Multiple sequence alignment - TraesCS7B01G277500

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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 TraesCS7B01G277500 chr7B 100.000 2615 0 0 1 2615 507837671 507835057 0.000000e+00 4830.0
1 TraesCS7B01G277500 chr7D 92.124 2349 85 35 59 2357 481838693 481836395 0.000000e+00 3221.0
2 TraesCS7B01G277500 chr7D 84.532 278 18 5 2342 2615 481836210 481835954 4.320000e-63 252.0
3 TraesCS7B01G277500 chr7A 88.075 1912 88 56 525 2383 549002430 549000606 0.000000e+00 2139.0
4 TraesCS7B01G277500 chr7A 90.213 235 23 0 2 236 549004000 549003766 9.090000e-80 307.0
5 TraesCS7B01G277500 chr7A 90.076 131 10 2 341 470 549002553 549002425 1.610000e-37 167.0
6 TraesCS7B01G277500 chr3D 100.000 35 0 0 476 510 588863468 588863434 6.040000e-07 65.8
7 TraesCS7B01G277500 chr3A 94.872 39 2 0 476 514 130834473 130834511 7.810000e-06 62.1
8 TraesCS7B01G277500 chr1B 94.872 39 2 0 470 508 668084848 668084886 7.810000e-06 62.1
9 TraesCS7B01G277500 chr1B 100.000 29 0 0 475 503 667325654 667325682 1.000000e-03 54.7
10 TraesCS7B01G277500 chr1A 93.023 43 2 1 469 510 418947078 418947120 7.810000e-06 62.1
11 TraesCS7B01G277500 chr6A 92.683 41 3 0 470 510 604662498 604662538 2.810000e-05 60.2


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 TraesCS7B01G277500 chr7B 507835057 507837671 2614 True 4830.0 4830 100.000000 1 2615 1 chr7B.!!$R1 2614
1 TraesCS7B01G277500 chr7D 481835954 481838693 2739 True 1736.5 3221 88.328000 59 2615 2 chr7D.!!$R1 2556
2 TraesCS7B01G277500 chr7A 549000606 549004000 3394 True 871.0 2139 89.454667 2 2383 3 chr7A.!!$R1 2381

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
559 1672 0.675522 ACCCGAACAATAGGCAACGG 60.676 55.0 0.0 0.0 46.39 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3222 0.459585 CATGTACACGACGGGGAAGG 60.46 60.0 0.43 0.0 0.0 3.46 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
24 25 3.689649 GTCAAGAGCCACAAACGGATATT 59.310 43.478 0.00 0.00 0.00 1.28
29 30 2.423538 AGCCACAAACGGATATTCAAGC 59.576 45.455 0.00 0.00 0.00 4.01
85 86 6.713762 TGTTCACAACATTTGAAAGGATCT 57.286 33.333 0.00 0.00 36.25 2.75
127 128 3.306641 GGCATCCATATCTTCTCGCTTCT 60.307 47.826 0.00 0.00 0.00 2.85
250 267 7.116948 ACATTCTAGATTGAGAGAACAACAACG 59.883 37.037 19.00 0.00 34.61 4.10
401 1513 4.703575 TGAAGCTGAGATGGGAGAAAAATG 59.296 41.667 0.00 0.00 0.00 2.32
440 1553 4.025360 CCATTCATGTGAATCAAAGGGGA 58.975 43.478 5.30 0.00 42.41 4.81
486 1599 4.880696 TGAAGAACAACATGACACATGTGA 59.119 37.500 31.94 11.45 31.80 3.58
495 1608 6.519679 ACATGACACATGTGATAAGCAATT 57.480 33.333 31.94 6.16 0.00 2.32
543 1656 7.645058 TTGGAGAAGAATGAAATATTGACCC 57.355 36.000 0.00 0.00 0.00 4.46
559 1672 0.675522 ACCCGAACAATAGGCAACGG 60.676 55.000 0.00 0.00 46.39 4.44
630 1745 3.896888 TGCACTTCAAATGGGATTGTTCT 59.103 39.130 0.00 0.00 0.00 3.01
673 1789 2.130395 GATGATGCATGTGTCGACGAT 58.870 47.619 2.46 2.34 0.00 3.73
674 1790 2.861462 TGATGCATGTGTCGACGATA 57.139 45.000 2.46 0.00 0.00 2.92
675 1791 2.731217 TGATGCATGTGTCGACGATAG 58.269 47.619 2.46 2.29 46.19 2.08
676 1792 2.357637 TGATGCATGTGTCGACGATAGA 59.642 45.455 2.46 0.00 41.38 1.98
677 1793 2.475200 TGCATGTGTCGACGATAGAG 57.525 50.000 11.62 0.00 41.38 2.43
678 1794 1.743394 TGCATGTGTCGACGATAGAGT 59.257 47.619 11.62 0.00 41.38 3.24
679 1795 2.223272 TGCATGTGTCGACGATAGAGTC 60.223 50.000 11.62 0.00 41.38 3.36
774 1890 6.368791 CACCACTCTTGTCTCATTCGATTTTA 59.631 38.462 0.00 0.00 0.00 1.52
775 1891 7.065085 CACCACTCTTGTCTCATTCGATTTTAT 59.935 37.037 0.00 0.00 0.00 1.40
776 1892 8.258007 ACCACTCTTGTCTCATTCGATTTTATA 58.742 33.333 0.00 0.00 0.00 0.98
777 1893 8.759641 CCACTCTTGTCTCATTCGATTTTATAG 58.240 37.037 0.00 0.00 0.00 1.31
778 1894 8.272176 CACTCTTGTCTCATTCGATTTTATAGC 58.728 37.037 0.00 0.00 0.00 2.97
779 1895 7.439655 ACTCTTGTCTCATTCGATTTTATAGCC 59.560 37.037 0.00 0.00 0.00 3.93
781 1897 7.987458 TCTTGTCTCATTCGATTTTATAGCCTT 59.013 33.333 0.00 0.00 0.00 4.35
782 1898 8.506168 TTGTCTCATTCGATTTTATAGCCTTT 57.494 30.769 0.00 0.00 0.00 3.11
790 1906 5.585445 TCGATTTTATAGCCTTTAAACGCCA 59.415 36.000 5.68 0.00 0.00 5.69
993 2113 4.314440 TGCGCGCCCTTCTGTTCT 62.314 61.111 30.77 0.00 0.00 3.01
1128 2251 2.747855 CAGCAGAACCGGAAGCCC 60.748 66.667 9.46 0.00 0.00 5.19
1257 2388 4.719106 AGGGCGTCGACCTCGTCT 62.719 66.667 15.92 0.00 35.03 4.18
1260 2391 2.688794 GGCGTCGACCTCGTCTTCT 61.689 63.158 10.58 0.00 40.80 2.85
1599 2736 2.759973 ATCTTCGGGCCGCTCTCA 60.760 61.111 23.83 0.00 0.00 3.27
1655 2792 0.247736 GGCGACATGGTCAGAAGTCT 59.752 55.000 0.00 0.00 32.09 3.24
1781 2923 4.461081 TGGTTCGGCAAGCTGTAAATTAAT 59.539 37.500 0.18 0.00 0.00 1.40
1782 2924 5.648526 TGGTTCGGCAAGCTGTAAATTAATA 59.351 36.000 0.18 0.00 0.00 0.98
1783 2925 6.183360 TGGTTCGGCAAGCTGTAAATTAATAG 60.183 38.462 0.18 0.00 0.00 1.73
1896 3039 2.436646 CCGGTGCACCCATGAGAC 60.437 66.667 29.95 2.66 0.00 3.36
2033 3176 7.468357 GCAGAAATGCAAGATATATATCCTGGC 60.468 40.741 18.73 18.07 32.38 4.85
2076 3222 2.420022 GACTGCACATATGTGGTTCCAC 59.580 50.000 31.63 17.24 45.72 4.02
2111 3261 1.001974 ACATGCGAACCACTTCTGCTA 59.998 47.619 0.00 0.00 31.34 3.49
2144 3295 2.931325 GCGTGTCGTATTTAATCCACCA 59.069 45.455 0.00 0.00 0.00 4.17
2146 3297 3.000925 CGTGTCGTATTTAATCCACCAGC 59.999 47.826 0.00 0.00 0.00 4.85
2182 3354 2.349580 CAGCTTGATCACCGTGTATGTG 59.650 50.000 0.00 0.00 35.01 3.21
2236 3410 2.222819 CGCGGCATTAGTCTTTCTGTTC 60.223 50.000 0.00 0.00 0.00 3.18
2270 3455 6.272558 ACCTGAGGGGGATTATACATTAAGAC 59.727 42.308 2.38 0.00 40.03 3.01
2364 3753 4.737765 CACGATCTTAGCTCTTCTGCTAAC 59.262 45.833 5.04 0.00 46.63 2.34
2429 3818 1.817357 TGCACAGAGATCAAAGGCAG 58.183 50.000 0.00 0.00 0.00 4.85
2434 3823 2.290768 ACAGAGATCAAAGGCAGTGCAT 60.291 45.455 18.61 7.05 0.00 3.96
2436 3825 4.135306 CAGAGATCAAAGGCAGTGCATAT 58.865 43.478 18.61 0.00 0.00 1.78
2446 3835 8.040727 TCAAAGGCAGTGCATATATATACGAAT 58.959 33.333 18.61 0.00 0.00 3.34
2448 3837 9.884636 AAAGGCAGTGCATATATATACGAATTA 57.115 29.630 18.61 0.00 0.00 1.40
2473 3862 1.876799 TGCTGACAACACCGGTAATTG 59.123 47.619 22.93 22.93 0.00 2.32
2504 3893 7.696872 GTGTGTCTTTTCCAAAGAAGAAGTAAC 59.303 37.037 0.47 0.00 34.00 2.50
2505 3894 6.905609 GTGTCTTTTCCAAAGAAGAAGTAACG 59.094 38.462 0.47 0.00 34.00 3.18
2506 3895 6.596497 TGTCTTTTCCAAAGAAGAAGTAACGT 59.404 34.615 0.47 0.00 34.00 3.99
2507 3896 7.765360 TGTCTTTTCCAAAGAAGAAGTAACGTA 59.235 33.333 0.47 0.00 34.00 3.57
2525 3914 9.831737 AGTAACGTAGTACTAACATTGTAGTTG 57.168 33.333 3.61 0.00 45.00 3.16
2526 3915 9.825972 GTAACGTAGTACTAACATTGTAGTTGA 57.174 33.333 3.61 0.00 45.00 3.18
2527 3916 8.733857 AACGTAGTACTAACATTGTAGTTGAC 57.266 34.615 3.61 0.00 45.00 3.18
2528 3917 7.874940 ACGTAGTACTAACATTGTAGTTGACA 58.125 34.615 3.61 0.00 41.94 3.58
2562 3951 0.597637 AGTTGACACCGTGCTTCTCG 60.598 55.000 0.00 0.00 0.00 4.04
2572 3961 4.516092 CCGTGCTTCTCGGTTTTAATAG 57.484 45.455 0.00 0.00 42.62 1.73
2573 3962 4.178540 CCGTGCTTCTCGGTTTTAATAGA 58.821 43.478 0.00 0.00 42.62 1.98
2576 3965 5.220228 CGTGCTTCTCGGTTTTAATAGAGTG 60.220 44.000 0.00 0.00 32.90 3.51
2586 3975 8.308931 TCGGTTTTAATAGAGTGACACAGTAAT 58.691 33.333 8.59 0.00 0.00 1.89
2596 3985 8.582657 AGAGTGACACAGTAATAATAGACACT 57.417 34.615 8.59 0.00 37.53 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.689813 TCCGTTTGTGGCTCTTGACTA 59.310 47.619 0.00 0.00 0.00 2.59
1 2 0.468226 TCCGTTTGTGGCTCTTGACT 59.532 50.000 0.00 0.00 0.00 3.41
2 3 1.523758 ATCCGTTTGTGGCTCTTGAC 58.476 50.000 0.00 0.00 0.00 3.18
3 4 3.627395 ATATCCGTTTGTGGCTCTTGA 57.373 42.857 0.00 0.00 0.00 3.02
4 5 3.689161 TGAATATCCGTTTGTGGCTCTTG 59.311 43.478 0.00 0.00 0.00 3.02
5 6 3.950397 TGAATATCCGTTTGTGGCTCTT 58.050 40.909 0.00 0.00 0.00 2.85
8 9 2.423538 GCTTGAATATCCGTTTGTGGCT 59.576 45.455 0.00 0.00 0.00 4.75
18 19 3.228188 TGGGGTGATGCTTGAATATCC 57.772 47.619 0.00 0.00 0.00 2.59
24 25 0.928505 ATGGATGGGGTGATGCTTGA 59.071 50.000 0.00 0.00 0.00 3.02
29 30 0.966179 CATGCATGGATGGGGTGATG 59.034 55.000 19.40 0.00 0.00 3.07
85 86 1.610038 CTTGCAGCAAGGTGATGACAA 59.390 47.619 25.40 1.31 35.45 3.18
192 193 4.652822 AGTAGCCTTTTGACGAAATCCTT 58.347 39.130 0.00 0.00 0.00 3.36
277 298 5.673568 GCGTCAACACATTGCTACATATGTT 60.674 40.000 14.77 0.00 35.63 2.71
357 1469 7.452880 TTCAAGACAGAAGTAAATGAATGGG 57.547 36.000 0.00 0.00 0.00 4.00
358 1470 7.025963 GCTTCAAGACAGAAGTAAATGAATGG 58.974 38.462 5.70 0.00 45.28 3.16
401 1513 4.651503 TGAATGGATGAAGGACTAGAGGAC 59.348 45.833 0.00 0.00 0.00 3.85
449 1562 8.287439 TGTTGTTCTTCAAATTTTACTCCAGA 57.713 30.769 0.00 0.00 37.81 3.86
450 1563 8.971321 CATGTTGTTCTTCAAATTTTACTCCAG 58.029 33.333 0.00 0.00 37.81 3.86
522 1635 7.065803 TGTTCGGGTCAATATTTCATTCTTCTC 59.934 37.037 0.00 0.00 0.00 2.87
535 1648 3.916359 TGCCTATTGTTCGGGTCAATA 57.084 42.857 0.00 0.00 36.92 1.90
543 1656 0.446222 CACCCGTTGCCTATTGTTCG 59.554 55.000 0.00 0.00 0.00 3.95
643 1758 4.038282 ACACATGCATCATCTCTCTCTCTC 59.962 45.833 0.00 0.00 0.00 3.20
644 1759 3.962063 ACACATGCATCATCTCTCTCTCT 59.038 43.478 0.00 0.00 0.00 3.10
645 1760 4.300803 GACACATGCATCATCTCTCTCTC 58.699 47.826 0.00 0.00 0.00 3.20
646 1761 3.243468 CGACACATGCATCATCTCTCTCT 60.243 47.826 0.00 0.00 0.00 3.10
647 1762 3.051327 CGACACATGCATCATCTCTCTC 58.949 50.000 0.00 0.00 0.00 3.20
673 1789 5.133941 CCCTAGTTGTGCTCTATGACTCTA 58.866 45.833 0.00 0.00 0.00 2.43
674 1790 3.957497 CCCTAGTTGTGCTCTATGACTCT 59.043 47.826 0.00 0.00 0.00 3.24
675 1791 3.491792 GCCCTAGTTGTGCTCTATGACTC 60.492 52.174 0.00 0.00 0.00 3.36
676 1792 2.432510 GCCCTAGTTGTGCTCTATGACT 59.567 50.000 0.00 0.00 0.00 3.41
677 1793 2.432510 AGCCCTAGTTGTGCTCTATGAC 59.567 50.000 0.00 0.00 0.00 3.06
678 1794 2.432146 CAGCCCTAGTTGTGCTCTATGA 59.568 50.000 0.00 0.00 31.77 2.15
679 1795 2.831333 CAGCCCTAGTTGTGCTCTATG 58.169 52.381 0.00 0.00 31.77 2.23
774 1890 2.421529 CCTCCTGGCGTTTAAAGGCTAT 60.422 50.000 26.70 0.00 39.58 2.97
775 1891 1.065709 CCTCCTGGCGTTTAAAGGCTA 60.066 52.381 26.70 21.78 39.58 3.93
776 1892 0.322546 CCTCCTGGCGTTTAAAGGCT 60.323 55.000 26.70 0.00 39.58 4.58
777 1893 2.180674 CCTCCTGGCGTTTAAAGGC 58.819 57.895 21.65 21.65 38.96 4.35
912 2028 3.627395 AATGGATAGGTGCGACTTTGA 57.373 42.857 0.00 0.00 0.00 2.69
993 2113 3.343326 GTGGTGGCCATGGGGGTA 61.343 66.667 9.72 0.00 39.65 3.69
1128 2251 3.384668 GGACACCATGTAGATGATGACG 58.615 50.000 0.19 0.00 26.29 4.35
1257 2388 3.387947 GCGGTCCTCGGGGAAGAA 61.388 66.667 5.00 0.00 44.15 2.52
1374 2505 2.109799 ACGTTCTGCTGCTGCTGT 59.890 55.556 17.00 4.90 40.48 4.40
1425 2562 1.070275 GAACAGGAACCCCGTCGTT 59.930 57.895 0.00 0.00 37.58 3.85
1599 2736 1.542767 CCCGATCATTGCTGCTGAGAT 60.543 52.381 0.00 1.05 0.00 2.75
1655 2792 7.122715 ACCCTAATGCATATTGAGTTGGTAAA 58.877 34.615 0.00 0.00 0.00 2.01
1781 2923 4.587976 ACTGCAGGAACCTAGACTACTA 57.412 45.455 19.93 0.00 0.00 1.82
1782 2924 3.459710 ACTGCAGGAACCTAGACTACT 57.540 47.619 19.93 0.00 0.00 2.57
1783 2925 5.360144 TCAATACTGCAGGAACCTAGACTAC 59.640 44.000 19.93 0.00 0.00 2.73
1896 3039 9.308623 CGAATCAACAAACAAATCAATTTCATG 57.691 29.630 0.00 0.00 0.00 3.07
2018 3161 4.959210 AGTCAAGCGCCAGGATATATATCT 59.041 41.667 19.72 5.94 33.28 1.98
2019 3162 5.046529 CAGTCAAGCGCCAGGATATATATC 58.953 45.833 13.50 13.50 0.00 1.63
2020 3163 4.711846 TCAGTCAAGCGCCAGGATATATAT 59.288 41.667 2.29 0.00 0.00 0.86
2021 3164 4.082190 GTCAGTCAAGCGCCAGGATATATA 60.082 45.833 2.29 0.00 0.00 0.86
2033 3176 1.403679 AGCTAGCTAGTCAGTCAAGCG 59.596 52.381 17.69 0.00 41.19 4.68
2076 3222 0.459585 CATGTACACGACGGGGAAGG 60.460 60.000 0.43 0.00 0.00 3.46
2111 3261 6.963049 AATACGACACGCTTAATTTCTTCT 57.037 33.333 0.00 0.00 0.00 2.85
2124 3274 3.000925 GCTGGTGGATTAAATACGACACG 59.999 47.826 0.00 0.00 0.00 4.49
2125 3275 3.000925 CGCTGGTGGATTAAATACGACAC 59.999 47.826 0.00 0.00 0.00 3.67
2144 3295 1.267261 GCTGTAGATCACCGTATCGCT 59.733 52.381 0.00 0.00 0.00 4.93
2146 3297 3.003378 TCAAGCTGTAGATCACCGTATCG 59.997 47.826 0.00 0.00 0.00 2.92
2182 3354 8.190784 ACTGCATGCCAACTATAAGAAAAATAC 58.809 33.333 16.68 0.00 0.00 1.89
2302 3487 6.262273 AGTTTGATTTTCACGCTCTTAAAGGA 59.738 34.615 0.00 0.00 0.00 3.36
2304 3489 7.096477 CCAAGTTTGATTTTCACGCTCTTAAAG 60.096 37.037 0.00 0.00 0.00 1.85
2307 3492 5.298276 ACCAAGTTTGATTTTCACGCTCTTA 59.702 36.000 0.00 0.00 0.00 2.10
2364 3753 3.005791 GGTTTTTGTGATCCCTTGAGTGG 59.994 47.826 0.00 0.00 0.00 4.00
2416 3805 9.039870 GTATATATATGCACTGCCTTTGATCTC 57.960 37.037 5.44 0.00 0.00 2.75
2446 3835 2.356382 CCGGTGTTGTCAGCAAAAGTAA 59.644 45.455 0.00 0.00 41.52 2.24
2448 3837 0.738389 CCGGTGTTGTCAGCAAAAGT 59.262 50.000 0.00 0.00 41.52 2.66
2473 3862 3.813166 TCTTTGGAAAAGACACACCGATC 59.187 43.478 0.00 0.00 0.00 3.69
2478 3867 6.196079 ACTTCTTCTTTGGAAAAGACACAC 57.804 37.500 1.98 0.00 31.46 3.82
2504 3893 8.732413 TTGTCAACTACAATGTTAGTACTACG 57.268 34.615 0.91 0.00 43.22 3.51
2532 3921 5.336744 CACGGTGTCAACTACAATGTTTTT 58.663 37.500 0.00 0.00 40.63 1.94
2533 3922 4.732355 GCACGGTGTCAACTACAATGTTTT 60.732 41.667 10.24 0.00 40.63 2.43
2534 3923 3.242936 GCACGGTGTCAACTACAATGTTT 60.243 43.478 10.24 0.00 40.63 2.83
2535 3924 2.289547 GCACGGTGTCAACTACAATGTT 59.710 45.455 10.24 0.00 40.63 2.71
2536 3925 1.871039 GCACGGTGTCAACTACAATGT 59.129 47.619 10.24 0.00 40.63 2.71
2537 3926 2.143122 AGCACGGTGTCAACTACAATG 58.857 47.619 10.24 0.00 40.63 2.82
2538 3927 2.543777 AGCACGGTGTCAACTACAAT 57.456 45.000 10.24 0.00 40.63 2.71
2539 3928 2.159014 AGAAGCACGGTGTCAACTACAA 60.159 45.455 10.24 0.00 40.63 2.41
2540 3929 1.411246 AGAAGCACGGTGTCAACTACA 59.589 47.619 10.24 0.00 35.06 2.74
2576 3965 9.530633 CCCTTTAGTGTCTATTATTACTGTGTC 57.469 37.037 0.00 0.00 0.00 3.67
2586 3975 6.727394 ACCAAATGCCCTTTAGTGTCTATTA 58.273 36.000 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.