Multiple sequence alignment - TraesCS7A01G493100

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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 TraesCS7A01G493100 chr7A 100.000 2507 0 0 1 2507 681817562 681820068 0.000000e+00 4630.0
1 TraesCS7A01G493100 chr7A 100.000 31 0 0 431 461 681817958 681817988 9.690000e-05 58.4
2 TraesCS7A01G493100 chr7A 100.000 31 0 0 397 427 681817992 681818022 9.690000e-05 58.4
3 TraesCS7A01G493100 chr7B 93.428 1826 78 16 686 2505 672395732 672393943 0.000000e+00 2669.0
4 TraesCS7A01G493100 chr7B 91.354 694 44 9 4 687 672396459 672395772 0.000000e+00 935.0
5 TraesCS7A01G493100 chr7B 100.000 31 0 0 397 427 672396031 672396001 9.690000e-05 58.4
6 TraesCS7A01G493100 chr7D 92.002 1688 66 21 687 2365 591295402 591297029 0.000000e+00 2305.0
7 TraesCS7A01G493100 chr7D 91.703 687 50 5 7 687 591294676 591295361 0.000000e+00 946.0
8 TraesCS7A01G493100 chr7D 91.139 158 10 2 2351 2507 591303463 591303617 7.030000e-51 211.0
9 TraesCS7A01G493100 chr2D 82.641 409 48 11 1732 2138 601290062 601289675 8.590000e-90 340.0
10 TraesCS7A01G493100 chr2B 81.106 434 63 9 1732 2158 730534751 730534330 1.860000e-86 329.0


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 TraesCS7A01G493100 chr7A 681817562 681820068 2506 False 1582.266667 4630 100.000000 1 2507 3 chr7A.!!$F1 2506
1 TraesCS7A01G493100 chr7B 672393943 672396459 2516 True 1220.800000 2669 94.927333 4 2505 3 chr7B.!!$R1 2501
2 TraesCS7A01G493100 chr7D 591294676 591297029 2353 False 1625.500000 2305 91.852500 7 2365 2 chr7D.!!$F2 2358

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
170 176 0.03601 ATGAGTGTCCGGCTCCTTTG 60.036 55.0 0.0 0.0 32.31 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2002 0.111704 CGTGCGTGTCTTCTTTGACG 60.112 55.0 0.0 0.0 39.64 4.35 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
111 115 1.274167 TGTGTCCGCCTTACAACTAGG 59.726 52.381 0.00 0.00 35.80 3.02
145 149 5.355596 TCAAACCGTGCTGAAAAATGAATT 58.644 33.333 0.00 0.00 0.00 2.17
149 153 5.222631 ACCGTGCTGAAAAATGAATTCTTC 58.777 37.500 7.05 2.78 0.00 2.87
170 176 0.036010 ATGAGTGTCCGGCTCCTTTG 60.036 55.000 0.00 0.00 32.31 2.77
175 181 1.547372 GTGTCCGGCTCCTTTGTAGTA 59.453 52.381 0.00 0.00 0.00 1.82
187 195 6.752815 GCTCCTTTGTAGTAGATCACTTGTAC 59.247 42.308 0.00 0.00 38.80 2.90
190 198 6.531948 CCTTTGTAGTAGATCACTTGTACTGC 59.468 42.308 0.00 0.00 38.80 4.40
272 280 1.006922 GCTGCAGCCAAAGTGGAAC 60.007 57.895 28.76 0.00 40.96 3.62
295 303 3.206964 GTGGGAGGCTAAGCTAATGAAC 58.793 50.000 0.00 0.00 0.00 3.18
374 385 9.449719 CTACTTTTGATCCAGGTTTTGTATAGT 57.550 33.333 0.00 0.00 0.00 2.12
391 402 1.382914 AGTTACCCCTCTTGGCCAAT 58.617 50.000 20.85 5.30 0.00 3.16
420 431 4.454678 TGGAGGATCAACAAGATGCATAC 58.545 43.478 0.00 0.00 46.54 2.39
427 438 6.916387 GGATCAACAAGATGCATACAAAGATG 59.084 38.462 0.00 0.00 43.85 2.90
521 532 2.234661 CCTGACTACCAGCTGTTGATCA 59.765 50.000 13.81 10.00 41.57 2.92
548 559 1.314730 GCCCCTCTTTGTTTCAACGA 58.685 50.000 0.00 0.00 0.00 3.85
618 629 5.648092 AGGTAAGGATTAACAAGATGCACAC 59.352 40.000 0.00 0.00 41.88 3.82
626 637 3.818961 ACAAGATGCACACAAAGATCG 57.181 42.857 0.00 0.00 0.00 3.69
656 670 7.952671 TCCAAGCCTGTCATAGTTATTACTAG 58.047 38.462 0.00 0.00 40.09 2.57
713 768 5.047872 TCAGGTGCAAGAATACGTACTGTTA 60.048 40.000 0.00 0.00 0.00 2.41
719 774 5.583457 GCAAGAATACGTACTGTTAATGGGT 59.417 40.000 0.00 0.00 0.00 4.51
735 790 9.715121 TGTTAATGGGTACTAAACTCTAAACAG 57.285 33.333 0.00 0.00 0.00 3.16
874 929 7.214467 TGTTTAAAGATCTTCATGGTGGAAC 57.786 36.000 8.78 6.00 0.00 3.62
922 977 4.455606 GCTACTTGCTCATCCAACCTTAT 58.544 43.478 0.00 0.00 38.95 1.73
1121 1176 3.659092 CGCAAACGAGGCCTGCAA 61.659 61.111 12.00 0.00 43.93 4.08
1182 1237 1.508632 GGCAGCTACTCAACGAAACA 58.491 50.000 0.00 0.00 0.00 2.83
1255 1310 1.131218 GACGACGACGACGATGACA 59.869 57.895 25.15 0.00 42.66 3.58
1260 1315 0.167470 ACGACGACGATGACAACGAT 59.833 50.000 15.32 0.00 42.66 3.73
1275 1330 1.584724 ACGATGAAGGGGGAGAACAT 58.415 50.000 0.00 0.00 0.00 2.71
1472 1533 3.075005 GGGCTGCGAGGTCACCTA 61.075 66.667 0.00 0.00 31.76 3.08
1692 1759 1.600013 ACTGAAGTCGGATCGATCGAG 59.400 52.381 23.84 14.96 38.42 4.04
1703 1770 5.870978 TCGGATCGATCGAGTACATTGTATA 59.129 40.000 23.84 0.00 32.51 1.47
1704 1771 6.537660 TCGGATCGATCGAGTACATTGTATAT 59.462 38.462 23.84 0.96 32.51 0.86
1705 1772 7.707893 TCGGATCGATCGAGTACATTGTATATA 59.292 37.037 23.84 0.00 32.51 0.86
1706 1773 8.496751 CGGATCGATCGAGTACATTGTATATAT 58.503 37.037 23.84 0.00 0.00 0.86
1831 1898 0.654683 GGTGATGAGATCGTTGCTGC 59.345 55.000 0.00 0.00 0.00 5.25
1876 1943 0.462581 GACCATCTGCCGCTCATCAA 60.463 55.000 0.00 0.00 0.00 2.57
1949 2016 0.507358 GGCGACGTCAAAGAAGACAC 59.493 55.000 17.16 0.00 38.43 3.67
1985 2052 3.124921 CACGGTCGCCCCAACATC 61.125 66.667 0.00 0.00 0.00 3.06
1986 2053 4.752879 ACGGTCGCCCCAACATCG 62.753 66.667 0.00 0.00 0.00 3.84
2038 2105 3.120025 CGACTCATCAGATACAGGATCGG 60.120 52.174 0.00 0.00 39.80 4.18
2041 2108 4.078537 CTCATCAGATACAGGATCGGTCT 58.921 47.826 0.00 0.00 39.80 3.85
2042 2109 4.474394 TCATCAGATACAGGATCGGTCTT 58.526 43.478 0.00 0.00 39.80 3.01
2043 2110 4.279420 TCATCAGATACAGGATCGGTCTTG 59.721 45.833 6.20 6.20 39.80 3.02
2044 2111 3.632333 TCAGATACAGGATCGGTCTTGT 58.368 45.455 18.13 18.13 45.43 3.16
2045 2112 3.381590 TCAGATACAGGATCGGTCTTGTG 59.618 47.826 22.47 6.74 43.60 3.33
2046 2113 2.695666 AGATACAGGATCGGTCTTGTGG 59.304 50.000 22.47 0.00 43.60 4.17
2047 2114 0.535335 TACAGGATCGGTCTTGTGGC 59.465 55.000 22.47 0.00 43.60 5.01
2048 2115 1.450312 CAGGATCGGTCTTGTGGCC 60.450 63.158 0.00 0.00 0.00 5.36
2054 2121 3.660111 GGTCTTGTGGCCGTGCAC 61.660 66.667 6.82 6.82 0.00 4.57
2055 2122 4.012895 GTCTTGTGGCCGTGCACG 62.013 66.667 31.77 31.77 39.44 5.34
2095 2171 4.329545 ACGCCGCTGACCCAATGT 62.330 61.111 0.00 0.00 0.00 2.71
2262 2338 3.617263 GTCTTTCATAGACGCCACGAAAT 59.383 43.478 0.00 0.00 43.59 2.17
2275 2351 3.592059 CCACGAAATTTTCTCGAGGGTA 58.408 45.455 13.56 0.00 41.58 3.69
2369 2445 5.243954 GCTTGAAGAATGGTTAGGGTTTCTT 59.756 40.000 0.00 0.00 40.22 2.52
2371 2447 6.648879 TGAAGAATGGTTAGGGTTTCTTTG 57.351 37.500 0.00 0.00 38.25 2.77
2393 2469 3.864003 GGTGAGGAAGTTACGATAAGTGC 59.136 47.826 0.00 0.00 0.00 4.40
2400 2476 5.063564 GGAAGTTACGATAAGTGCCTCAAAG 59.936 44.000 0.00 0.00 0.00 2.77
2405 2481 1.032114 ATAAGTGCCTCAAAGCCCGC 61.032 55.000 0.00 0.00 0.00 6.13
2434 2510 1.538276 GCGTTCTGAATTTGGCATCG 58.462 50.000 0.00 0.00 0.00 3.84
2443 2519 0.038166 ATTTGGCATCGTGGACCTGT 59.962 50.000 0.00 0.00 0.00 4.00
2462 2538 0.459489 TTTGTTGTTGCCTCACTGCC 59.541 50.000 0.00 0.00 0.00 4.85
2477 2553 5.105595 CCTCACTGCCATATTCATCGAGATA 60.106 44.000 0.00 0.00 0.00 1.98
2505 2581 0.933097 CCCATCATGTTTCTCGCTCG 59.067 55.000 0.00 0.00 0.00 5.03
2506 2582 0.302890 CCATCATGTTTCTCGCTCGC 59.697 55.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.693120 TCTGTAGATATGGAAAGTACCTACAG 57.307 38.462 17.21 17.21 46.69 2.74
1 2 7.724506 CCTCTGTAGATATGGAAAGTACCTACA 59.275 40.741 0.00 0.00 35.28 2.74
2 3 7.724951 ACCTCTGTAGATATGGAAAGTACCTAC 59.275 40.741 0.00 0.00 0.00 3.18
16 17 6.928348 TGGTCAAGAAAACCTCTGTAGATA 57.072 37.500 0.00 0.00 37.69 1.98
17 18 5.825593 TGGTCAAGAAAACCTCTGTAGAT 57.174 39.130 0.00 0.00 37.69 1.98
18 19 5.825593 ATGGTCAAGAAAACCTCTGTAGA 57.174 39.130 0.00 0.00 37.69 2.59
19 20 6.464222 TGTATGGTCAAGAAAACCTCTGTAG 58.536 40.000 0.00 0.00 37.69 2.74
20 21 6.428083 TGTATGGTCAAGAAAACCTCTGTA 57.572 37.500 0.00 0.00 37.69 2.74
111 115 2.336667 CACGGTTTGAATGCCAAATCC 58.663 47.619 0.00 0.00 45.48 3.01
145 149 0.965866 AGCCGGACACTCATCGAAGA 60.966 55.000 5.05 0.00 45.75 2.87
149 153 1.949847 AAGGAGCCGGACACTCATCG 61.950 60.000 5.05 0.00 35.79 3.84
170 176 6.796426 TGATGCAGTACAAGTGATCTACTAC 58.204 40.000 0.00 0.00 39.18 2.73
175 181 5.067805 TCGTATGATGCAGTACAAGTGATCT 59.932 40.000 0.00 0.00 0.00 2.75
187 195 3.672397 CGATTCTCCTTCGTATGATGCAG 59.328 47.826 0.00 0.00 32.08 4.41
272 280 2.435805 TCATTAGCTTAGCCTCCCACAG 59.564 50.000 0.00 0.00 0.00 3.66
374 385 4.264623 ACAATTATTGGCCAAGAGGGGTAA 60.265 41.667 24.94 16.00 37.04 2.85
420 431 3.349927 TGATCCTCCAACTGCATCTTTG 58.650 45.455 0.00 0.00 0.00 2.77
427 438 2.783135 TCTTGTTGATCCTCCAACTGC 58.217 47.619 0.00 0.00 44.87 4.40
521 532 3.525800 AACAAAGAGGGGCAGTTATGT 57.474 42.857 0.00 0.00 0.00 2.29
548 559 3.368531 GCAGACGAGAAGATGGGTAGTTT 60.369 47.826 0.00 0.00 0.00 2.66
618 629 3.806521 CAGGCTTGGATCTACGATCTTTG 59.193 47.826 4.10 0.00 0.00 2.77
626 637 4.946478 ACTATGACAGGCTTGGATCTAC 57.054 45.455 0.00 0.00 0.00 2.59
713 768 7.876582 GTGTCTGTTTAGAGTTTAGTACCCATT 59.123 37.037 0.00 0.00 32.48 3.16
735 790 8.948145 ACGGTATATCTAGTGATAATCTGTGTC 58.052 37.037 0.00 0.00 38.50 3.67
922 977 1.879380 CTGCTGTGATTCGGTTTTGGA 59.121 47.619 0.00 0.00 0.00 3.53
995 1050 0.609151 TACGGTTTTCTCCATGCCGA 59.391 50.000 11.84 0.00 44.57 5.54
1116 1171 0.322008 GGAAGGTCCTCAGGTTGCAG 60.322 60.000 0.00 0.00 32.53 4.41
1121 1176 2.284699 CCGGGAAGGTCCTCAGGT 60.285 66.667 0.00 0.00 36.57 4.00
1182 1237 2.564975 GGTGTCGTCGACGTGGAT 59.435 61.111 34.40 0.00 40.80 3.41
1255 1310 1.358152 TGTTCTCCCCCTTCATCGTT 58.642 50.000 0.00 0.00 0.00 3.85
1260 1315 1.289160 CCTCATGTTCTCCCCCTTCA 58.711 55.000 0.00 0.00 0.00 3.02
1704 1771 9.893634 TCCGGATTACAGTGAGAAAATAAAATA 57.106 29.630 0.00 0.00 0.00 1.40
1705 1772 8.801882 TCCGGATTACAGTGAGAAAATAAAAT 57.198 30.769 0.00 0.00 0.00 1.82
1706 1773 8.508875 GTTCCGGATTACAGTGAGAAAATAAAA 58.491 33.333 4.15 0.00 0.00 1.52
1814 1881 0.807275 CGGCAGCAACGATCTCATCA 60.807 55.000 0.00 0.00 0.00 3.07
1831 1898 3.610669 CCTGGCGGAGGATCTCGG 61.611 72.222 0.00 0.00 46.33 4.63
1858 1925 0.745845 GTTGATGAGCGGCAGATGGT 60.746 55.000 1.45 0.00 0.00 3.55
1876 1943 2.117156 ATGAGGCGCTACCGTACGT 61.117 57.895 15.21 5.08 46.52 3.57
1935 2002 0.111704 CGTGCGTGTCTTCTTTGACG 60.112 55.000 0.00 0.00 39.64 4.35
1984 2051 2.822561 AGATGAGACTGAAGCAAGACGA 59.177 45.455 0.00 0.00 0.00 4.20
1985 2052 3.178267 GAGATGAGACTGAAGCAAGACG 58.822 50.000 0.00 0.00 0.00 4.18
1986 2053 3.520569 GGAGATGAGACTGAAGCAAGAC 58.479 50.000 0.00 0.00 0.00 3.01
2038 2105 4.012895 CGTGCACGGCCACAAGAC 62.013 66.667 31.15 0.00 35.47 3.01
2041 2108 3.882013 CAACGTGCACGGCCACAA 61.882 61.111 39.21 0.00 44.95 3.33
2052 2119 4.025401 GACTTGGGCCGCAACGTG 62.025 66.667 0.00 0.00 0.00 4.49
2053 2120 4.250305 AGACTTGGGCCGCAACGT 62.250 61.111 0.00 3.09 0.00 3.99
2054 2121 3.726517 CAGACTTGGGCCGCAACG 61.727 66.667 0.00 0.00 0.00 4.10
2055 2122 4.043200 GCAGACTTGGGCCGCAAC 62.043 66.667 0.00 0.00 0.00 4.17
2089 2165 2.159627 GCTACGTTCAGGTTGACATTGG 59.840 50.000 0.00 0.00 0.00 3.16
2095 2171 1.373748 GCGGCTACGTTCAGGTTGA 60.374 57.895 0.00 0.00 43.45 3.18
2166 2242 1.627297 GGATCGGCACCTTCCCTTCT 61.627 60.000 0.00 0.00 0.00 2.85
2262 2338 3.579586 TGGCTAAACTACCCTCGAGAAAA 59.420 43.478 15.71 0.00 0.00 2.29
2330 2406 5.734720 TCTTCAAGCCAGTCGAATCTTAAT 58.265 37.500 0.00 0.00 0.00 1.40
2369 2445 5.475719 CACTTATCGTAACTTCCTCACCAA 58.524 41.667 0.00 0.00 0.00 3.67
2371 2447 3.864003 GCACTTATCGTAACTTCCTCACC 59.136 47.826 0.00 0.00 0.00 4.02
2434 2510 1.470805 GGCAACAACAAACAGGTCCAC 60.471 52.381 0.00 0.00 0.00 4.02
2443 2519 0.459489 GGCAGTGAGGCAACAACAAA 59.541 50.000 0.00 0.00 43.51 2.83
2462 2538 6.423302 GGCCTATGCTTATCTCGATGAATATG 59.577 42.308 0.00 0.00 37.74 1.78
2477 2553 2.761786 AACATGATGGGCCTATGCTT 57.238 45.000 6.22 0.00 37.74 3.91


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

AutoCloner maintained by Alex Coulton.