Multiple sequence alignment - TraesCS7A01G559500

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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 TraesCS7A01G559500 chr7A 100.000 2576 0 0 1 2576 731390095 731387520 0.000000e+00 4758.0
1 TraesCS7A01G559500 chr7A 86.771 1663 181 26 508 2142 731252594 731254245 0.000000e+00 1816.0
2 TraesCS7A01G559500 chr7A 86.071 1723 188 26 861 2576 731236443 731238120 0.000000e+00 1805.0
3 TraesCS7A01G559500 chr7A 86.938 1447 173 10 1015 2453 731283062 731281624 0.000000e+00 1611.0
4 TraesCS7A01G559500 chr7A 84.861 502 58 10 2073 2571 731019029 731019515 8.280000e-135 490.0
5 TraesCS7A01G559500 chr7A 84.274 496 65 4 2076 2571 731499928 731499446 3.000000e-129 472.0
6 TraesCS7A01G559500 chr7A 88.629 299 29 2 22 316 731016974 731017271 2.440000e-95 359.0
7 TraesCS7A01G559500 chr7A 87.625 299 31 3 22 316 731422156 731421860 2.450000e-90 342.0
8 TraesCS7A01G559500 chr7D 94.044 2082 103 10 508 2576 634669546 634671619 0.000000e+00 3138.0
9 TraesCS7A01G559500 chr7D 85.294 2006 213 38 508 2453 634677584 634679567 0.000000e+00 1995.0
10 TraesCS7A01G559500 chr7D 86.590 1663 186 27 508 2142 634710094 634708441 0.000000e+00 1801.0
11 TraesCS7A01G559500 chr7D 92.354 497 29 6 21 512 634669027 634669519 0.000000e+00 699.0
12 TraesCS7A01G559500 chr7B 93.077 1979 123 10 508 2477 741548913 741550886 0.000000e+00 2883.0
13 TraesCS7A01G559500 chr7B 92.766 1963 108 15 508 2460 741620186 741618248 0.000000e+00 2808.0
14 TraesCS7A01G559500 chr7B 83.739 2011 241 43 508 2455 741588815 741586828 0.000000e+00 1823.0
15 TraesCS7A01G559500 chr7B 91.919 495 36 4 25 515 741620708 741620214 0.000000e+00 689.0
16 TraesCS7A01G559500 chr7B 92.500 440 33 0 2037 2476 741554162 741554601 4.680000e-177 630.0
17 TraesCS7A01G559500 chr7B 79.104 134 19 9 371 496 672892228 672892096 1.640000e-12 84.2
18 TraesCS7A01G559500 chr4B 86.547 1509 159 27 508 1992 625077810 625079298 0.000000e+00 1622.0
19 TraesCS7A01G559500 chr4B 83.660 306 34 8 15 316 625077474 625077767 9.080000e-70 274.0
20 TraesCS7A01G559500 chr6D 84.444 180 22 5 320 495 5926871 5926694 3.410000e-39 172.0
21 TraesCS7A01G559500 chr6D 82.873 181 25 5 320 496 5926680 5926502 9.540000e-35 158.0
22 TraesCS7A01G559500 chr3B 76.440 191 32 9 316 497 2994294 2994480 9.820000e-15 91.6
23 TraesCS7A01G559500 chr6B 80.531 113 20 2 321 432 612269547 612269658 4.570000e-13 86.1
24 TraesCS7A01G559500 chr6B 80.220 91 16 2 382 470 706998373 706998463 1.650000e-07 67.6
25 TraesCS7A01G559500 chr1A 75.573 131 25 6 372 497 452288595 452288467 9.960000e-05 58.4


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 TraesCS7A01G559500 chr7A 731387520 731390095 2575 True 4758.0 4758 100.0000 1 2576 1 chr7A.!!$R2 2575
1 TraesCS7A01G559500 chr7A 731252594 731254245 1651 False 1816.0 1816 86.7710 508 2142 1 chr7A.!!$F2 1634
2 TraesCS7A01G559500 chr7A 731236443 731238120 1677 False 1805.0 1805 86.0710 861 2576 1 chr7A.!!$F1 1715
3 TraesCS7A01G559500 chr7A 731281624 731283062 1438 True 1611.0 1611 86.9380 1015 2453 1 chr7A.!!$R1 1438
4 TraesCS7A01G559500 chr7A 731016974 731019515 2541 False 424.5 490 86.7450 22 2571 2 chr7A.!!$F3 2549
5 TraesCS7A01G559500 chr7D 634677584 634679567 1983 False 1995.0 1995 85.2940 508 2453 1 chr7D.!!$F1 1945
6 TraesCS7A01G559500 chr7D 634669027 634671619 2592 False 1918.5 3138 93.1990 21 2576 2 chr7D.!!$F2 2555
7 TraesCS7A01G559500 chr7D 634708441 634710094 1653 True 1801.0 1801 86.5900 508 2142 1 chr7D.!!$R1 1634
8 TraesCS7A01G559500 chr7B 741586828 741588815 1987 True 1823.0 1823 83.7390 508 2455 1 chr7B.!!$R2 1947
9 TraesCS7A01G559500 chr7B 741548913 741554601 5688 False 1756.5 2883 92.7885 508 2477 2 chr7B.!!$F1 1969
10 TraesCS7A01G559500 chr7B 741618248 741620708 2460 True 1748.5 2808 92.3425 25 2460 2 chr7B.!!$R3 2435
11 TraesCS7A01G559500 chr4B 625077474 625079298 1824 False 948.0 1622 85.1035 15 1992 2 chr4B.!!$F1 1977

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
342 349 0.387239 GCAACATTCACGGGCTCAAC 60.387 55.0 0.00 0.0 0.00 3.18 F
1290 1427 0.107312 AGCGCATTGAGAAGCTCCAT 60.107 50.0 11.47 0.0 34.48 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1564 0.373024 GATGCTCTTGAGAAGCACGC 59.627 55.0 0.0 0.0 41.61 5.34 R
2384 2761 0.396435 AATGTTGTCCTCCTGTGCGA 59.604 50.0 0.0 0.0 0.00 5.10 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
28 29 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
47 50 5.353123 TGTGTTTTCAAAGAGGTGAGTGTAC 59.647 40.000 0.00 0.00 0.00 2.90
51 54 2.691526 TCAAAGAGGTGAGTGTACGTGT 59.308 45.455 0.00 0.00 0.00 4.49
52 55 3.884693 TCAAAGAGGTGAGTGTACGTGTA 59.115 43.478 0.00 0.00 0.00 2.90
79 82 7.174253 TGTTGTTGGATATCTCACACTTTTACC 59.826 37.037 2.05 0.00 0.00 2.85
89 92 7.962964 TCTCACACTTTTACCATCAAAGTAG 57.037 36.000 0.00 0.00 41.58 2.57
249 256 4.599047 TTCATGTACTTTTTGGCCTTGG 57.401 40.909 3.32 0.00 0.00 3.61
342 349 0.387239 GCAACATTCACGGGCTCAAC 60.387 55.000 0.00 0.00 0.00 3.18
353 360 2.626780 GGCTCAACACGGGGCTTTC 61.627 63.158 0.00 0.00 0.00 2.62
376 385 2.708216 TTGTCACTCTGAGTTGGCAA 57.292 45.000 17.31 17.31 0.00 4.52
448 461 3.032459 GGGGGCGGGTTTAATTAAATGA 58.968 45.455 13.54 0.00 0.00 2.57
458 472 5.290885 GGTTTAATTAAATGAAAGCAGCCCG 59.709 40.000 13.54 0.00 32.26 6.13
481 496 1.604604 AAGCATGTAAACAGCCGTGT 58.395 45.000 0.00 0.00 39.19 4.49
608 666 2.284190 GATAGGAGCAAGGCTTGTGTC 58.716 52.381 26.71 21.93 39.88 3.67
659 717 1.543607 TTGAAGGATGGCATTGCGAA 58.456 45.000 0.00 0.00 0.00 4.70
690 765 5.537674 AGCTTAACATCATGGGGAAATCATC 59.462 40.000 0.00 0.00 0.00 2.92
703 779 3.248602 GGAAATCATCAGCACGGTATGAC 59.751 47.826 0.00 0.00 32.74 3.06
736 812 2.099263 CCGTGATATCGGGAGCGATATT 59.901 50.000 0.67 0.00 45.88 1.28
739 816 3.130516 GTGATATCGGGAGCGATATTGGA 59.869 47.826 0.67 0.00 40.41 3.53
828 919 6.677913 CACAATTAAAGTCGGGTCAAAGATT 58.322 36.000 0.00 0.00 0.00 2.40
843 934 7.307455 GGGTCAAAGATTTGCTAGATATTCGAC 60.307 40.741 0.00 0.00 38.05 4.20
992 1113 3.118738 TCCTTCGCTGGTTTTATCCTCTC 60.119 47.826 0.00 0.00 0.00 3.20
1006 1127 1.748122 CTCTCGCCAGCAATGCCTT 60.748 57.895 0.00 0.00 0.00 4.35
1050 1187 4.129737 CATGACTCGACCCGGCGT 62.130 66.667 6.01 0.00 0.00 5.68
1227 1364 0.607489 TCAAAAGCCTGCCAGAGCTC 60.607 55.000 5.27 5.27 38.74 4.09
1229 1366 2.116983 AAAAGCCTGCCAGAGCTCGA 62.117 55.000 8.37 0.00 38.74 4.04
1290 1427 0.107312 AGCGCATTGAGAAGCTCCAT 60.107 50.000 11.47 0.00 34.48 3.41
1348 1485 1.757699 GCGAGATCAGGTACCTCCTTT 59.242 52.381 12.84 0.00 45.67 3.11
1401 1538 0.250684 TTGGCCTCAACATCGAGCAA 60.251 50.000 3.32 0.00 0.00 3.91
1427 1564 2.035832 CCAAAGTTGGCTACAAAGTGGG 59.964 50.000 1.24 0.00 42.21 4.61
1507 1644 0.250901 AGCTTCATGTGTCACCACCC 60.251 55.000 0.00 0.00 41.09 4.61
1565 1702 0.115349 ACCACCTCAGTAGCAGGAGT 59.885 55.000 0.00 0.00 34.75 3.85
1688 1825 4.016444 GCAGTTCTTTGATATGGGGTTCA 58.984 43.478 0.00 0.00 0.00 3.18
1698 1835 2.024176 ATGGGGTTCAGTTCGATTCG 57.976 50.000 0.00 0.00 0.00 3.34
1782 1925 5.294552 GCTTTGGTGGTTAGTATGAGACATC 59.705 44.000 0.00 0.00 0.00 3.06
2031 2403 4.928661 ACGTGCTAGACAATTGATTGAC 57.071 40.909 13.59 4.60 40.14 3.18
2172 2547 8.627403 CAAGCTAAATGTGATGGATGACTAATT 58.373 33.333 0.00 0.00 0.00 1.40
2185 2560 6.547141 TGGATGACTAATTTTTGCCTGGATAG 59.453 38.462 0.00 0.00 0.00 2.08
2359 2736 5.808366 AGTTGGAGTCATGTTCTCTGTTA 57.192 39.130 15.82 3.68 33.06 2.41
2369 2746 6.650807 GTCATGTTCTCTGTTATTCAGACCAA 59.349 38.462 0.00 0.00 46.77 3.67
2384 2761 5.087323 TCAGACCAACCTTCATTCTAGAGT 58.913 41.667 0.00 0.00 0.00 3.24
2462 6562 0.980231 AGGAGACATGGTGGCCTCTC 60.980 60.000 3.32 6.59 0.00 3.20
2512 6612 5.105106 TGGTAGCCGAAATCTTGACTCATTA 60.105 40.000 0.00 0.00 0.00 1.90
2524 6624 0.392706 ACTCATTATCGGCGCCATCA 59.607 50.000 28.98 10.08 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.863740 ACACACACACACACATTCTACG 59.136 45.455 0.00 0.00 0.00 3.51
1 2 3.621268 ACACACACACACACACATTCTAC 59.379 43.478 0.00 0.00 0.00 2.59
2 3 3.620821 CACACACACACACACACATTCTA 59.379 43.478 0.00 0.00 0.00 2.10
3 4 2.419673 CACACACACACACACACATTCT 59.580 45.455 0.00 0.00 0.00 2.40
5 6 2.095314 CACACACACACACACACACATT 60.095 45.455 0.00 0.00 0.00 2.71
6 7 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
7 8 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
8 9 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
9 10 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
10 11 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
11 12 2.618709 TGAAAACACACACACACACACA 59.381 40.909 0.00 0.00 0.00 3.72
12 13 3.275400 TGAAAACACACACACACACAC 57.725 42.857 0.00 0.00 0.00 3.82
13 14 3.990318 TTGAAAACACACACACACACA 57.010 38.095 0.00 0.00 0.00 3.72
14 15 4.541779 TCTTTGAAAACACACACACACAC 58.458 39.130 0.00 0.00 0.00 3.82
15 16 4.320861 CCTCTTTGAAAACACACACACACA 60.321 41.667 0.00 0.00 0.00 3.72
16 17 4.165779 CCTCTTTGAAAACACACACACAC 58.834 43.478 0.00 0.00 0.00 3.82
17 18 3.823873 ACCTCTTTGAAAACACACACACA 59.176 39.130 0.00 0.00 0.00 3.72
18 19 4.083003 TCACCTCTTTGAAAACACACACAC 60.083 41.667 0.00 0.00 0.00 3.82
19 20 4.075682 TCACCTCTTTGAAAACACACACA 58.924 39.130 0.00 0.00 0.00 3.72
28 29 4.116961 CACGTACACTCACCTCTTTGAAA 58.883 43.478 0.00 0.00 0.00 2.69
47 50 5.810074 TGTGAGATATCCAACAACATACACG 59.190 40.000 0.00 0.00 0.00 4.49
51 54 8.862325 AAAAGTGTGAGATATCCAACAACATA 57.138 30.769 9.10 0.00 0.00 2.29
52 55 7.765695 AAAAGTGTGAGATATCCAACAACAT 57.234 32.000 9.10 0.00 0.00 2.71
342 349 0.240945 GACAATGTGAAAGCCCCGTG 59.759 55.000 0.00 0.00 0.00 4.94
353 360 2.225019 GCCAACTCAGAGTGACAATGTG 59.775 50.000 3.05 0.00 0.00 3.21
376 385 2.247372 CCCCCTTAATCCAATCAACCCT 59.753 50.000 0.00 0.00 0.00 4.34
433 446 5.584649 GGGCTGCTTTCATTTAATTAAACCC 59.415 40.000 12.74 11.22 0.00 4.11
448 461 1.067635 CATGCTTTTACGGGCTGCTTT 60.068 47.619 0.00 0.00 0.00 3.51
458 472 3.911964 CACGGCTGTTTACATGCTTTTAC 59.088 43.478 0.00 0.00 0.00 2.01
481 496 5.700373 GCTCAAATCCCAAAAATGCTAAACA 59.300 36.000 0.00 0.00 0.00 2.83
608 666 0.390124 CATCCAAATGAATGGGCCGG 59.610 55.000 0.00 0.00 41.05 6.13
690 765 2.196749 GAGACATGTCATACCGTGCTG 58.803 52.381 27.02 0.00 0.00 4.41
703 779 0.668535 TATCACGGGAGCGAGACATG 59.331 55.000 0.00 0.00 0.00 3.21
736 812 1.600511 TAGCGCATGACGTTCCTCCA 61.601 55.000 11.47 0.00 46.11 3.86
739 816 0.595053 CGATAGCGCATGACGTTCCT 60.595 55.000 11.47 0.00 46.11 3.36
828 919 1.335810 ACGCGGTCGAATATCTAGCAA 59.664 47.619 12.47 0.00 39.41 3.91
843 934 5.220340 CCTTATTTAGTACTTGTGAACGCGG 60.220 44.000 12.47 0.00 0.00 6.46
883 974 7.771361 TGATTTGGTAAGAGTTTACTGTGACAA 59.229 33.333 0.00 0.00 39.30 3.18
1006 1127 2.107378 TGTATTGGAGGGTCACTTTGCA 59.893 45.455 0.00 0.00 0.00 4.08
1011 1147 2.127708 GGGATGTATTGGAGGGTCACT 58.872 52.381 0.00 0.00 0.00 3.41
1050 1187 3.132824 TGAGGCGCTTCTTGAATCTATCA 59.867 43.478 20.92 0.00 35.85 2.15
1290 1427 1.658114 CGTCTTGTCGACCTGGTCA 59.342 57.895 25.42 10.75 39.56 4.02
1348 1485 3.446873 GGGTCACCATGCATGATTTTGTA 59.553 43.478 28.31 3.23 36.50 2.41
1427 1564 0.373024 GATGCTCTTGAGAAGCACGC 59.627 55.000 0.00 0.00 41.61 5.34
1507 1644 1.299541 GACCCCATGTCTATGTTGCG 58.700 55.000 0.00 0.00 41.03 4.85
1565 1702 1.879372 GCTCACCATGTCAAGTCAGCA 60.879 52.381 0.00 0.00 0.00 4.41
1688 1825 1.347320 GGAGCGAAACGAATCGAACT 58.653 50.000 10.55 6.62 45.48 3.01
1698 1835 1.369625 CTGGTACATGGGAGCGAAAC 58.630 55.000 0.00 0.00 38.20 2.78
1805 1948 1.672363 ACGACGCACATAGACGGATAA 59.328 47.619 0.00 0.00 0.00 1.75
2005 2377 5.748630 CAATCAATTGTCTAGCACGTAGCTA 59.251 40.000 15.64 15.64 42.42 3.32
2031 2403 0.532862 ACACGACCAAGGTTCAGCAG 60.533 55.000 0.00 0.00 0.00 4.24
2172 2547 7.953005 TTCACAAATATCTATCCAGGCAAAA 57.047 32.000 0.00 0.00 0.00 2.44
2359 2736 6.214412 ACTCTAGAATGAAGGTTGGTCTGAAT 59.786 38.462 0.00 0.00 0.00 2.57
2369 2746 2.826128 TGTGCGACTCTAGAATGAAGGT 59.174 45.455 0.00 0.00 0.00 3.50
2384 2761 0.396435 AATGTTGTCCTCCTGTGCGA 59.604 50.000 0.00 0.00 0.00 5.10
2462 6562 1.010350 GATTGCATGAAGGCGAGCG 60.010 57.895 0.00 0.00 36.28 5.03
2512 6612 2.592574 CCACATGATGGCGCCGAT 60.593 61.111 23.90 16.46 43.24 4.18
2524 6624 1.919600 GAGCCTCAGGGAAGCCACAT 61.920 60.000 0.00 0.00 33.58 3.21


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

AutoCloner maintained by Alex Coulton.