Multiple sequence alignment - TraesCS5A01G250400

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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 TraesCS5A01G250400 chr5A 100.000 2591 0 0 1 2591 465998089 465995499 0.000000e+00 4785
1 TraesCS5A01G250400 chr5D 93.788 2624 76 30 1 2591 364672004 364669435 0.000000e+00 3862
2 TraesCS5A01G250400 chr5B 94.342 1944 57 23 1 1914 430681308 430679388 0.000000e+00 2931
3 TraesCS5A01G250400 chr5B 95.210 689 26 6 1908 2591 430674729 430674043 0.000000e+00 1083
4 TraesCS5A01G250400 chr7B 83.396 265 42 1 1251 1513 99130817 99130553 7.160000e-61 244
5 TraesCS5A01G250400 chr7D 82.609 276 46 2 1265 1539 136253355 136253081 2.580000e-60 243
6 TraesCS5A01G250400 chr7A 83.333 252 36 6 1265 1513 135901495 135901247 7.210000e-56 228


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 TraesCS5A01G250400 chr5A 465995499 465998089 2590 True 4785 4785 100.000 1 2591 1 chr5A.!!$R1 2590
1 TraesCS5A01G250400 chr5D 364669435 364672004 2569 True 3862 3862 93.788 1 2591 1 chr5D.!!$R1 2590
2 TraesCS5A01G250400 chr5B 430679388 430681308 1920 True 2931 2931 94.342 1 1914 1 chr5B.!!$R2 1913
3 TraesCS5A01G250400 chr5B 430674043 430674729 686 True 1083 1083 95.210 1908 2591 1 chr5B.!!$R1 683

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
791 836 0.397941 TCTGGACTGAGGCAAACTGG 59.602 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2266 1.92651 TGCGTGTGAGATCATTTAGCG 59.073 47.619 0.0 0.0 0.0 4.26 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
69 86 1.446445 CCAAACCACCATGCATGCG 60.446 57.895 21.69 16.19 0.00 4.73
70 87 1.289694 CAAACCACCATGCATGCGT 59.710 52.632 21.69 16.83 0.00 5.24
71 88 0.733566 CAAACCACCATGCATGCGTC 60.734 55.000 21.69 0.00 0.00 5.19
72 89 1.876497 AAACCACCATGCATGCGTCC 61.876 55.000 21.69 0.00 0.00 4.79
73 90 2.438975 CCACCATGCATGCGTCCT 60.439 61.111 21.69 0.00 0.00 3.85
74 91 2.048023 CCACCATGCATGCGTCCTT 61.048 57.895 21.69 0.00 0.00 3.36
75 92 1.138036 CACCATGCATGCGTCCTTG 59.862 57.895 21.69 8.18 0.00 3.61
76 93 2.103538 CCATGCATGCGTCCTTGC 59.896 61.111 21.69 0.00 41.18 4.01
77 94 2.412323 CCATGCATGCGTCCTTGCT 61.412 57.895 21.69 0.00 41.32 3.91
78 95 1.063649 CATGCATGCGTCCTTGCTC 59.936 57.895 14.93 0.00 41.32 4.26
79 96 2.466982 ATGCATGCGTCCTTGCTCG 61.467 57.895 14.09 0.00 41.32 5.03
80 97 3.121030 GCATGCGTCCTTGCTCGT 61.121 61.111 0.00 0.00 38.64 4.18
81 98 1.809619 GCATGCGTCCTTGCTCGTA 60.810 57.895 0.00 0.00 38.64 3.43
82 99 1.756375 GCATGCGTCCTTGCTCGTAG 61.756 60.000 0.00 0.00 38.64 3.51
83 100 1.141881 ATGCGTCCTTGCTCGTAGG 59.858 57.895 0.00 0.00 35.36 3.18
84 101 2.886124 GCGTCCTTGCTCGTAGGC 60.886 66.667 0.00 0.00 32.59 3.93
262 279 3.621715 GTGGCCTAACTATTTCTGTTCGG 59.378 47.826 3.32 0.00 34.58 4.30
377 394 3.060602 GCGCAAGAGTTTAGTTCTGTCT 58.939 45.455 0.30 0.00 43.02 3.41
527 546 2.786777 TGCGGTAGACAAGACTACTCA 58.213 47.619 9.00 5.75 41.45 3.41
557 576 2.453521 AGTCATGGAATGTGCAAGCAT 58.546 42.857 0.00 0.00 46.80 3.79
558 577 2.165641 AGTCATGGAATGTGCAAGCATG 59.834 45.455 0.00 0.00 46.80 4.06
559 578 2.164827 GTCATGGAATGTGCAAGCATGA 59.835 45.455 0.00 0.00 46.80 3.07
560 579 2.425668 TCATGGAATGTGCAAGCATGAG 59.574 45.455 0.00 0.00 46.80 2.90
569 598 7.545265 GGAATGTGCAAGCATGAGTAAATTAAA 59.455 33.333 0.00 0.00 0.00 1.52
585 621 8.021396 AGTAAATTAAACCGCAATGTTCTCTTC 58.979 33.333 0.00 0.00 0.00 2.87
602 638 5.313712 TCTCTTCGGAAAGCAAAGGTTAAT 58.686 37.500 0.00 0.00 32.18 1.40
615 651 6.441604 AGCAAAGGTTAATTGATGGAGGATTT 59.558 34.615 0.00 0.00 0.00 2.17
616 652 7.619302 AGCAAAGGTTAATTGATGGAGGATTTA 59.381 33.333 0.00 0.00 0.00 1.40
617 653 8.257306 GCAAAGGTTAATTGATGGAGGATTTAA 58.743 33.333 0.00 0.00 0.00 1.52
633 669 8.336987 GGAGGATTTAAATATAAGGGGCATAGT 58.663 37.037 0.00 0.00 0.00 2.12
678 715 2.038033 CGAAAGGAGAAAGGTGGTGGTA 59.962 50.000 0.00 0.00 0.00 3.25
788 833 3.239861 CCTCTGGACTGAGGCAAAC 57.760 57.895 11.56 0.00 45.84 2.93
789 834 0.689623 CCTCTGGACTGAGGCAAACT 59.310 55.000 11.56 0.00 45.84 2.66
790 835 1.610102 CCTCTGGACTGAGGCAAACTG 60.610 57.143 11.56 0.00 45.84 3.16
791 836 0.397941 TCTGGACTGAGGCAAACTGG 59.602 55.000 0.00 0.00 0.00 4.00
792 837 1.228245 TGGACTGAGGCAAACTGGC 60.228 57.895 0.00 0.00 44.10 4.85
793 838 1.228245 GGACTGAGGCAAACTGGCA 60.228 57.895 2.87 0.00 46.46 4.92
794 839 0.823356 GGACTGAGGCAAACTGGCAA 60.823 55.000 2.87 0.00 46.46 4.52
795 840 1.032014 GACTGAGGCAAACTGGCAAA 58.968 50.000 2.87 0.00 46.46 3.68
928 973 2.781595 AAGCGAAACCGAGCCACGAT 62.782 55.000 2.48 0.00 45.77 3.73
930 975 1.445410 CGAAACCGAGCCACGATCA 60.445 57.895 2.48 0.00 45.77 2.92
931 976 0.806102 CGAAACCGAGCCACGATCAT 60.806 55.000 2.48 0.00 45.77 2.45
932 977 0.931005 GAAACCGAGCCACGATCATC 59.069 55.000 2.48 0.00 45.77 2.92
933 978 0.806102 AAACCGAGCCACGATCATCG 60.806 55.000 5.22 5.22 46.93 3.84
1249 1300 1.134007 GTGATGACATCCATGGCCAGA 60.134 52.381 13.05 3.90 35.17 3.86
1250 1301 1.134007 TGATGACATCCATGGCCAGAC 60.134 52.381 13.05 0.00 35.17 3.51
1311 1362 2.028484 GTGTCCAACCGCGAGTCA 59.972 61.111 8.23 0.00 0.00 3.41
1362 1413 4.383861 CTCAGCGAGCTGTGGGCA 62.384 66.667 22.47 4.34 43.96 5.36
1566 1617 0.663153 GCGAGAAAAACACCACTGCT 59.337 50.000 0.00 0.00 0.00 4.24
1574 1625 4.039357 CACCACTGCTGCTGCTGC 62.039 66.667 22.51 22.51 41.07 5.25
1575 1626 4.266543 ACCACTGCTGCTGCTGCT 62.267 61.111 27.67 9.87 41.07 4.24
1576 1627 3.738246 CCACTGCTGCTGCTGCTG 61.738 66.667 27.75 27.75 41.07 4.41
1623 1674 9.331282 CTTATCTTCTCAATTTAACTACCAGGG 57.669 37.037 0.00 0.00 0.00 4.45
1883 1934 3.210227 TGATGAAACAAGAAACCGCTCA 58.790 40.909 0.00 0.00 0.00 4.26
1895 1946 0.393808 ACCGCTCAAAACCAGTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
2150 2203 7.011016 CCTTGTTTTAACTTCAGCGGAAAAATT 59.989 33.333 0.00 0.00 31.35 1.82
2364 2427 6.252441 CAGTAGCAAGTCTCGAAGATACAAAG 59.748 42.308 0.00 0.00 35.99 2.77
2433 2497 5.545658 AATTTGTATGTACGTGCCAAGAG 57.454 39.130 0.00 0.00 0.00 2.85
2462 2526 9.480053 AATATGAAAATTATGCAGTAACATGGC 57.520 29.630 0.00 0.00 0.00 4.40
2463 2527 6.278172 TGAAAATTATGCAGTAACATGGCA 57.722 33.333 0.00 0.00 42.43 4.92
2517 2584 1.179152 CAGGATTCAGGTGCATTGCA 58.821 50.000 7.38 7.38 35.60 4.08
2585 2652 4.065423 CGTGAGCGTGTGAATACAAAAT 57.935 40.909 0.00 0.00 38.82 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.635278 TTATCTCCTGCATCTGATTTCCA 57.365 39.130 0.00 0.00 0.00 3.53
69 86 1.226717 CGAGCCTACGAGCAAGGAC 60.227 63.158 0.00 0.00 36.08 3.85
70 87 1.378119 TCGAGCCTACGAGCAAGGA 60.378 57.895 0.00 0.00 37.37 3.36
71 88 1.226717 GTCGAGCCTACGAGCAAGG 60.227 63.158 0.00 0.00 42.88 3.61
72 89 0.798771 GTGTCGAGCCTACGAGCAAG 60.799 60.000 0.00 0.00 42.88 4.01
73 90 1.211969 GTGTCGAGCCTACGAGCAA 59.788 57.895 0.00 0.00 42.88 3.91
74 91 2.697761 GGTGTCGAGCCTACGAGCA 61.698 63.158 0.00 0.00 42.88 4.26
75 92 2.005960 ATGGTGTCGAGCCTACGAGC 62.006 60.000 7.38 0.00 42.88 5.03
76 93 0.248661 CATGGTGTCGAGCCTACGAG 60.249 60.000 7.38 0.00 42.88 4.18
77 94 1.807226 CATGGTGTCGAGCCTACGA 59.193 57.895 7.38 0.00 40.00 3.43
78 95 1.878522 GCATGGTGTCGAGCCTACG 60.879 63.158 7.38 0.00 0.00 3.51
79 96 0.744874 TAGCATGGTGTCGAGCCTAC 59.255 55.000 7.89 0.00 0.00 3.18
80 97 1.032794 CTAGCATGGTGTCGAGCCTA 58.967 55.000 7.89 0.00 0.00 3.93
81 98 0.972983 ACTAGCATGGTGTCGAGCCT 60.973 55.000 7.89 0.00 0.00 4.58
82 99 0.807667 CACTAGCATGGTGTCGAGCC 60.808 60.000 7.89 0.00 43.23 4.70
83 100 2.670635 CACTAGCATGGTGTCGAGC 58.329 57.895 7.89 0.00 43.23 5.03
211 228 3.775202 CCAGTGAAGTAGATCAACTCGG 58.225 50.000 0.00 0.00 0.00 4.63
262 279 3.007635 GTGTAGCCACTGTGGGAATAAC 58.992 50.000 27.02 10.08 38.19 1.89
283 300 0.536724 TGATGATGGACACCAGGACG 59.463 55.000 0.00 0.00 36.75 4.79
320 337 0.984230 GAGATCCACCACAGGGACAA 59.016 55.000 0.00 0.00 37.23 3.18
377 394 4.160814 TCACCCGCATTAGTTTAGCTTAGA 59.839 41.667 0.00 0.00 0.00 2.10
508 527 2.097791 CCTGAGTAGTCTTGTCTACCGC 59.902 54.545 0.00 0.00 40.56 5.68
527 546 2.957402 TTCCATGACTTGACTTGCCT 57.043 45.000 0.00 0.00 0.00 4.75
557 576 7.174253 AGAGAACATTGCGGTTTAATTTACTCA 59.826 33.333 0.00 0.00 0.00 3.41
558 577 7.527457 AGAGAACATTGCGGTTTAATTTACTC 58.473 34.615 0.00 0.00 0.00 2.59
559 578 7.448748 AGAGAACATTGCGGTTTAATTTACT 57.551 32.000 0.00 0.00 0.00 2.24
560 579 7.007099 CGAAGAGAACATTGCGGTTTAATTTAC 59.993 37.037 0.00 0.00 0.00 2.01
569 598 0.320374 TCCGAAGAGAACATTGCGGT 59.680 50.000 0.00 0.00 39.70 5.68
585 621 4.864247 CCATCAATTAACCTTTGCTTTCCG 59.136 41.667 0.00 0.00 0.00 4.30
602 638 7.673926 GCCCCTTATATTTAAATCCTCCATCAA 59.326 37.037 3.39 0.00 0.00 2.57
617 653 9.088987 CCAAAACAATACTATGCCCCTTATATT 57.911 33.333 0.00 0.00 0.00 1.28
618 654 8.452868 TCCAAAACAATACTATGCCCCTTATAT 58.547 33.333 0.00 0.00 0.00 0.86
623 659 4.601406 TCCAAAACAATACTATGCCCCT 57.399 40.909 0.00 0.00 0.00 4.79
624 660 7.888546 ACTATATCCAAAACAATACTATGCCCC 59.111 37.037 0.00 0.00 0.00 5.80
633 669 5.836358 GGGGCCAACTATATCCAAAACAATA 59.164 40.000 4.39 0.00 0.00 1.90
678 715 1.962822 CATGAGGCGCACACACACT 60.963 57.895 10.83 0.00 0.00 3.55
700 741 4.182693 TCGTCTTGTCGATTTGGTACAT 57.817 40.909 0.00 0.00 34.39 2.29
787 832 1.602888 CTCTGCCTGCTTTGCCAGT 60.603 57.895 0.00 0.00 0.00 4.00
788 833 2.991076 GCTCTGCCTGCTTTGCCAG 61.991 63.158 0.00 0.00 0.00 4.85
789 834 2.987547 GCTCTGCCTGCTTTGCCA 60.988 61.111 0.00 0.00 0.00 4.92
790 835 3.756727 GGCTCTGCCTGCTTTGCC 61.757 66.667 0.73 0.00 46.69 4.52
928 973 1.483827 AGCCAGAAAGCAGATCGATGA 59.516 47.619 0.54 0.00 34.23 2.92
930 975 1.202627 GGAGCCAGAAAGCAGATCGAT 60.203 52.381 0.00 0.00 34.23 3.59
931 976 0.176680 GGAGCCAGAAAGCAGATCGA 59.823 55.000 0.00 0.00 34.23 3.59
932 977 0.177604 AGGAGCCAGAAAGCAGATCG 59.822 55.000 0.00 0.00 34.23 3.69
933 978 1.209019 TCAGGAGCCAGAAAGCAGATC 59.791 52.381 0.00 0.00 34.23 2.75
1229 1280 1.134007 TCTGGCCATGGATGTCATCAC 60.134 52.381 18.40 4.98 32.92 3.06
1230 1281 1.134007 GTCTGGCCATGGATGTCATCA 60.134 52.381 18.40 1.75 32.92 3.07
1231 1282 1.602311 GTCTGGCCATGGATGTCATC 58.398 55.000 18.40 4.06 32.92 2.92
1574 1625 0.099436 GGTTTATTCAGCAGCGGCAG 59.901 55.000 12.44 2.56 44.61 4.85
1575 1626 0.607762 TGGTTTATTCAGCAGCGGCA 60.608 50.000 12.44 0.00 44.61 5.69
1576 1627 0.740737 ATGGTTTATTCAGCAGCGGC 59.259 50.000 0.00 0.00 41.61 6.53
1718 1769 7.821846 AGTAGTACGTAGCTAAGGGTATGTATC 59.178 40.741 11.48 5.47 44.42 2.24
1883 1934 5.654650 TGGTTTCTCATTACACACTGGTTTT 59.345 36.000 0.00 0.00 0.00 2.43
1895 1946 9.130661 CCAATGGTATTGTATGGTTTCTCATTA 57.869 33.333 0.00 0.00 0.00 1.90
2212 2266 1.926510 TGCGTGTGAGATCATTTAGCG 59.073 47.619 0.00 0.00 0.00 4.26
2364 2427 4.335594 ACTCTGCACACTTTTGTTTAGGAC 59.664 41.667 0.00 0.00 31.66 3.85
2423 2487 9.950680 ATAATTTTCATATTAACTCTTGGCACG 57.049 29.630 0.00 0.00 0.00 5.34
2461 2525 7.391148 TGGTTTTTGGTTCTATATTCTCTGC 57.609 36.000 0.00 0.00 0.00 4.26
2463 2527 9.628500 GGTATGGTTTTTGGTTCTATATTCTCT 57.372 33.333 0.00 0.00 0.00 3.10
2495 2562 2.028748 GCAATGCACCTGAATCCTGTTT 60.029 45.455 0.00 0.00 0.00 2.83
2530 2597 3.570975 ACTTGATTTGATGACAGCTTGCA 59.429 39.130 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.