTATTGCAGGACC 59.834 50.000 18.73 0.00 0.00 4.46
1814 1830 2.044492 AGGACCAAGGATCTGTACAGGA 59.956 50.000 22.48 9.94 0.00 3.86
1885 1911 0.109272 TAGCCTATATGCGCGTCAGC 60.109 55.000 4.79 5.10 40.74 4.26
1996 2022 6.186957 TGCATGACCTTGTAAATCCTATGTT 58.813 36.000 0.00 0.00 0.00 2.71
2162 2835 1.270358 GCGGATCCCTACATCAAGGTC 60.270 57.143 6.06 0.00 34.56 3.85
2225 2899 3.771160 CCTCCTGCCGGCGTTACT 61.771 66.667 23.90 0.00 0.00 2.24
2226 2900 2.509336 CTCCTGCCGGCGTTACTG 60.509 66.667 23.90 5.74 0.00 2.74
2248 2922 2.361119 CCAATCTGCATCATCTTGTGGG 59.639 50.000 0.00 0.00 0.00 4.61
2254 2928 1.952296 GCATCATCTTGTGGGCTTAGG 59.048 52.381 0.00 0.00 0.00 2.69
2257 2931 1.559682 TCATCTTGTGGGCTTAGGACC 59.440 52.381 0.00 0.00 42.24 4.46
2263 5062 4.986467 GGGCTTAGGACCATGGTG 57.014 61.111 25.52 8.65 41.30 4.17
2356 5161 6.541111 AGAGAAAAACTTAACGTCCATCAC 57.459 37.500 0.00 0.00 0.00 3.06
2357 5162 6.053005 AGAGAAAAACTTAACGTCCATCACA 58.947 36.000 0.00 0.00 0.00 3.58
2380 5185 9.378551 CACACTATAGCTACCACAAAAGAATAA 57.621 33.333 0.00 0.00 0.00 1.40
2406 5211 4.741321 AATATGGTTCAATTGCACCCAG 57.259 40.909 22.27 0.00 29.93 4.45
2530 5339 2.084610 TGCTTCATCAGTGTCTTCCG 57.915 50.000 0.00 0.00 0.00 4.30
2544 5353 4.989168 GTGTCTTCCGTAACTTGATCAACT 59.011 41.667 3.38 0.00 0.00 3.16
2685 5494 6.539103 AGGCAAAATTCCTTTACGAGATCTAC 59.461 38.462 0.00 0.00 0.00 2.59
2700 5509 4.688021 AGATCTACAGGATTGAAAGCGAC 58.312 43.478 0.00 0.00 34.33 5.19
2716 5525 8.552083 TGAAAGCGACATATAATAGCATCATT 57.448 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 4.735132 CCGCCGCTCCGACTTTCA 62.735 66.667 0.00 0.00 0.00 2.69
170 171 4.796231 CGACTTCCACTCCGGCCG 62.796 72.222 21.04 21.04 33.14 6.13
321 323 1.887198 AGACGACACCCTACAACAGAG 59.113 52.381 0.00 0.00 0.00 3.35
342 344 2.172505 ACACTGTCATCCAAGTGACCAA 59.827 45.455 9.63 0.00 46.17 3.67
368 370 2.356313 CTGCGCACCACTCGAGTT 60.356 61.111 17.26 0.00 0.00 3.01
405 407 4.521130 AACCGATACATCTGCGATACAT 57.479 40.909 0.00 0.00 0.00 2.29
480 482 1.295423 GCAACCGGCAGGAGTTCTA 59.705 57.895 10.86 0.00 43.97 2.10
516 518 1.358787 TCCATCAGGTTTGAGCCCAAT 59.641 47.619 0.00 0.00 36.61 3.16
606 616 1.969923 CCCAAAAGAATGCCAGTGGAA 59.030 47.619 15.20 1.11 0.00 3.53
612 622 0.965439 CGGTTCCCAAAAGAATGCCA 59.035 50.000 0.00 0.00 0.00 4.92
619 634 1.977009 GGGCCTCGGTTCCCAAAAG 60.977 63.158 0.84 0.00 42.18 2.27
626 641 3.384532 TACGGTGGGCCTCGGTTC 61.385 66.667 21.42 0.00 0.00 3.62
631 646 1.542187 AAGAGTGTACGGTGGGCCTC 61.542 60.000 4.53 0.00 0.00 4.70
706 722 0.394565 GCCTGATGGAGCCGTATTCT 59.605 55.000 0.00 0.00 34.57 2.40
832 848 7.372714 AGTTTCGGTGGGAACAAAAATAATAC 58.627 34.615 0.00 0.00 46.06 1.89
833 849 7.309316 GGAGTTTCGGTGGGAACAAAAATAATA 60.309 37.037 0.00 0.00 46.06 0.98
866 882 1.338389 GCCATTTTTCAGTGCCATGCT 60.338 47.619 0.00 0.00 0.00 3.79
944 960 1.682344 GGAGGGTGGCAAATGTCCC 60.682 63.158 1.93 1.93 40.16 4.46
977 993 4.922026 GTCACGTGTTGGGGCCGT 62.922 66.667 16.51 0.00 34.71 5.68
1145 1161 5.065346 TCTCTCTCTTGATACACAGCTAACG 59.935 44.000 0.00 0.00 0.00 3.18
1161 1177 1.494721 CCCTGCCTCTAGTCTCTCTCT 59.505 57.143 0.00 0.00 0.00 3.10
1170 1186 1.152355 CTCCCTCCCCTGCCTCTAG 60.152 68.421 0.00 0.00 0.00 2.43
1176 1192 0.544120 CTAGATCCTCCCTCCCCTGC 60.544 65.000 0.00 0.00 0.00 4.85
1187 1203 2.576191 CCGATCCCTCTCTCTAGATCCT 59.424 54.545 0.00 0.00 33.13 3.24
1188 1204 2.356741 CCCGATCCCTCTCTCTAGATCC 60.357 59.091 0.00 0.00 33.13 3.36
1204 1220 0.838122 CTATCTTGGCCCCTCCCGAT 60.838 60.000 0.00 0.00 0.00 4.18
1360 1376 2.042435 CTCCTCCGCCTCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
1534 1550 1.085893 TCGCGTACCTGTATTCGTCA 58.914 50.000 5.77 0.00 0.00 4.35
1555 1571 2.159014 AGAGAGAGAGACGCGTATCTGT 60.159 50.000 38.07 34.16 30.29 3.41
1718 1734 1.134226 GTTTTCGTGGTCGTCATCGT 58.866 50.000 0.00 0.00 38.33 3.73
1762 1778 7.993101 ACGTAGACAGTAATAGCAATCTGTAA 58.007 34.615 0.00 0.00 40.53 2.41
1798 1814 6.037172 CGGTTTATTTCCTGTACAGATCCTTG 59.963 42.308 24.68 6.34 0.00 3.61
1814 1830 0.996583 TCAGGGGAGCCGGTTTATTT 59.003 50.000 1.90 0.00 0.00 1.40
1996 2022 6.003326 ACATGACATTTACACCATGAGTTCA 58.997 36.000 0.00 0.00 38.83 3.18
2121 2783 2.483714 CCCACGGATACATGTTGAGGAG 60.484 54.545 2.30 0.00 0.00 3.69
2145 2807 3.970640 AGGAAGACCTTGATGTAGGGATC 59.029 47.826 0.00 0.00 45.36 3.36
2162 2835 1.301293 GCTTGTGGGGAGGAGGAAG 59.699 63.158 0.00 0.00 0.00 3.46
2226 2900 2.223735 CCACAAGATGATGCAGATTGGC 60.224 50.000 0.00 0.00 0.00 4.52
2248 2922 1.972872 CCATCACCATGGTCCTAAGC 58.027 55.000 16.53 0.00 44.46 3.09
2257 2931 0.749091 ATCACGCCACCATCACCATG 60.749 55.000 0.00 0.00 0.00 3.66
2258 2932 0.749091 CATCACGCCACCATCACCAT 60.749 55.000 0.00 0.00 0.00 3.55
2259 2933 1.377072 CATCACGCCACCATCACCA 60.377 57.895 0.00 0.00 0.00 4.17
2260 2934 2.764314 GCATCACGCCACCATCACC 61.764 63.158 0.00 0.00 32.94 4.02
2261 2935 1.985447 CTGCATCACGCCACCATCAC 61.985 60.000 0.00 0.00 41.33 3.06
2263 5062 1.746615 ACTGCATCACGCCACCATC 60.747 57.895 0.00 0.00 41.33 3.51
2291 5092 0.677731 CCGAAGCTTGCTCCAATCCA 60.678 55.000 2.10 0.00 0.00 3.41
2356 5161 9.601217 AGTTATTCTTTTGTGGTAGCTATAGTG 57.399 33.333 0.00 0.00 0.00 2.74
2357 5162 9.819267 GAGTTATTCTTTTGTGGTAGCTATAGT 57.181 33.333 0.00 0.00 0.00 2.12
2380 5185 5.337491 GGGTGCAATTGAACCATATTTGAGT 60.337 40.000 32.46 0.00 46.04 3.41
2530 5339 8.142994 TCTTCTTTCACAGTTGATCAAGTTAC 57.857 34.615 13.25 0.00 0.00 2.50
2544 5353 2.092429 AGGTGTTGGCTCTTCTTTCACA 60.092 45.455 0.00 0.00 0.00 3.58
2685 5494 7.118245 TGCTATTATATGTCGCTTTCAATCCTG 59.882 37.037 0.00 0.00 0.00 3.86
2716 5525 6.972328 GCGAGAAATATTTGCAAAGGTTGATA 59.028 34.615 18.19 4.24 0.00 2.15


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

AutoCloner maintained by Alex Coulton.