Multiple sequence alignment - TraesCS1A01G167000

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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 TraesCS1A01G167000 chr1A 100.000 2594 0 0 1 2594 299718197 299720790 0.000000e+00 4791.0
1 TraesCS1A01G167000 chr1D 94.005 2135 68 17 1 2110 247508654 247506555 0.000000e+00 3179.0
2 TraesCS1A01G167000 chr1D 93.407 455 28 1 2124 2576 247506381 247505927 0.000000e+00 673.0
3 TraesCS1A01G167000 chr1B 94.180 2079 72 21 64 2113 330230637 330232695 0.000000e+00 3123.0
4 TraesCS1A01G167000 chr1B 89.899 396 36 2 2183 2576 330233047 330233440 8.280000e-140 507.0
5 TraesCS1A01G167000 chr1B 93.421 76 5 0 1 76 330230543 330230618 2.110000e-21 113.0
6 TraesCS1A01G167000 chr1B 96.875 64 2 0 2124 2187 330232870 330232933 9.820000e-20 108.0
7 TraesCS1A01G167000 chr5B 79.960 504 95 5 1101 1600 609484550 609485051 1.470000e-97 366.0
8 TraesCS1A01G167000 chr5B 79.600 500 97 4 1101 1597 609481805 609482302 1.140000e-93 353.0
9 TraesCS1A01G167000 chr5B 79.600 500 97 4 1101 1597 609494605 609495102 1.140000e-93 353.0
10 TraesCS1A01G167000 chr5B 79.242 501 98 5 1101 1597 609492092 609492590 6.870000e-91 344.0
11 TraesCS1A01G167000 chr5B 79.042 501 98 6 1101 1597 609464431 609464928 1.150000e-88 337.0
12 TraesCS1A01G167000 chr5D 79.918 488 94 3 1112 1597 493777645 493778130 3.170000e-94 355.0
13 TraesCS1A01G167000 chr7A 81.208 447 77 6 1153 1597 624772639 624773080 1.140000e-93 353.0
14 TraesCS1A01G167000 chr6A 95.000 40 2 0 2084 2123 522037119 522037158 2.160000e-06 63.9


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 TraesCS1A01G167000 chr1A 299718197 299720790 2593 False 4791.00 4791 100.00000 1 2594 1 chr1A.!!$F1 2593
1 TraesCS1A01G167000 chr1D 247505927 247508654 2727 True 1926.00 3179 93.70600 1 2576 2 chr1D.!!$R1 2575
2 TraesCS1A01G167000 chr1B 330230543 330233440 2897 False 962.75 3123 93.59375 1 2576 4 chr1B.!!$F1 2575
3 TraesCS1A01G167000 chr5B 609481805 609485051 3246 False 359.50 366 79.78000 1101 1600 2 chr5B.!!$F2 499
4 TraesCS1A01G167000 chr5B 609492092 609495102 3010 False 348.50 353 79.42100 1101 1597 2 chr5B.!!$F3 496

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
545 596 0.963962 ATGCCAGTTTCAACCAGCAG 59.036 50.0 9.38 0.0 39.71 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 5665 0.399091 CCCAGACTATGAGAGGGCCA 60.399 60.0 6.18 0.0 31.81 5.36 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
145 182 8.312669 AGAGCTACTTCTATGGAGTAATTTGT 57.687 34.615 0.00 0.00 0.00 2.83
186 223 5.472148 CAAACTTGCAATGCCTTTATCTGA 58.528 37.500 1.53 0.00 0.00 3.27
187 224 5.726980 AACTTGCAATGCCTTTATCTGAA 57.273 34.783 1.53 0.00 0.00 3.02
188 225 5.320549 ACTTGCAATGCCTTTATCTGAAG 57.679 39.130 1.53 0.00 0.00 3.02
275 314 3.499338 AGCCAAATCATCCAGAAACACA 58.501 40.909 0.00 0.00 0.00 3.72
303 342 4.082787 TGGATGCGGTTTTTCTCAATTCTC 60.083 41.667 0.00 0.00 0.00 2.87
326 365 2.232452 AGTGTCCAGGAAATCTGAGACG 59.768 50.000 0.00 0.00 46.18 4.18
333 372 3.433615 CAGGAAATCTGAGACGGTCAAAC 59.566 47.826 11.27 2.29 46.18 2.93
339 378 4.066646 TCTGAGACGGTCAAACAATCAA 57.933 40.909 11.27 0.00 33.60 2.57
378 417 5.867903 AATTGATCAAACCAGGACAAACA 57.132 34.783 13.09 0.00 0.00 2.83
384 423 2.361757 CAAACCAGGACAAACATGCTGA 59.638 45.455 0.00 0.00 40.28 4.26
418 457 6.021596 GCCAAAATGTTCAGTTATACACTCG 58.978 40.000 0.00 0.00 30.92 4.18
425 465 4.978083 TCAGTTATACACTCGGTTCTCC 57.022 45.455 0.00 0.00 30.92 3.71
438 478 6.912591 CACTCGGTTCTCCATTTATTTTATGC 59.087 38.462 0.00 0.00 0.00 3.14
545 596 0.963962 ATGCCAGTTTCAACCAGCAG 59.036 50.000 9.38 0.00 39.71 4.24
554 605 5.632347 CAGTTTCAACCAGCAGAATGATTTC 59.368 40.000 0.00 0.00 39.69 2.17
564 615 4.040376 GCAGAATGATTTCCTCGCAATTC 58.960 43.478 0.00 0.00 39.69 2.17
781 838 6.047231 GCCTAGTTAAACCAGTGGTATAGTG 58.953 44.000 17.09 3.16 33.12 2.74
782 839 6.351626 GCCTAGTTAAACCAGTGGTATAGTGT 60.352 42.308 17.09 0.00 33.12 3.55
926 983 9.656040 AATTGCTGATTTCTGAGCTCTATATAG 57.344 33.333 16.19 3.10 36.11 1.31
1569 4377 5.335191 GCTCAACAAGAACATCGGAGAATTT 60.335 40.000 0.00 0.00 43.58 1.82
1669 4477 0.108585 GGGAACTGTGTGCTCCTCAA 59.891 55.000 0.00 0.00 31.75 3.02
1699 4507 2.503331 CCATATGGTGTGTGTGTGTGT 58.497 47.619 14.09 0.00 0.00 3.72
1700 4508 2.226200 CCATATGGTGTGTGTGTGTGTG 59.774 50.000 14.09 0.00 0.00 3.82
1701 4509 2.700722 TATGGTGTGTGTGTGTGTGT 57.299 45.000 0.00 0.00 0.00 3.72
1702 4510 1.093972 ATGGTGTGTGTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
1703 4511 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
1704 4512 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
1741 4571 5.997129 TGTGTGTGTGTGATGATAATCTTGT 59.003 36.000 0.00 0.00 0.00 3.16
1742 4572 6.486320 TGTGTGTGTGTGATGATAATCTTGTT 59.514 34.615 0.00 0.00 0.00 2.83
1787 4617 3.820467 TGCTATCCCAAGAAAAGTGTGTG 59.180 43.478 0.00 0.00 0.00 3.82
1976 4806 3.565482 TCAGATGTTTGAACAGTTCAGCC 59.435 43.478 15.61 10.84 43.04 4.85
1985 4815 5.336150 TGAACAGTTCAGCCATTTGAAAA 57.664 34.783 12.24 0.00 38.69 2.29
2013 4848 6.645790 AATCAAAGAGAACAAGACAATGCT 57.354 33.333 0.00 0.00 0.00 3.79
2091 4926 7.228652 AGAAGTACCTTAAGAGATACTCCCT 57.771 40.000 3.36 7.13 0.00 4.20
2096 4931 5.844601 ACCTTAAGAGATACTCCCTCTGTT 58.155 41.667 3.36 0.00 40.58 3.16
2099 4934 4.618378 AAGAGATACTCCCTCTGTTCCT 57.382 45.455 0.00 0.00 40.58 3.36
2100 4935 5.735733 AAGAGATACTCCCTCTGTTCCTA 57.264 43.478 0.00 0.00 40.58 2.94
2102 4937 5.451354 AGAGATACTCCCTCTGTTCCTAAC 58.549 45.833 0.00 0.00 39.36 2.34
2110 4945 6.834969 ACTCCCTCTGTTCCTAACTATAAGAC 59.165 42.308 0.00 0.00 0.00 3.01
2112 4947 6.068379 TCCCTCTGTTCCTAACTATAAGACCT 60.068 42.308 0.00 0.00 0.00 3.85
2113 4948 6.265876 CCCTCTGTTCCTAACTATAAGACCTC 59.734 46.154 0.00 0.00 0.00 3.85
2116 4951 9.629878 CTCTGTTCCTAACTATAAGACCTCTTA 57.370 37.037 0.00 0.00 42.04 2.10
2117 4952 9.986157 TCTGTTCCTAACTATAAGACCTCTTAA 57.014 33.333 0.00 0.00 41.27 1.85
2191 5309 7.633193 AGTCTACTCACAGTCTAATAGGTTG 57.367 40.000 0.00 0.00 0.00 3.77
2255 5373 1.066002 CAACTATTTGGCCTGGCATCG 59.934 52.381 22.05 4.28 0.00 3.84
2351 5469 6.042777 TGCACGGAAACAACAATCAAATAAA 58.957 32.000 0.00 0.00 0.00 1.40
2526 5646 2.350458 CCCACAGCAAATTCCGGGG 61.350 63.158 0.00 0.00 0.00 5.73
2543 5665 2.039418 GGGGTTTTTCAGAGCAAAGGT 58.961 47.619 0.00 0.00 0.00 3.50
2576 5698 9.331282 CTCATAGTCTGGGTTTTATTAGAAAGG 57.669 37.037 0.00 0.00 0.00 3.11
2577 5699 8.272173 TCATAGTCTGGGTTTTATTAGAAAGGG 58.728 37.037 0.00 0.00 0.00 3.95
2578 5700 6.713731 AGTCTGGGTTTTATTAGAAAGGGA 57.286 37.500 0.00 0.00 0.00 4.20
2579 5701 7.098845 AGTCTGGGTTTTATTAGAAAGGGAA 57.901 36.000 0.00 0.00 0.00 3.97
2580 5702 7.532199 AGTCTGGGTTTTATTAGAAAGGGAAA 58.468 34.615 0.00 0.00 0.00 3.13
2581 5703 8.008332 AGTCTGGGTTTTATTAGAAAGGGAAAA 58.992 33.333 0.00 0.00 0.00 2.29
2582 5704 8.304596 GTCTGGGTTTTATTAGAAAGGGAAAAG 58.695 37.037 0.00 0.00 0.00 2.27
2583 5705 8.008332 TCTGGGTTTTATTAGAAAGGGAAAAGT 58.992 33.333 0.00 0.00 0.00 2.66
2584 5706 9.304335 CTGGGTTTTATTAGAAAGGGAAAAGTA 57.696 33.333 0.00 0.00 0.00 2.24
2585 5707 9.831682 TGGGTTTTATTAGAAAGGGAAAAGTAT 57.168 29.630 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 182 1.074775 GGGGGTTGTCTGTGCATCA 59.925 57.895 0.00 0.00 0.00 3.07
197 236 7.324178 ACATCCTGTGTAGTCACTTAATTCTC 58.676 38.462 0.00 0.00 44.14 2.87
229 268 5.221641 CCCGGGATTGTCTCAATATGTCTTA 60.222 44.000 18.48 0.00 0.00 2.10
275 314 2.293399 GAGAAAAACCGCATCCAAGTGT 59.707 45.455 0.00 0.00 0.00 3.55
303 342 2.568956 TCTCAGATTTCCTGGACACTGG 59.431 50.000 17.70 11.69 43.12 4.00
326 365 7.158021 TGGAAATATGGTTTGATTGTTTGACC 58.842 34.615 0.00 0.00 0.00 4.02
418 457 7.346751 TGGAGCATAAAATAAATGGAGAACC 57.653 36.000 0.00 0.00 0.00 3.62
438 478 8.833231 TTTAAAACAGAGACTAACAGATGGAG 57.167 34.615 0.00 0.00 0.00 3.86
545 596 5.824429 TGATGAATTGCGAGGAAATCATTC 58.176 37.500 8.82 4.52 34.66 2.67
554 605 3.270027 TGGTAGTTGATGAATTGCGAGG 58.730 45.455 0.00 0.00 0.00 4.63
596 647 9.347240 ACTCGGTAGTAGCTTTAGTGATTAATA 57.653 33.333 0.00 0.00 32.84 0.98
597 648 8.235359 ACTCGGTAGTAGCTTTAGTGATTAAT 57.765 34.615 0.00 0.00 32.84 1.40
599 650 8.737168 TTACTCGGTAGTAGCTTTAGTGATTA 57.263 34.615 0.00 0.00 39.36 1.75
600 651 7.636150 TTACTCGGTAGTAGCTTTAGTGATT 57.364 36.000 0.00 0.00 39.36 2.57
601 652 7.820578 ATTACTCGGTAGTAGCTTTAGTGAT 57.179 36.000 0.00 0.00 39.36 3.06
602 653 8.737168 TTATTACTCGGTAGTAGCTTTAGTGA 57.263 34.615 0.00 0.00 39.36 3.41
603 654 9.395707 CATTATTACTCGGTAGTAGCTTTAGTG 57.604 37.037 0.00 0.00 39.36 2.74
604 655 9.129532 ACATTATTACTCGGTAGTAGCTTTAGT 57.870 33.333 0.00 1.72 39.36 2.24
781 838 0.531090 TGCTACCGTGTGTTCACCAC 60.531 55.000 0.37 0.00 44.78 4.16
782 839 0.394938 ATGCTACCGTGTGTTCACCA 59.605 50.000 0.37 0.00 41.09 4.17
926 983 2.835764 TCAAGTGTATGGGTGGGTACTC 59.164 50.000 0.00 0.00 0.00 2.59
1569 4377 5.245977 TCACACATCAGACCAAGTGATCTTA 59.754 40.000 0.00 0.00 32.06 2.10
1687 4495 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1688 4496 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1689 4497 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1690 4498 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1691 4499 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1692 4500 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1693 4501 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1694 4502 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1695 4503 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1696 4504 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1697 4505 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1698 4506 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1699 4507 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1700 4508 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1701 4509 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1702 4510 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1703 4511 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1704 4512 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1741 4571 2.722094 ACGGCTTATTTGCTCCATCAA 58.278 42.857 0.00 0.00 0.00 2.57
1742 4572 2.418368 ACGGCTTATTTGCTCCATCA 57.582 45.000 0.00 0.00 0.00 3.07
1787 4617 8.487176 CACACATAGTTTTGGAAATTAACAAGC 58.513 33.333 0.00 0.00 0.00 4.01
1913 4743 3.440173 CCGCACAAAACCAGAGTCATTAT 59.560 43.478 0.00 0.00 0.00 1.28
1994 4829 3.005155 GCCAGCATTGTCTTGTTCTCTTT 59.995 43.478 0.00 0.00 0.00 2.52
2003 4838 4.312443 CTGAAATTTGCCAGCATTGTCTT 58.688 39.130 0.00 0.00 0.00 3.01
2013 4848 7.531857 TTTCTATAACACCTGAAATTTGCCA 57.468 32.000 0.00 0.00 0.00 4.92
2091 4926 9.986157 TTAAGAGGTCTTATAGTTAGGAACAGA 57.014 33.333 0.29 0.00 38.16 3.41
2110 4945 4.580580 AGCGCCCAAATAATCTTTAAGAGG 59.419 41.667 2.29 0.00 0.00 3.69
2112 4947 6.037830 GTGTAGCGCCCAAATAATCTTTAAGA 59.962 38.462 2.29 0.00 0.00 2.10
2113 4948 6.038271 AGTGTAGCGCCCAAATAATCTTTAAG 59.962 38.462 2.29 0.00 0.00 1.85
2116 4951 4.270008 AGTGTAGCGCCCAAATAATCTTT 58.730 39.130 2.29 0.00 0.00 2.52
2117 4952 3.886123 AGTGTAGCGCCCAAATAATCTT 58.114 40.909 2.29 0.00 0.00 2.40
2118 4953 3.560636 AGTGTAGCGCCCAAATAATCT 57.439 42.857 2.29 0.00 0.00 2.40
2119 4954 5.941948 ATAAGTGTAGCGCCCAAATAATC 57.058 39.130 2.29 0.00 0.00 1.75
2121 4956 9.590451 GTATATATAAGTGTAGCGCCCAAATAA 57.410 33.333 2.29 0.00 0.00 1.40
2122 4957 8.199449 GGTATATATAAGTGTAGCGCCCAAATA 58.801 37.037 2.29 1.36 0.00 1.40
2191 5309 5.505654 CGATGGGCCAATAACAAGTAATGTC 60.506 44.000 11.89 0.00 42.99 3.06
2255 5373 5.281727 GGTTTCAAATGAGTTGTGACTTCC 58.718 41.667 0.00 0.00 38.47 3.46
2331 5449 7.922505 TGACTTTATTTGATTGTTGTTTCCG 57.077 32.000 0.00 0.00 0.00 4.30
2351 5469 6.770746 ACGGTAGTGTTATGAGTTATGACT 57.229 37.500 0.00 0.00 39.32 3.41
2526 5646 2.473816 GCCACCTTTGCTCTGAAAAAC 58.526 47.619 0.00 0.00 0.00 2.43
2543 5665 0.399091 CCCAGACTATGAGAGGGCCA 60.399 60.000 6.18 0.00 31.81 5.36


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

AutoCloner maintained by Alex Coulton.