Multiple sequence alignment - TraesCS7B01G465300

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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 TraesCS7B01G465300 chr7B 100.000 2782 0 0 297 3078 721435191 721437972 0.000000e+00 5138
1 TraesCS7B01G465300 chr7B 100.000 93 0 0 1 93 721434895 721434987 4.080000e-39 172
2 TraesCS7B01G465300 chr5B 97.466 2762 69 1 317 3078 491862399 491859639 0.000000e+00 4711
3 TraesCS7B01G465300 chr5B 97.185 2771 76 2 308 3078 13301101 13298333 0.000000e+00 4684
4 TraesCS7B01G465300 chr5B 97.041 2771 82 0 308 3078 290698527 290701297 0.000000e+00 4663
5 TraesCS7B01G465300 chr3B 97.329 2771 74 0 308 3078 765959012 765961782 0.000000e+00 4708
6 TraesCS7B01G465300 chr3B 96.978 2780 84 0 299 3078 436519114 436521893 0.000000e+00 4669
7 TraesCS7B01G465300 chr3B 97.176 2762 78 0 317 3078 765937137 765939898 0.000000e+00 4669
8 TraesCS7B01G465300 chr3B 97.041 2771 79 2 308 3078 706906314 706909081 0.000000e+00 4660
9 TraesCS7B01G465300 chr2B 97.191 2777 75 2 305 3078 616543037 616540261 0.000000e+00 4693
10 TraesCS7B01G465300 chr4A 97.252 2766 74 2 313 3078 675635369 675632606 0.000000e+00 4686
11 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 83561092 83561179 1.910000e-32 150
12 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 328634647 328634560 1.910000e-32 150
13 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 374494780 374494693 1.910000e-32 150
14 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 404471784 404471871 1.910000e-32 150
15 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 423303781 423303694 1.910000e-32 150
16 TraesCS7B01G465300 chrUn 97.727 88 1 1 1 87 448604332 448604245 1.910000e-32 150
17 TraesCS7B01G465300 chr4B 97.727 88 1 1 1 87 91196903 91196990 1.910000e-32 150
18 TraesCS7B01G465300 chr1B 97.727 88 1 1 1 87 123415081 123414994 1.910000e-32 150
19 TraesCS7B01G465300 chr1B 97.727 88 1 1 1 87 150784895 150784982 1.910000e-32 150


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 TraesCS7B01G465300 chr7B 721434895 721437972 3077 False 2655 5138 100.000 1 3078 2 chr7B.!!$F1 3077
1 TraesCS7B01G465300 chr5B 491859639 491862399 2760 True 4711 4711 97.466 317 3078 1 chr5B.!!$R2 2761
2 TraesCS7B01G465300 chr5B 13298333 13301101 2768 True 4684 4684 97.185 308 3078 1 chr5B.!!$R1 2770
3 TraesCS7B01G465300 chr5B 290698527 290701297 2770 False 4663 4663 97.041 308 3078 1 chr5B.!!$F1 2770
4 TraesCS7B01G465300 chr3B 765959012 765961782 2770 False 4708 4708 97.329 308 3078 1 chr3B.!!$F4 2770
5 TraesCS7B01G465300 chr3B 436519114 436521893 2779 False 4669 4669 96.978 299 3078 1 chr3B.!!$F1 2779
6 TraesCS7B01G465300 chr3B 765937137 765939898 2761 False 4669 4669 97.176 317 3078 1 chr3B.!!$F3 2761
7 TraesCS7B01G465300 chr3B 706906314 706909081 2767 False 4660 4660 97.041 308 3078 1 chr3B.!!$F2 2770
8 TraesCS7B01G465300 chr2B 616540261 616543037 2776 True 4693 4693 97.191 305 3078 1 chr2B.!!$R1 2773
9 TraesCS7B01G465300 chr4A 675632606 675635369 2763 True 4686 4686 97.252 313 3078 1 chr4A.!!$R1 2765

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
46 47 0.235144 GATCACATCTGCTCATGCGC 59.765 55.000 0.00 0.00 43.34 6.09 F
47 48 0.463116 ATCACATCTGCTCATGCGCA 60.463 50.000 14.96 14.96 43.34 6.09 F
48 49 1.062047 CACATCTGCTCATGCGCAC 59.938 57.895 14.90 0.00 43.34 5.34 F
76 77 1.081641 CGTTCCTTTGCTGCTGCTG 60.082 57.895 17.00 0.77 40.48 4.41 F
765 767 1.203237 TCATCACCATGTCCACCGAT 58.797 50.000 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1437 0.389948 GCTCCAGTACAGGACGGTTG 60.390 60.000 2.26 0.0 33.19 3.77 R
1621 1624 0.397564 TGCTCAACACTCAGATGGCA 59.602 50.000 0.00 0.0 0.00 4.92 R
1971 1975 2.643551 CACCAATCGGTAGGCTGAAAT 58.356 47.619 0.00 0.0 46.94 2.17 R
2026 2030 8.463930 TGGTAAGAAGAGAACAATGAAATGTT 57.536 30.769 0.00 0.0 45.82 2.71 R
2087 2091 0.174389 ATGATCAGAAGCACTCGCGT 59.826 50.000 5.77 0.0 45.49 6.01 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
17 18 3.547247 GTCCCCTAACCCTAGCCG 58.453 66.667 0.00 0.00 0.00 5.52
18 19 2.445274 TCCCCTAACCCTAGCCGC 60.445 66.667 0.00 0.00 0.00 6.53
19 20 3.557290 CCCCTAACCCTAGCCGCC 61.557 72.222 0.00 0.00 0.00 6.13
20 21 2.766651 CCCTAACCCTAGCCGCCA 60.767 66.667 0.00 0.00 0.00 5.69
21 22 2.504519 CCTAACCCTAGCCGCCAC 59.495 66.667 0.00 0.00 0.00 5.01
22 23 2.106332 CTAACCCTAGCCGCCACG 59.894 66.667 0.00 0.00 0.00 4.94
23 24 2.362760 TAACCCTAGCCGCCACGA 60.363 61.111 0.00 0.00 0.00 4.35
24 25 1.952102 CTAACCCTAGCCGCCACGAA 61.952 60.000 0.00 0.00 0.00 3.85
25 26 2.229690 TAACCCTAGCCGCCACGAAC 62.230 60.000 0.00 0.00 0.00 3.95
26 27 4.077184 CCCTAGCCGCCACGAACA 62.077 66.667 0.00 0.00 0.00 3.18
27 28 2.509336 CCTAGCCGCCACGAACAG 60.509 66.667 0.00 0.00 0.00 3.16
28 29 2.571757 CTAGCCGCCACGAACAGA 59.428 61.111 0.00 0.00 0.00 3.41
29 30 1.141881 CTAGCCGCCACGAACAGAT 59.858 57.895 0.00 0.00 0.00 2.90
30 31 0.872021 CTAGCCGCCACGAACAGATC 60.872 60.000 0.00 0.00 0.00 2.75
31 32 1.600511 TAGCCGCCACGAACAGATCA 61.601 55.000 0.00 0.00 0.00 2.92
32 33 2.740714 GCCGCCACGAACAGATCAC 61.741 63.158 0.00 0.00 0.00 3.06
33 34 1.374125 CCGCCACGAACAGATCACA 60.374 57.895 0.00 0.00 0.00 3.58
34 35 0.740868 CCGCCACGAACAGATCACAT 60.741 55.000 0.00 0.00 0.00 3.21
35 36 0.647410 CGCCACGAACAGATCACATC 59.353 55.000 0.00 0.00 0.00 3.06
36 37 1.737029 CGCCACGAACAGATCACATCT 60.737 52.381 0.00 0.00 41.15 2.90
45 46 1.867166 AGATCACATCTGCTCATGCG 58.133 50.000 0.00 0.00 43.34 4.73
46 47 0.235144 GATCACATCTGCTCATGCGC 59.765 55.000 0.00 0.00 43.34 6.09
47 48 0.463116 ATCACATCTGCTCATGCGCA 60.463 50.000 14.96 14.96 43.34 6.09
48 49 1.062047 CACATCTGCTCATGCGCAC 59.938 57.895 14.90 0.00 43.34 5.34
49 50 2.323447 CATCTGCTCATGCGCACG 59.677 61.111 14.90 3.71 43.34 5.34
50 51 3.570638 ATCTGCTCATGCGCACGC 61.571 61.111 14.90 16.95 43.34 5.34
65 66 4.675029 CGCCCACCGTCGTTCCTT 62.675 66.667 0.00 0.00 0.00 3.36
66 67 2.281276 GCCCACCGTCGTTCCTTT 60.281 61.111 0.00 0.00 0.00 3.11
67 68 2.613506 GCCCACCGTCGTTCCTTTG 61.614 63.158 0.00 0.00 0.00 2.77
68 69 2.613506 CCCACCGTCGTTCCTTTGC 61.614 63.158 0.00 0.00 0.00 3.68
69 70 1.597027 CCACCGTCGTTCCTTTGCT 60.597 57.895 0.00 0.00 0.00 3.91
70 71 1.569493 CACCGTCGTTCCTTTGCTG 59.431 57.895 0.00 0.00 0.00 4.41
71 72 2.251642 ACCGTCGTTCCTTTGCTGC 61.252 57.895 0.00 0.00 0.00 5.25
72 73 1.961277 CCGTCGTTCCTTTGCTGCT 60.961 57.895 0.00 0.00 0.00 4.24
73 74 1.205064 CGTCGTTCCTTTGCTGCTG 59.795 57.895 0.00 0.00 0.00 4.41
74 75 1.081840 GTCGTTCCTTTGCTGCTGC 60.082 57.895 8.89 8.89 40.20 5.25
75 76 1.227943 TCGTTCCTTTGCTGCTGCT 60.228 52.632 17.00 0.00 40.48 4.24
76 77 1.081641 CGTTCCTTTGCTGCTGCTG 60.082 57.895 17.00 0.77 40.48 4.41
77 78 1.372623 GTTCCTTTGCTGCTGCTGC 60.373 57.895 22.51 22.51 40.48 5.25
78 79 2.567497 TTCCTTTGCTGCTGCTGCC 61.567 57.895 25.44 10.66 40.48 4.85
79 80 4.415332 CCTTTGCTGCTGCTGCCG 62.415 66.667 25.44 14.88 40.48 5.69
407 408 4.314440 TGACAGCAGGGCCACGAC 62.314 66.667 6.18 0.00 0.00 4.34
476 477 3.506096 CGTCTCTCCACGCGGCTA 61.506 66.667 12.47 0.00 31.96 3.93
480 481 3.338126 CTCTCCACGCGGCTACGTT 62.338 63.158 12.47 0.00 45.75 3.99
765 767 1.203237 TCATCACCATGTCCACCGAT 58.797 50.000 0.00 0.00 0.00 4.18
973 975 5.689383 ACGTGCATGTTTAGATCAAAGTT 57.311 34.783 5.51 0.00 0.00 2.66
979 981 8.717821 GTGCATGTTTAGATCAAAGTTAGTACA 58.282 33.333 0.00 0.00 0.00 2.90
1119 1122 3.286751 GCCGCAGCACTGAAACCA 61.287 61.111 0.81 0.00 39.53 3.67
1158 1161 3.726782 CGTATTTTAAGCGTTGGCAGACC 60.727 47.826 0.00 0.00 43.41 3.85
1434 1437 4.843728 TCCAGGATTACAAGATGGTTGAC 58.156 43.478 0.00 0.00 32.68 3.18
1605 1608 2.234661 ACATCAGAGGCGTGAATTCTCA 59.765 45.455 7.05 0.00 0.00 3.27
1621 1624 4.916041 TTCTCAGTGGAGGATGTCATTT 57.084 40.909 0.00 0.00 41.69 2.32
1905 1909 2.975489 ACAGGACTCCAAGTCTGTCAAT 59.025 45.455 7.02 0.00 44.46 2.57
1908 1912 5.105146 ACAGGACTCCAAGTCTGTCAATATC 60.105 44.000 7.02 0.00 44.46 1.63
2026 2030 2.493035 CAGGTGTTCATGTGTGTGCTA 58.507 47.619 0.00 0.00 0.00 3.49
2060 2064 3.845860 TCTCTTCTTACCAGGTCACAGT 58.154 45.455 0.00 0.00 0.00 3.55
2087 2091 2.105821 GGTCCGTATTGATGGGGAATGA 59.894 50.000 0.00 0.00 31.86 2.57
2115 2119 2.224843 TGCTTCTGATCATGGTGTTGGT 60.225 45.455 0.00 0.00 0.00 3.67
2176 2180 0.867746 GAAGAACGTGCAGCATGTCA 59.132 50.000 20.75 0.00 39.31 3.58
2402 2406 2.693074 AGGTTTGGCATTCACGTCTTTT 59.307 40.909 0.00 0.00 0.00 2.27
2552 2556 0.681733 GAGGAGAGACACTTGGCACA 59.318 55.000 0.00 0.00 0.00 4.57
3027 3031 1.274712 CTCCCTATGAGAGATGGGCC 58.725 60.000 0.00 0.00 44.42 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.804912 GCGGCTAGGGTTAGGGGAC 61.805 68.421 0.00 0.00 0.00 4.46
1 2 2.445274 GCGGCTAGGGTTAGGGGA 60.445 66.667 0.00 0.00 0.00 4.81
2 3 3.557290 GGCGGCTAGGGTTAGGGG 61.557 72.222 0.00 0.00 0.00 4.79
4 5 2.504519 GTGGCGGCTAGGGTTAGG 59.495 66.667 11.43 0.00 0.00 2.69
6 7 1.983481 TTCGTGGCGGCTAGGGTTA 60.983 57.895 11.43 0.00 0.00 2.85
7 8 3.315949 TTCGTGGCGGCTAGGGTT 61.316 61.111 11.43 0.00 0.00 4.11
8 9 4.078516 GTTCGTGGCGGCTAGGGT 62.079 66.667 11.43 0.00 0.00 4.34
9 10 4.077184 TGTTCGTGGCGGCTAGGG 62.077 66.667 11.43 0.00 0.00 3.53
10 11 2.298158 ATCTGTTCGTGGCGGCTAGG 62.298 60.000 11.43 0.00 0.00 3.02
11 12 0.872021 GATCTGTTCGTGGCGGCTAG 60.872 60.000 11.43 4.04 0.00 3.42
12 13 1.141019 GATCTGTTCGTGGCGGCTA 59.859 57.895 11.43 0.00 0.00 3.93
13 14 2.125512 GATCTGTTCGTGGCGGCT 60.126 61.111 11.43 0.00 0.00 5.52
14 15 2.434185 TGATCTGTTCGTGGCGGC 60.434 61.111 0.00 0.00 0.00 6.53
15 16 0.740868 ATGTGATCTGTTCGTGGCGG 60.741 55.000 0.00 0.00 0.00 6.13
16 17 0.647410 GATGTGATCTGTTCGTGGCG 59.353 55.000 0.00 0.00 0.00 5.69
17 18 2.015736 AGATGTGATCTGTTCGTGGC 57.984 50.000 0.00 0.00 38.44 5.01
26 27 1.867166 CGCATGAGCAGATGTGATCT 58.133 50.000 9.69 0.00 39.98 2.75
27 28 0.235144 GCGCATGAGCAGATGTGATC 59.765 55.000 17.16 0.31 42.27 2.92
28 29 0.463116 TGCGCATGAGCAGATGTGAT 60.463 50.000 20.84 0.00 42.92 3.06
29 30 1.078988 TGCGCATGAGCAGATGTGA 60.079 52.632 20.84 0.00 42.92 3.58
30 31 3.493213 TGCGCATGAGCAGATGTG 58.507 55.556 20.84 4.58 42.92 3.21
48 49 4.675029 AAGGAACGACGGTGGGCG 62.675 66.667 0.00 0.00 0.00 6.13
49 50 2.281276 AAAGGAACGACGGTGGGC 60.281 61.111 0.00 0.00 0.00 5.36
50 51 2.613506 GCAAAGGAACGACGGTGGG 61.614 63.158 0.00 0.00 0.00 4.61
51 52 1.597027 AGCAAAGGAACGACGGTGG 60.597 57.895 0.00 0.00 0.00 4.61
52 53 1.569493 CAGCAAAGGAACGACGGTG 59.431 57.895 0.00 0.00 0.00 4.94
53 54 2.251642 GCAGCAAAGGAACGACGGT 61.252 57.895 0.00 0.00 0.00 4.83
54 55 1.961277 AGCAGCAAAGGAACGACGG 60.961 57.895 0.00 0.00 0.00 4.79
55 56 1.205064 CAGCAGCAAAGGAACGACG 59.795 57.895 0.00 0.00 0.00 5.12
56 57 1.081840 GCAGCAGCAAAGGAACGAC 60.082 57.895 0.00 0.00 41.58 4.34
57 58 1.227943 AGCAGCAGCAAAGGAACGA 60.228 52.632 3.17 0.00 45.49 3.85
58 59 1.081641 CAGCAGCAGCAAAGGAACG 60.082 57.895 3.17 0.00 45.49 3.95
59 60 1.372623 GCAGCAGCAGCAAAGGAAC 60.373 57.895 4.63 0.00 45.49 3.62
60 61 2.567497 GGCAGCAGCAGCAAAGGAA 61.567 57.895 12.41 0.00 45.49 3.36
61 62 2.987547 GGCAGCAGCAGCAAAGGA 60.988 61.111 12.41 0.00 45.49 3.36
62 63 4.415332 CGGCAGCAGCAGCAAAGG 62.415 66.667 12.41 0.00 45.49 3.11
348 349 3.948473 TGGCAAAAATAAGCGCATAGGTA 59.052 39.130 11.47 0.00 0.00 3.08
476 477 6.369615 GGGACACAACACACTTATATAAACGT 59.630 38.462 0.00 0.00 0.00 3.99
480 481 6.630203 AGGGGACACAACACACTTATATAA 57.370 37.500 0.00 0.00 0.00 0.98
554 555 2.256461 GCAGCAGCAAAGGAACGG 59.744 61.111 0.00 0.00 41.58 4.44
973 975 7.710907 GGCATTGACTAAGTTGATGATGTACTA 59.289 37.037 0.00 0.00 0.00 1.82
979 981 5.221185 GCATGGCATTGACTAAGTTGATGAT 60.221 40.000 0.00 0.00 0.00 2.45
1229 1232 1.347707 TGAACGCCTTCTCCTGTTCAT 59.652 47.619 2.77 0.00 44.01 2.57
1384 1387 7.057264 TGCTCTATAATATACATCTCGCTCCT 58.943 38.462 0.00 0.00 0.00 3.69
1434 1437 0.389948 GCTCCAGTACAGGACGGTTG 60.390 60.000 2.26 0.00 33.19 3.77
1605 1608 1.355381 TGGCAAATGACATCCTCCACT 59.645 47.619 0.00 0.00 0.00 4.00
1621 1624 0.397564 TGCTCAACACTCAGATGGCA 59.602 50.000 0.00 0.00 0.00 4.92
1713 1716 4.340617 TGAACTTGTGGGAGTTGAAGTTT 58.659 39.130 0.00 0.00 39.84 2.66
1971 1975 2.643551 CACCAATCGGTAGGCTGAAAT 58.356 47.619 0.00 0.00 46.94 2.17
2026 2030 8.463930 TGGTAAGAAGAGAACAATGAAATGTT 57.536 30.769 0.00 0.00 45.82 2.71
2087 2091 0.174389 ATGATCAGAAGCACTCGCGT 59.826 50.000 5.77 0.00 45.49 6.01
2102 2106 1.404986 CGACCGTACCAACACCATGAT 60.405 52.381 0.00 0.00 0.00 2.45
2115 2119 5.633830 AAGTAAACTTCAGATCGACCGTA 57.366 39.130 0.00 0.00 0.00 4.02
2176 2180 0.693049 AGGTTCTTCTTGATGGCGGT 59.307 50.000 0.00 0.00 0.00 5.68
2402 2406 7.356540 CGTCATAACACCAAAACTTATGTGAA 58.643 34.615 0.00 0.00 32.12 3.18
3027 3031 4.810790 ACGAGAGTGTTGTCCTTCTATTG 58.189 43.478 0.00 0.00 46.97 1.90


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

AutoCloner maintained by Alex Coulton.