Multiple sequence alignment - TraesCS7B01G111600

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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 TraesCS7B01G111600 chr7B 100.000 2695 0 0 1 2695 128301694 128304388 0.000000e+00 4977.0
1 TraesCS7B01G111600 chr7D 93.174 2725 124 29 2 2695 164868008 164870701 0.000000e+00 3945.0
2 TraesCS7B01G111600 chr7D 85.000 100 11 3 1406 1502 447035348 447035446 6.140000e-17 99.0
3 TraesCS7B01G111600 chr7A 88.893 2674 187 55 66 2671 166745363 166747994 0.000000e+00 3192.0
4 TraesCS7B01G111600 chr3D 86.667 105 10 2 1401 1502 562472333 562472230 2.190000e-21 113.0
5 TraesCS7B01G111600 chr3B 84.314 102 12 3 1416 1514 157241609 157241709 2.210000e-16 97.1
6 TraesCS7B01G111600 chr3A 84.314 102 12 3 1416 1514 550423794 550423694 2.210000e-16 97.1
7 TraesCS7B01G111600 chr6D 94.118 51 3 0 1638 1688 384444900 384444850 8.000000e-11 78.7
8 TraesCS7B01G111600 chr6B 94.118 51 3 0 1638 1688 574724809 574724759 8.000000e-11 78.7
9 TraesCS7B01G111600 chr6A 94.118 51 3 0 1638 1688 529025052 529025002 8.000000e-11 78.7


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 TraesCS7B01G111600 chr7B 128301694 128304388 2694 False 4977 4977 100.000 1 2695 1 chr7B.!!$F1 2694
1 TraesCS7B01G111600 chr7D 164868008 164870701 2693 False 3945 3945 93.174 2 2695 1 chr7D.!!$F1 2693
2 TraesCS7B01G111600 chr7A 166745363 166747994 2631 False 3192 3192 88.893 66 2671 1 chr7A.!!$F1 2605

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
686 703 0.319728 CCAAGGGAGCATCGATCGAT 59.68 55.0 24.6 24.6 34.37 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1783 0.179215 CATTCAGTCCGCTTTCACGC 60.179 55.0 0.0 0.0 0.0 5.34 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 7.979537 TGCATCTATAAAATCAAGACAGTACGT 59.020 33.333 0.00 0.00 0.00 3.57
32 33 9.999009 TCTATAAAATCAAGACAGTACGTAGTG 57.001 33.333 25.36 25.36 45.73 2.74
39 40 0.901580 ACAGTACGTAGTGGGTGGGG 60.902 60.000 29.05 7.58 45.73 4.96
48 49 3.543626 TGGGTGGGGTGGGGAGTA 61.544 66.667 0.00 0.00 0.00 2.59
51 52 2.453054 GTGGGGTGGGGAGTAGGA 59.547 66.667 0.00 0.00 0.00 2.94
52 53 1.689582 GTGGGGTGGGGAGTAGGAG 60.690 68.421 0.00 0.00 0.00 3.69
53 54 2.181773 TGGGGTGGGGAGTAGGAGT 61.182 63.158 0.00 0.00 0.00 3.85
544 556 4.777366 TCAGATCAAGTTGTAGACCCATCA 59.223 41.667 2.11 0.00 0.00 3.07
548 560 0.902531 AGTTGTAGACCCATCACCCG 59.097 55.000 0.00 0.00 0.00 5.28
552 564 2.538222 TGTAGACCCATCACCCGTTTA 58.462 47.619 0.00 0.00 0.00 2.01
564 576 3.254657 TCACCCGTTTAAAATGCTGGAAG 59.745 43.478 0.00 0.00 0.00 3.46
583 595 4.681483 GGAAGCTCTGTGCAAATTTTACAC 59.319 41.667 12.26 12.26 45.94 2.90
590 602 5.968848 TCTGTGCAAATTTTACACGAACTTC 59.031 36.000 13.64 0.00 37.11 3.01
626 638 6.171213 ACACTTTATAGTAGCTGGTGGTTTC 58.829 40.000 0.00 0.00 31.96 2.78
631 643 1.623811 AGTAGCTGGTGGTTTCGTGAT 59.376 47.619 0.00 0.00 0.00 3.06
641 653 2.635915 TGGTTTCGTGATACAAGACCCT 59.364 45.455 0.00 0.00 0.00 4.34
643 655 3.683340 GGTTTCGTGATACAAGACCCTTC 59.317 47.826 0.00 0.00 0.00 3.46
645 657 2.816411 TCGTGATACAAGACCCTTCCT 58.184 47.619 0.00 0.00 0.00 3.36
686 703 0.319728 CCAAGGGAGCATCGATCGAT 59.680 55.000 24.60 24.60 34.37 3.59
750 767 2.052766 GCATATGCGCGCACAGTC 60.053 61.111 39.05 21.82 0.00 3.51
944 967 0.614979 CCCTTCGTCTTCCTCCTCCA 60.615 60.000 0.00 0.00 0.00 3.86
948 971 0.903454 TCGTCTTCCTCCTCCAACCC 60.903 60.000 0.00 0.00 0.00 4.11
964 987 1.065410 ACCCTCACCATTCACCACCA 61.065 55.000 0.00 0.00 0.00 4.17
1019 1053 1.919956 ATGGACCTCGACGACGACAC 61.920 60.000 5.75 0.89 43.81 3.67
1065 1099 4.501285 TCGCCGTCCTCCTCCGAT 62.501 66.667 0.00 0.00 0.00 4.18
1068 1102 2.851071 GCCGTCCTCCTCCGATCTG 61.851 68.421 0.00 0.00 0.00 2.90
1087 1121 2.361438 CTGGACACCGAGGTAGTTATCC 59.639 54.545 0.00 0.00 0.00 2.59
1110 1144 3.365265 CTTGGCTGGGTGCGGTTC 61.365 66.667 0.00 0.00 44.05 3.62
1122 1156 2.706123 GCGGTTCGTTGCATTTGCG 61.706 57.895 0.00 0.00 45.83 4.85
1123 1157 1.369930 CGGTTCGTTGCATTTGCGT 60.370 52.632 0.00 0.00 45.83 5.24
1161 1195 1.444250 ACGGAGTTGTCGGCTTTGA 59.556 52.632 0.00 0.00 37.78 2.69
1181 1215 4.980805 TGTTGGCAGTCGACGGGC 62.981 66.667 30.29 30.29 37.15 6.13
1328 1362 4.785453 GCAACGGAGGGGCAGGAG 62.785 72.222 0.00 0.00 0.00 3.69
1744 1783 3.419759 GGGCGCTTACGTGGTGTG 61.420 66.667 7.64 0.00 42.83 3.82
1765 1804 0.179215 GTGAAAGCGGACTGAATGCG 60.179 55.000 0.00 0.00 46.53 4.73
2029 2078 5.697633 TGTTACACCCGTCAGTTTTTATCTC 59.302 40.000 0.00 0.00 0.00 2.75
2054 2107 9.109393 TCATGTACTCCTGTAAATATCAAAAGC 57.891 33.333 0.00 0.00 0.00 3.51
2079 2132 7.696453 GCAATAAGAGAATTTTACGCAAAGCTA 59.304 33.333 0.00 0.00 0.00 3.32
2084 2137 6.872020 AGAGAATTTTACGCAAAGCTACAGTA 59.128 34.615 0.00 0.00 0.00 2.74
2086 2139 6.872020 AGAATTTTACGCAAAGCTACAGTAGA 59.128 34.615 12.15 0.00 0.00 2.59
2087 2140 6.648725 ATTTTACGCAAAGCTACAGTAGAG 57.351 37.500 12.15 0.00 0.00 2.43
2099 2152 8.411991 AAGCTACAGTAGAGAAAGTAAAGTCT 57.588 34.615 12.15 0.00 0.00 3.24
2209 2269 2.258286 GCGCCGTGGCATTTTCTT 59.742 55.556 12.06 0.00 42.06 2.52
2210 2270 1.801512 GCGCCGTGGCATTTTCTTC 60.802 57.895 12.06 0.00 42.06 2.87
2216 2276 1.613437 CGTGGCATTTTCTTCCCTGTT 59.387 47.619 0.00 0.00 0.00 3.16
2297 2357 1.548357 ATTCGAGTGCCAGCTGACCT 61.548 55.000 17.39 7.41 0.00 3.85
2328 2394 4.974989 ACGAAACCCCGACGCCAC 62.975 66.667 0.00 0.00 0.00 5.01
2386 2452 1.144057 ATGGGTTCGTCCTCATCGC 59.856 57.895 0.30 0.00 36.25 4.58
2495 2597 5.303845 CAGAATGATGAGGAGGAGATGTACA 59.696 44.000 0.00 0.00 39.69 2.90
2497 2599 3.300388 TGATGAGGAGGAGATGTACACC 58.700 50.000 0.00 0.00 0.00 4.16
2546 2648 1.755783 GATTCCAGCAAGGGCCCAG 60.756 63.158 27.56 17.84 42.56 4.45
2569 2671 1.507141 CCAGAAAAAGACGCGGCACT 61.507 55.000 17.71 5.72 0.00 4.40
2604 2706 1.068125 TGACATGTCTACCAACGGACG 60.068 52.381 25.55 0.00 35.45 4.79
2609 2711 1.271325 TGTCTACCAACGGACGAGGTA 60.271 52.381 15.65 15.65 36.87 3.08
2684 2792 5.471456 AGCTTGGAATGTTCAAGTAGAGTTG 59.529 40.000 0.00 0.00 42.44 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.891150 CCACCCACTACGTACTGTCTT 59.109 52.381 0.00 0.00 0.00 3.01
26 27 3.712907 CCCACCCCACCCACTACG 61.713 72.222 0.00 0.00 0.00 3.51
28 29 3.543626 TCCCCACCCCACCCACTA 61.544 66.667 0.00 0.00 0.00 2.74
32 33 2.691252 CTACTCCCCACCCCACCC 60.691 72.222 0.00 0.00 0.00 4.61
39 40 6.496144 ACATATTTTACTCCTACTCCCCAC 57.504 41.667 0.00 0.00 0.00 4.61
48 49 9.213777 TCCTCATGAACTACATATTTTACTCCT 57.786 33.333 0.00 0.00 37.46 3.69
102 105 4.599241 CCCTGTCCCTATCCTATTGTTCAT 59.401 45.833 0.00 0.00 0.00 2.57
544 556 2.029380 GCTTCCAGCATTTTAAACGGGT 60.029 45.455 0.00 0.00 41.89 5.28
548 560 4.919754 CACAGAGCTTCCAGCATTTTAAAC 59.080 41.667 0.00 0.00 45.56 2.01
552 564 1.271656 GCACAGAGCTTCCAGCATTTT 59.728 47.619 0.00 0.00 45.56 1.82
564 576 3.884169 TCGTGTAAAATTTGCACAGAGC 58.116 40.909 22.73 0.51 45.05 4.09
567 579 5.741510 TGAAGTTCGTGTAAAATTTGCACAG 59.258 36.000 22.73 16.18 45.05 3.66
568 580 5.641709 TGAAGTTCGTGTAAAATTTGCACA 58.358 33.333 22.73 12.22 45.05 4.57
583 595 6.991485 AGTGTAAATTTTGCATGAAGTTCG 57.009 33.333 0.00 0.00 0.00 3.95
626 638 3.952323 TCTAGGAAGGGTCTTGTATCACG 59.048 47.826 0.00 0.00 0.00 4.35
631 643 5.900437 TCTTCTTCTAGGAAGGGTCTTGTA 58.100 41.667 8.38 0.00 41.94 2.41
641 653 7.502060 ACATTTGGATCTCTTCTTCTAGGAA 57.498 36.000 0.00 0.00 0.00 3.36
643 655 6.765512 GGAACATTTGGATCTCTTCTTCTAGG 59.234 42.308 0.00 0.00 0.00 3.02
645 657 7.257790 TGGAACATTTGGATCTCTTCTTCTA 57.742 36.000 0.00 0.00 0.00 2.10
686 703 2.031674 ATGCAGCCCGTGATCGATCA 62.032 55.000 23.99 23.99 39.71 2.92
687 704 0.038251 TATGCAGCCCGTGATCGATC 60.038 55.000 18.72 18.72 39.71 3.69
688 705 0.392706 TTATGCAGCCCGTGATCGAT 59.607 50.000 0.00 0.00 39.71 3.59
689 706 0.392706 ATTATGCAGCCCGTGATCGA 59.607 50.000 0.00 0.00 39.71 3.59
690 707 0.514255 CATTATGCAGCCCGTGATCG 59.486 55.000 0.00 0.00 0.00 3.69
691 708 1.597742 ACATTATGCAGCCCGTGATC 58.402 50.000 0.00 0.00 0.00 2.92
692 709 2.158827 TGTACATTATGCAGCCCGTGAT 60.159 45.455 0.00 0.00 0.00 3.06
750 767 4.415501 GCGCAAGTGCACGACTCG 62.416 66.667 12.01 14.31 42.21 4.18
944 967 0.112412 GGTGGTGAATGGTGAGGGTT 59.888 55.000 0.00 0.00 0.00 4.11
948 971 0.609131 GGGTGGTGGTGAATGGTGAG 60.609 60.000 0.00 0.00 0.00 3.51
1019 1053 0.892814 GGAGGGGGAGTACGGTATCG 60.893 65.000 0.00 0.00 43.02 2.92
1065 1099 2.885135 TAACTACCTCGGTGTCCAGA 57.115 50.000 0.00 0.00 0.00 3.86
1068 1102 2.381911 TGGATAACTACCTCGGTGTCC 58.618 52.381 0.00 0.17 0.00 4.02
1087 1121 0.388907 CGCACCCAGCCAAGAAATTG 60.389 55.000 0.00 0.00 41.38 2.32
1110 1144 0.843242 AAAACGACGCAAATGCAACG 59.157 45.000 15.73 15.73 42.21 4.10
1122 1156 2.347168 GCGCACGCAAGAAAACGAC 61.347 57.895 10.65 0.00 41.49 4.34
1123 1157 2.052590 GCGCACGCAAGAAAACGA 60.053 55.556 10.65 0.00 41.49 3.85
1153 1187 2.256391 TGCCAACAGATCAAAGCCG 58.744 52.632 0.00 0.00 0.00 5.52
1181 1215 1.205893 CTCCGGTCAGGGAAGAAAGAG 59.794 57.143 0.00 0.00 41.52 2.85
1277 1311 4.704103 TCGCTCTCCTGCCCTGGT 62.704 66.667 0.00 0.00 0.00 4.00
1280 1314 2.441901 CTCTCGCTCTCCTGCCCT 60.442 66.667 0.00 0.00 0.00 5.19
1744 1783 0.179215 CATTCAGTCCGCTTTCACGC 60.179 55.000 0.00 0.00 0.00 5.34
1841 1884 1.953686 AGGGACCGAACAACAACAATG 59.046 47.619 0.00 0.00 0.00 2.82
2029 2078 8.892723 TGCTTTTGATATTTACAGGAGTACATG 58.107 33.333 0.00 0.00 0.00 3.21
2047 2100 8.079203 TGCGTAAAATTCTCTTATTGCTTTTGA 58.921 29.630 0.00 0.00 0.00 2.69
2054 2107 9.000018 GTAGCTTTGCGTAAAATTCTCTTATTG 58.000 33.333 0.00 0.00 0.00 1.90
2079 2132 8.240267 ACAAGAGACTTTACTTTCTCTACTGT 57.760 34.615 1.65 1.69 46.48 3.55
2115 2170 3.458189 GGCAGCACGAAATAGTACAGAT 58.542 45.455 0.00 0.00 0.00 2.90
2209 2269 2.280797 GCAGTGCACGAACAGGGA 60.281 61.111 11.09 0.00 0.00 4.20
2210 2270 2.591429 TGCAGTGCACGAACAGGG 60.591 61.111 15.37 0.00 31.71 4.45
2235 2295 2.815308 GTCCGTGCGATGGGATCT 59.185 61.111 0.00 0.00 34.25 2.75
2328 2394 1.083015 CGTGCAAAGGTTCGTTCGG 60.083 57.895 0.00 0.00 0.00 4.30
2376 2442 1.008995 GAGAGCGAGCGATGAGGAC 60.009 63.158 0.00 0.00 0.00 3.85
2379 2445 2.051435 CCGAGAGCGAGCGATGAG 60.051 66.667 0.00 0.00 40.82 2.90
2386 2452 0.523966 AACTTGACTCCGAGAGCGAG 59.476 55.000 1.33 5.70 40.82 5.03
2497 2599 0.941542 TTCAAACCGGAAGCAACTCG 59.058 50.000 9.46 0.00 0.00 4.18
2546 2648 1.497722 CGCGTCTTTTTCTGGCCTC 59.502 57.895 3.32 0.00 0.00 4.70
2578 2680 3.073678 GTTGGTAGACATGTCATGTGCA 58.926 45.455 27.02 7.52 45.03 4.57
2604 2706 6.567891 GCTTCAGGTTAAACATGTGTTACCTC 60.568 42.308 21.39 8.86 42.20 3.85
2609 2711 5.852282 AAGCTTCAGGTTAAACATGTGTT 57.148 34.783 0.00 0.00 40.50 3.32


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

AutoCloner maintained by Alex Coulton.