Multiple sequence alignment - TraesCS6A01G157100

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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 TraesCS6A01G157100 chr6A 100.000 2401 0 0 1 2401 146481457 146479057 0.000000e+00 4434.0
1 TraesCS6A01G157100 chr6D 90.727 2092 147 24 1 2061 117359538 117361613 0.000000e+00 2745.0
2 TraesCS6A01G157100 chr6D 89.877 326 24 3 2078 2401 117361599 117361917 6.180000e-111 411.0
3 TraesCS6A01G157100 chr6B 90.537 2124 128 30 1 2061 207958676 207956563 0.000000e+00 2741.0
4 TraesCS6A01G157100 chr6B 91.385 325 28 0 2077 2401 207956578 207956254 1.690000e-121 446.0
5 TraesCS6A01G157100 chr7D 97.059 34 1 0 2368 2401 271924355 271924388 9.270000e-05 58.4
6 TraesCS6A01G157100 chr7B 100.000 30 0 0 2370 2399 410464756 410464785 3.330000e-04 56.5


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 TraesCS6A01G157100 chr6A 146479057 146481457 2400 True 4434.0 4434 100.000 1 2401 1 chr6A.!!$R1 2400
1 TraesCS6A01G157100 chr6D 117359538 117361917 2379 False 1578.0 2745 90.302 1 2401 2 chr6D.!!$F1 2400
2 TraesCS6A01G157100 chr6B 207956254 207958676 2422 True 1593.5 2741 90.961 1 2401 2 chr6B.!!$R1 2400

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
632 636 1.934589 GGTGCCTGAACCAACAAAAC 58.065 50.0 0.0 0.0 40.22 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1817 0.250727 ATGAACAAGTGGACCACCGG 60.251 55.0 21.32 15.45 39.42 5.28 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
163 164 5.491078 ACATCTGGACCCAAAGGAATAACTA 59.509 40.000 0.00 0.00 36.73 2.24
179 180 8.907885 AGGAATAACTAGATTTTCAAAGGCATC 58.092 33.333 0.00 0.00 0.00 3.91
199 200 2.304761 TCGCTCCAAGTATCAACCCTTT 59.695 45.455 0.00 0.00 0.00 3.11
212 213 3.053245 TCAACCCTTTGGAAAGAACTCCA 60.053 43.478 0.47 0.00 43.99 3.86
215 216 3.117131 ACCCTTTGGAAAGAACTCCACAT 60.117 43.478 0.47 0.00 45.37 3.21
252 253 8.345724 AGAAAGTGTGCATTAATCAAAGAGAT 57.654 30.769 0.00 0.00 39.09 2.75
324 328 2.277084 CATGTTACCTAGAACCGGTGC 58.723 52.381 8.52 5.95 35.98 5.01
357 361 9.836864 ATTTGTATTCTCTTTCTTTGGCTTTTT 57.163 25.926 0.00 0.00 0.00 1.94
480 484 2.242708 AGTGGTAGTGTTGGGTTTTCCA 59.757 45.455 0.00 0.00 45.43 3.53
632 636 1.934589 GGTGCCTGAACCAACAAAAC 58.065 50.000 0.00 0.00 40.22 2.43
649 653 7.386573 CCAACAAAACTTTAAAGTGTTCACCTT 59.613 33.333 21.22 7.42 39.66 3.50
654 658 4.338400 ACTTTAAAGTGTTCACCTTGGAGC 59.662 41.667 19.94 0.00 37.98 4.70
706 710 3.553105 ACGGAACACAACTTCGAAAGTAC 59.447 43.478 0.00 0.00 41.91 2.73
732 740 9.667107 CAGTATAAAGACCTCCAATGAACTTTA 57.333 33.333 0.00 0.00 35.40 1.85
811 841 9.599866 CATTTATTTCACACAGTACCAGATCTA 57.400 33.333 0.00 0.00 0.00 1.98
833 863 8.601047 TCTAGTAGCAAGGATATATGCAGATT 57.399 34.615 0.00 0.00 44.95 2.40
895 925 7.337938 TGTGTATCCATTTCAGAAGCAATCTA 58.662 34.615 0.00 0.00 36.32 1.98
969 1000 3.567478 ATAAATGGACACTGAGCCCTC 57.433 47.619 0.00 0.00 0.00 4.30
972 1003 3.403558 GGACACTGAGCCCTCCCC 61.404 72.222 0.00 0.00 0.00 4.81
1195 1226 6.375174 TGTTGATTGATTGATTGAGTAGGTGG 59.625 38.462 0.00 0.00 0.00 4.61
1259 1290 1.452145 GGTGCACCCACAACGACAAT 61.452 55.000 26.31 0.00 43.88 2.71
1263 1294 1.202359 GCACCCACAACGACAATTGTT 60.202 47.619 13.36 0.00 40.89 2.83
1265 1296 3.516615 CACCCACAACGACAATTGTTTT 58.483 40.909 13.36 6.55 40.89 2.43
1410 1441 6.183360 GGAAATGATGATCTGACTGAAGTGTG 60.183 42.308 0.00 0.00 0.00 3.82
1435 1466 6.552629 CCTGAGATTTGAGTTGATGACAATG 58.447 40.000 0.00 0.00 38.32 2.82
1439 1470 8.799367 TGAGATTTGAGTTGATGACAATGAAAT 58.201 29.630 0.00 0.00 38.32 2.17
1572 1603 3.066291 AGACAAACCATATGCCGACAA 57.934 42.857 0.00 0.00 0.00 3.18
1644 1675 6.225981 AGAAAGAACTTTGACCTTTGCATT 57.774 33.333 4.48 0.00 32.11 3.56
1680 1711 9.748708 ACACATCCATGCATTAATTATTGTAAC 57.251 29.630 0.00 0.00 0.00 2.50
1681 1712 9.747293 CACATCCATGCATTAATTATTGTAACA 57.253 29.630 0.00 0.67 0.00 2.41
1783 1817 1.542030 TGTTTGGTGTGTTGGTGTGTC 59.458 47.619 0.00 0.00 0.00 3.67
1791 1825 1.890510 GTTGGTGTGTCCGGTGGTC 60.891 63.158 0.00 0.00 39.52 4.02
1833 1895 4.160252 GTGCCCATTCTACATGATTTTGGT 59.840 41.667 0.00 0.00 0.00 3.67
1907 1969 6.886178 ATGTAGTGGTACTATTGGGTTTCT 57.114 37.500 0.00 0.00 32.65 2.52
1995 2059 9.267096 GAAGAAAGATTGCTAACAAAGATTACG 57.733 33.333 0.00 0.00 39.77 3.18
2034 2099 4.385447 CAGTATTTGCGTTTTCCATGTTGG 59.615 41.667 0.00 0.00 39.43 3.77
2058 2123 4.264460 TGTTGCTTGAACCAACAAAAGT 57.736 36.364 3.72 0.00 46.66 2.66
2059 2124 4.636249 TGTTGCTTGAACCAACAAAAGTT 58.364 34.783 3.72 0.00 46.66 2.66
2060 2125 5.059833 TGTTGCTTGAACCAACAAAAGTTT 58.940 33.333 3.72 0.00 46.66 2.66
2061 2126 5.529060 TGTTGCTTGAACCAACAAAAGTTTT 59.471 32.000 3.72 0.00 46.66 2.43
2062 2127 6.038714 TGTTGCTTGAACCAACAAAAGTTTTT 59.961 30.769 3.72 0.00 46.66 1.94
2100 2165 6.869388 GGAACCAACAAAAGTTTGAAGTGTTA 59.131 34.615 10.66 0.00 40.55 2.41
2105 2170 7.596995 CCAACAAAAGTTTGAAGTGTTAACTCA 59.403 33.333 10.66 0.00 40.55 3.41
2107 2172 6.806739 ACAAAAGTTTGAAGTGTTAACTCAGC 59.193 34.615 10.66 0.54 40.55 4.26
2113 2178 1.779569 AGTGTTAACTCAGCGTTCCG 58.220 50.000 7.22 0.00 37.05 4.30
2146 2211 4.346709 TCCAGTTTAGACTCATGGAACACA 59.653 41.667 0.00 0.00 35.43 3.72
2163 2228 7.607250 TGGAACACAACTTCAAAAGTACAAAT 58.393 30.769 0.00 0.00 41.91 2.32
2169 2234 7.860872 CACAACTTCAAAAGTACAAATACCTCC 59.139 37.037 0.00 0.00 41.91 4.30
2175 2240 4.467198 AAGTACAAATACCTCCGGTGAG 57.533 45.455 4.76 0.00 36.19 3.51
2240 2307 8.235226 CACCATGAGAAGATATGCACATTTATC 58.765 37.037 0.00 0.00 0.00 1.75
2300 2367 9.225436 TGCACATAAATGTTCACTAACTTCATA 57.775 29.630 0.00 0.00 39.39 2.15
2321 2388 6.435591 TCATAGTATCCAAAAACCAACATGCA 59.564 34.615 0.00 0.00 0.00 3.96
2324 2391 7.422465 AGTATCCAAAAACCAACATGCATAT 57.578 32.000 0.00 0.00 0.00 1.78
2325 2392 7.491682 AGTATCCAAAAACCAACATGCATATC 58.508 34.615 0.00 0.00 0.00 1.63
2326 2393 5.083533 TCCAAAAACCAACATGCATATCC 57.916 39.130 0.00 0.00 0.00 2.59
2327 2394 4.529769 TCCAAAAACCAACATGCATATCCA 59.470 37.500 0.00 0.00 0.00 3.41
2328 2395 5.189342 TCCAAAAACCAACATGCATATCCAT 59.811 36.000 0.00 0.00 0.00 3.41
2329 2396 5.881443 CCAAAAACCAACATGCATATCCATT 59.119 36.000 0.00 0.00 0.00 3.16
2344 2417 7.040892 TGCATATCCATTTCAGAAGCAATCTAC 60.041 37.037 0.00 0.00 36.32 2.59
2394 2468 2.354805 CCCTCAGGTCCTTTTTACTCCG 60.355 54.545 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.444933 TGGGGTGATGAAGTCCAAGT 58.555 50.000 0.00 0.00 0.00 3.16
22 23 1.971149 AGATGGGGTGATGAAGTCCA 58.029 50.000 0.00 0.00 0.00 4.02
163 164 2.424956 GGAGCGATGCCTTTGAAAATCT 59.575 45.455 0.00 0.00 0.00 2.40
179 180 2.403252 AAGGGTTGATACTTGGAGCG 57.597 50.000 0.00 0.00 0.00 5.03
199 200 5.305585 GTCTTGTATGTGGAGTTCTTTCCA 58.694 41.667 0.00 0.00 44.84 3.53
212 213 6.692486 CACACTTTCTCTAGGTCTTGTATGT 58.308 40.000 0.00 0.00 0.00 2.29
215 216 4.587262 TGCACACTTTCTCTAGGTCTTGTA 59.413 41.667 0.00 0.00 0.00 2.41
264 265 4.705110 TTCACAATCCAGGTCTTGAAGA 57.295 40.909 10.41 0.00 0.00 2.87
302 303 2.235402 CACCGGTTCTAGGTAACATGGT 59.765 50.000 2.97 0.00 40.59 3.55
303 304 2.901249 CACCGGTTCTAGGTAACATGG 58.099 52.381 2.97 0.00 40.59 3.66
596 600 4.463891 AGGCACCAAATCGAGATGAAAAAT 59.536 37.500 2.02 0.00 0.00 1.82
632 636 4.580580 AGCTCCAAGGTGAACACTTTAAAG 59.419 41.667 13.76 13.76 0.00 1.85
649 653 2.327325 AGTTTCAGTAGGGAGCTCCA 57.673 50.000 33.29 12.26 38.24 3.86
654 658 1.550976 AGGCGAAGTTTCAGTAGGGAG 59.449 52.381 0.00 0.00 0.00 4.30
706 710 8.567285 AAAGTTCATTGGAGGTCTTTATACTG 57.433 34.615 0.00 0.00 0.00 2.74
732 740 5.615289 GCTGGACAGTAAATATCCATGAGT 58.385 41.667 0.00 0.00 41.65 3.41
750 758 2.491621 CGACATCTCTGCGCTGGA 59.508 61.111 14.70 10.71 0.00 3.86
811 841 9.610705 CATTAATCTGCATATATCCTTGCTACT 57.389 33.333 0.00 0.00 39.60 2.57
872 902 8.212995 TCATAGATTGCTTCTGAAATGGATACA 58.787 33.333 0.00 0.00 43.68 2.29
895 925 6.258727 CGAGGAGTGTGTAGCATTTAATTCAT 59.741 38.462 0.00 0.00 0.00 2.57
972 1003 2.230992 GGATCGAGATGTGATGAGAGGG 59.769 54.545 0.00 0.00 0.00 4.30
1195 1226 1.294659 CTTGCACAACTCGGCCTCTC 61.295 60.000 0.00 0.00 0.00 3.20
1381 1412 4.649218 TCAGTCAGATCATCATTTCCGGTA 59.351 41.667 0.00 0.00 0.00 4.02
1410 1441 4.005650 TGTCATCAACTCAAATCTCAGGC 58.994 43.478 0.00 0.00 0.00 4.85
1435 1466 8.214721 CCAGGTTTTGGTAGAGAGATAATTTC 57.785 38.462 0.00 0.00 42.41 2.17
1499 1530 7.554118 GCTACTGCAATGGTATATTGGTATCAT 59.446 37.037 0.00 0.00 39.41 2.45
1500 1531 6.878923 GCTACTGCAATGGTATATTGGTATCA 59.121 38.462 0.00 0.00 39.41 2.15
1533 1564 6.524101 TGTCTTTTCAGCTGTAAAAGGTTT 57.476 33.333 30.01 0.00 41.92 3.27
1584 1615 2.884012 CAACAGCAACAACACAGGGATA 59.116 45.455 0.00 0.00 0.00 2.59
1644 1675 2.684374 GCATGGATGTGTGCATTACTCA 59.316 45.455 0.00 0.00 40.94 3.41
1680 1711 8.619146 ACATTTTGTAGCGAATCATGTAAATG 57.381 30.769 0.00 0.00 36.83 2.32
1681 1712 9.935682 CTACATTTTGTAGCGAATCATGTAAAT 57.064 29.630 2.01 0.00 43.11 1.40
1783 1817 0.250727 ATGAACAAGTGGACCACCGG 60.251 55.000 21.32 15.45 39.42 5.28
1791 1825 1.531149 ACGAAAGCGATGAACAAGTGG 59.469 47.619 0.00 0.00 41.64 4.00
1885 1947 5.781306 TGAGAAACCCAATAGTACCACTACA 59.219 40.000 0.00 0.00 32.84 2.74
1886 1948 6.290294 TGAGAAACCCAATAGTACCACTAC 57.710 41.667 0.00 0.00 32.84 2.73
2012 2077 4.038642 ACCAACATGGAAAACGCAAATACT 59.961 37.500 2.85 0.00 40.96 2.12
2013 2078 4.303282 ACCAACATGGAAAACGCAAATAC 58.697 39.130 2.85 0.00 40.96 1.89
2065 2130 0.976073 TGTTGGTTCCCCCGCAAAAA 60.976 50.000 0.00 0.00 35.15 1.94
2066 2131 0.976073 TTGTTGGTTCCCCCGCAAAA 60.976 50.000 0.00 0.00 35.15 2.44
2067 2132 0.976073 TTTGTTGGTTCCCCCGCAAA 60.976 50.000 0.00 0.00 37.94 3.68
2068 2133 0.976073 TTTTGTTGGTTCCCCCGCAA 60.976 50.000 0.00 0.00 35.15 4.85
2069 2134 1.381327 TTTTGTTGGTTCCCCCGCA 60.381 52.632 0.00 0.00 35.15 5.69
2070 2135 1.365999 CTTTTGTTGGTTCCCCCGC 59.634 57.895 0.00 0.00 35.15 6.13
2071 2136 1.116308 AACTTTTGTTGGTTCCCCCG 58.884 50.000 0.00 0.00 41.77 5.73
2072 2137 2.502130 TCAAACTTTTGTTGGTTCCCCC 59.498 45.455 1.75 0.00 42.67 5.40
2073 2138 3.897141 TCAAACTTTTGTTGGTTCCCC 57.103 42.857 1.75 0.00 42.67 4.81
2074 2139 4.629634 CACTTCAAACTTTTGTTGGTTCCC 59.370 41.667 1.75 0.00 42.67 3.97
2075 2140 5.234752 ACACTTCAAACTTTTGTTGGTTCC 58.765 37.500 1.75 0.00 42.67 3.62
2076 2141 6.779115 AACACTTCAAACTTTTGTTGGTTC 57.221 33.333 1.75 0.00 42.67 3.62
2077 2142 7.929245 AGTTAACACTTCAAACTTTTGTTGGTT 59.071 29.630 8.61 5.67 42.67 3.67
2078 2143 7.438564 AGTTAACACTTCAAACTTTTGTTGGT 58.561 30.769 8.61 0.52 42.67 3.67
2079 2144 7.596995 TGAGTTAACACTTCAAACTTTTGTTGG 59.403 33.333 8.61 0.00 36.59 3.77
2080 2145 8.514136 TGAGTTAACACTTCAAACTTTTGTTG 57.486 30.769 8.61 1.67 36.59 3.33
2081 2146 7.328493 GCTGAGTTAACACTTCAAACTTTTGTT 59.672 33.333 8.61 0.00 37.58 2.83
2082 2147 6.806739 GCTGAGTTAACACTTCAAACTTTTGT 59.193 34.615 8.61 0.00 34.89 2.83
2083 2148 6.021468 CGCTGAGTTAACACTTCAAACTTTTG 60.021 38.462 8.61 0.00 33.72 2.44
2084 2149 6.027749 CGCTGAGTTAACACTTCAAACTTTT 58.972 36.000 8.61 0.00 33.72 2.27
2113 2178 6.746120 TGAGTCTAAACTGGAGTTTGAGTAC 58.254 40.000 13.87 7.27 46.56 2.73
2146 2211 7.198306 CGGAGGTATTTGTACTTTTGAAGTT 57.802 36.000 0.00 0.00 42.81 2.66
2175 2240 7.391554 TGGCTAGTAAATATCCATGAGAAATGC 59.608 37.037 0.00 0.00 0.00 3.56
2240 2307 7.994425 ACTATGAGATCTGGTACTATGTGAG 57.006 40.000 0.00 0.00 0.00 3.51
2300 2367 5.743636 ATGCATGTTGGTTTTTGGATACT 57.256 34.783 0.00 0.00 37.61 2.12
2321 2388 7.445121 TCGTAGATTGCTTCTGAAATGGATAT 58.555 34.615 0.00 0.00 35.79 1.63
2324 2391 5.084818 TCGTAGATTGCTTCTGAAATGGA 57.915 39.130 0.00 0.00 35.79 3.41
2325 2392 5.801350 TTCGTAGATTGCTTCTGAAATGG 57.199 39.130 0.00 0.00 35.79 3.16
2326 2393 9.773328 TTTAATTCGTAGATTGCTTCTGAAATG 57.227 29.630 0.00 0.00 35.79 2.32
2328 2395 9.773328 CATTTAATTCGTAGATTGCTTCTGAAA 57.227 29.630 0.00 0.00 35.79 2.69
2329 2396 7.910162 GCATTTAATTCGTAGATTGCTTCTGAA 59.090 33.333 0.62 0.00 35.79 3.02
2367 2441 2.715763 AAAGGACCTGAGGGAGTACA 57.284 50.000 2.38 0.00 36.25 2.90
2378 2452 5.494390 AATACACGGAGTAAAAAGGACCT 57.506 39.130 0.00 0.00 41.61 3.85


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

AutoCloner maintained by Alex Coulton.