Multiple sequence alignment - TraesCS2D01G410500

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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 TraesCS2D01G410500 chr2D 100.000 2393 0 0 1 2393 525289859 525292251 0.000000e+00 4420
1 TraesCS2D01G410500 chr2D 97.727 220 5 0 1569 1788 525291318 525291537 1.740000e-101 379
2 TraesCS2D01G410500 chr2D 97.727 220 5 0 1460 1679 525291427 525291646 1.740000e-101 379
3 TraesCS2D01G410500 chr2D 97.297 111 3 0 1678 1788 525291318 525291428 3.140000e-44 189
4 TraesCS2D01G410500 chr2D 97.297 111 3 0 1460 1570 525291536 525291646 3.140000e-44 189
5 TraesCS2D01G410500 chr2B 94.900 2412 79 16 4 2393 622640982 622638593 0.000000e+00 3733
6 TraesCS2D01G410500 chr2B 97.273 220 6 0 1460 1679 622639414 622639195 8.080000e-100 374
7 TraesCS2D01G410500 chr2B 94.545 220 8 1 1569 1788 622639519 622639304 1.060000e-88 337
8 TraesCS2D01G410500 chr2B 97.297 111 3 0 1460 1570 622639305 622639195 3.140000e-44 189
9 TraesCS2D01G410500 chr2B 93.694 111 3 1 1678 1788 622639519 622639413 1.900000e-36 163
10 TraesCS2D01G410500 chr2A 93.000 500 26 5 1901 2393 671279900 671279403 0.000000e+00 721


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 TraesCS2D01G410500 chr2D 525289859 525292251 2392 False 1111.2 4420 98.0096 1 2393 5 chr2D.!!$F1 2392
1 TraesCS2D01G410500 chr2B 622638593 622640982 2389 True 959.2 3733 95.5418 4 2393 5 chr2B.!!$R1 2389

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
212 213 0.036952 CTGTGAACTCTCCATGCGGT 60.037 55.000 0.00 0.0 0.00 5.68 F
393 394 1.133025 GGATCCATGCTTTGGTTGTCG 59.867 52.381 6.95 0.0 46.52 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1021 1039 0.385974 GCATGCAAACACCAGTCGTC 60.386 55.0 14.21 0.0 0.0 4.20 R
1579 1597 0.596577 GGTTCTCTTTTGCCCCGTTC 59.403 55.0 0.00 0.0 0.0 3.95 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
56 57 0.409876 ACTCTCCCAGCACCTCACTA 59.590 55.000 0.00 0.00 0.00 2.74
69 70 1.144913 CCTCACTAGGCTAGAGCTCCT 59.855 57.143 27.59 3.13 41.70 3.69
74 75 0.747255 TAGGCTAGAGCTCCTTTGCG 59.253 55.000 10.93 0.00 41.70 4.85
94 95 0.955428 TCCGCTGCGCTCTTGATTTT 60.955 50.000 18.00 0.00 0.00 1.82
139 140 2.350522 CTTAAGATGGAGCAGTGCGTT 58.649 47.619 10.00 0.00 0.00 4.84
186 187 0.243907 TCCTTGCGACAGCTGAGTAC 59.756 55.000 23.35 7.27 45.42 2.73
209 210 1.085091 CTGCTGTGAACTCTCCATGC 58.915 55.000 0.00 0.00 0.00 4.06
212 213 0.036952 CTGTGAACTCTCCATGCGGT 60.037 55.000 0.00 0.00 0.00 5.68
224 225 2.427812 TCCATGCGGTATCGTACTCAAA 59.572 45.455 0.00 0.00 38.89 2.69
275 276 8.902806 TGGAATTAATTAATTGTGCTGGTAGAG 58.097 33.333 24.60 0.00 36.13 2.43
373 374 1.638133 CGTCAGGCTGTCTTGATGAG 58.362 55.000 15.27 0.00 0.00 2.90
393 394 1.133025 GGATCCATGCTTTGGTTGTCG 59.867 52.381 6.95 0.00 46.52 4.35
464 465 1.940613 GTTTGTCTCGAGCCAAACACT 59.059 47.619 34.82 0.00 46.06 3.55
509 510 1.298602 TGCGGTATGTATGCTTGCAG 58.701 50.000 0.87 0.00 0.00 4.41
529 530 4.705023 GCAGCCCCTTTATTTTGTCTTCTA 59.295 41.667 0.00 0.00 0.00 2.10
562 563 7.418337 TCAAGAACTATACCATCAGCTAACA 57.582 36.000 0.00 0.00 0.00 2.41
645 646 8.175925 TCAACCAACATCATAATTCAGTCAAA 57.824 30.769 0.00 0.00 0.00 2.69
646 647 8.637099 TCAACCAACATCATAATTCAGTCAAAA 58.363 29.630 0.00 0.00 0.00 2.44
656 657 9.844790 TCATAATTCAGTCAAAATTTAGTGCAG 57.155 29.630 0.00 0.00 0.00 4.41
657 658 9.630098 CATAATTCAGTCAAAATTTAGTGCAGT 57.370 29.630 0.00 0.00 0.00 4.40
658 659 9.846248 ATAATTCAGTCAAAATTTAGTGCAGTC 57.154 29.630 0.00 0.00 0.00 3.51
659 660 6.691754 TTCAGTCAAAATTTAGTGCAGTCA 57.308 33.333 0.00 0.00 0.00 3.41
660 661 6.304356 TCAGTCAAAATTTAGTGCAGTCAG 57.696 37.500 0.00 0.00 0.00 3.51
661 662 4.913924 CAGTCAAAATTTAGTGCAGTCAGC 59.086 41.667 0.00 0.00 45.96 4.26
731 732 2.978278 AGGAATCCCCTCATGATCTGAC 59.022 50.000 0.00 0.00 43.31 3.51
740 741 4.768968 CCCTCATGATCTGACCTTTTTGTT 59.231 41.667 0.00 0.00 0.00 2.83
903 921 4.878397 ACCGAAATGATTGGTCTCATTCTC 59.122 41.667 0.21 1.29 43.37 2.87
917 935 9.152327 TGGTCTCATTCTCTACATAAATGATCT 57.848 33.333 0.00 0.00 38.39 2.75
931 949 5.620738 AAATGATCTAGCAGGCTTACTCA 57.379 39.130 0.00 0.72 0.00 3.41
1021 1039 6.816640 TCCCATGTTAAAGACTTTGATACTCG 59.183 38.462 10.80 2.68 0.00 4.18
1103 1121 7.065204 GCCAAATCTTGAGAAGGTTACTCTTAG 59.935 40.741 0.00 0.00 35.66 2.18
1147 1165 4.164030 TGTGGATGGATAGCTGTGTGTTAT 59.836 41.667 0.00 0.00 0.00 1.89
1419 1437 7.495934 CCTGGATGTGAGTTAAAAGTATCGAAT 59.504 37.037 0.00 0.00 0.00 3.34
1453 1471 7.573283 GCTTCTTCTGTTTACGCTATTTTCCTT 60.573 37.037 0.00 0.00 0.00 3.36
1586 1604 6.091713 CAGTGTAGTTTTACTTATGAACGGGG 59.908 42.308 0.00 0.00 0.00 5.73
1607 1625 4.363138 GGCAAAAGAGAACCTCAAACTTG 58.637 43.478 0.00 0.00 32.06 3.16
1710 1728 0.250727 CGGGGCAAAAGAGAACCTCA 60.251 55.000 0.00 0.00 32.06 3.86
1712 1730 1.889170 GGGGCAAAAGAGAACCTCAAG 59.111 52.381 0.00 0.00 32.06 3.02
1775 1793 8.827177 AGAAACATAGAAACTACATTCGTGAA 57.173 30.769 0.00 0.00 34.46 3.18
1844 1862 8.887264 ATTACACCATATCAGTTTGGGTTAAA 57.113 30.769 0.00 0.00 37.32 1.52
1893 1911 2.589798 ATTTGCTGCCATTCGGATTG 57.410 45.000 0.00 0.00 0.00 2.67
1909 1927 6.417191 TCGGATTGCACTTATGAAAACTAC 57.583 37.500 0.00 0.00 0.00 2.73
1917 1935 5.407387 GCACTTATGAAAACTACCGTCTGAA 59.593 40.000 0.00 0.00 0.00 3.02
1969 1992 0.749454 CTCTGTATGGGTGCCCTTGC 60.749 60.000 8.91 6.56 36.94 4.01
1994 2017 7.174772 GCCCATGAAAACTTTCCATTTTTATGT 59.825 33.333 11.59 0.00 39.53 2.29
1995 2018 9.717942 CCCATGAAAACTTTCCATTTTTATGTA 57.282 29.630 11.59 0.00 39.53 2.29
2026 2049 6.042777 TGTCTGATGGTCGAAATGAACTATC 58.957 40.000 0.00 0.00 34.43 2.08
2095 2118 9.301153 GAGTTGATTGTGTTGTTTGAATACTTT 57.699 29.630 0.00 0.00 0.00 2.66
2130 2153 1.526917 GTGTGCACAGGTTCCAGCT 60.527 57.895 22.40 0.00 0.00 4.24
2152 2175 5.877564 GCTTCAGCTAAAGGTAAGAAGATGT 59.122 40.000 9.62 0.00 35.67 3.06
2154 2177 6.605471 TCAGCTAAAGGTAAGAAGATGTGA 57.395 37.500 0.00 0.00 0.00 3.58
2175 2198 2.851195 TCTGCTGGTCTTTCCAACTTC 58.149 47.619 0.00 0.00 46.59 3.01
2246 2269 2.496070 TGTAGCTGTCTGCCGTAAATCT 59.504 45.455 0.00 0.00 44.23 2.40
2250 2273 2.688507 CTGTCTGCCGTAAATCTGTGT 58.311 47.619 0.00 0.00 0.00 3.72
2251 2274 3.067106 CTGTCTGCCGTAAATCTGTGTT 58.933 45.455 0.00 0.00 0.00 3.32
2259 2282 5.092781 GCCGTAAATCTGTGTTAATGGTTG 58.907 41.667 0.00 0.00 0.00 3.77
2356 2379 2.681848 GCAACCCTCTGTCATGAAGATG 59.318 50.000 0.00 0.63 0.00 2.90
2375 2398 5.255687 AGATGATCATGTTTGCTTGTGGTA 58.744 37.500 14.30 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.565391 TCAGATAGTTGCTCGGGAAACA 59.435 45.455 9.34 0.00 33.49 2.83
1 2 3.247006 TCAGATAGTTGCTCGGGAAAC 57.753 47.619 0.00 0.00 0.00 2.78
2 3 3.973206 TTCAGATAGTTGCTCGGGAAA 57.027 42.857 0.00 0.00 0.00 3.13
56 57 1.261238 ACGCAAAGGAGCTCTAGCCT 61.261 55.000 14.64 0.00 43.38 4.58
94 95 1.888436 CTAGCACTGGACAGCCCGAA 61.888 60.000 0.00 0.00 37.93 4.30
139 140 3.569277 ACAACATTTCAGCAGCATGTGTA 59.431 39.130 0.00 0.00 39.31 2.90
186 187 0.389166 GGAGAGTTCACAGCAGACCG 60.389 60.000 0.00 0.00 0.00 4.79
209 210 6.638468 GGTAAGGTTATTTGAGTACGATACCG 59.362 42.308 0.00 0.00 42.50 4.02
212 213 7.566760 TCGGTAAGGTTATTTGAGTACGATA 57.433 36.000 0.00 0.00 0.00 2.92
224 225 4.569564 GCGAACAAGATTCGGTAAGGTTAT 59.430 41.667 10.71 0.00 41.76 1.89
275 276 4.237724 GGCAAGCTTTCAAGTAATGGAAC 58.762 43.478 0.00 0.00 0.00 3.62
354 355 1.638133 CTCATCAAGACAGCCTGACG 58.362 55.000 0.00 0.00 0.00 4.35
393 394 7.467557 TGAGCAATGAACTCAAAATGAAAAC 57.532 32.000 0.00 0.00 41.10 2.43
509 510 7.170393 ACATTAGAAGACAAAATAAAGGGGC 57.830 36.000 0.00 0.00 0.00 5.80
546 547 5.868454 ACATGCATGTTAGCTGATGGTATA 58.132 37.500 26.61 0.00 37.90 1.47
556 557 2.643551 ACTGGGTACATGCATGTTAGC 58.356 47.619 35.45 26.47 41.97 3.09
562 563 3.885297 GAGCATAAACTGGGTACATGCAT 59.115 43.478 12.82 0.00 43.46 3.96
645 646 3.077359 GACTGGCTGACTGCACTAAATT 58.923 45.455 6.65 0.00 45.15 1.82
646 647 2.038952 TGACTGGCTGACTGCACTAAAT 59.961 45.455 6.65 0.00 45.15 1.40
649 650 0.318441 GTGACTGGCTGACTGCACTA 59.682 55.000 6.65 0.00 45.15 2.74
650 651 1.070445 GTGACTGGCTGACTGCACT 59.930 57.895 6.65 0.00 45.15 4.40
651 652 0.604780 ATGTGACTGGCTGACTGCAC 60.605 55.000 6.65 7.60 45.15 4.57
652 653 0.109153 AATGTGACTGGCTGACTGCA 59.891 50.000 6.65 0.00 45.15 4.41
653 654 0.801251 GAATGTGACTGGCTGACTGC 59.199 55.000 0.00 0.00 41.94 4.40
654 655 2.174363 TGAATGTGACTGGCTGACTG 57.826 50.000 0.00 0.00 0.00 3.51
655 656 3.079578 CAATGAATGTGACTGGCTGACT 58.920 45.455 0.00 0.00 0.00 3.41
656 657 2.816087 ACAATGAATGTGACTGGCTGAC 59.184 45.455 0.00 0.00 41.93 3.51
657 658 3.076621 GACAATGAATGTGACTGGCTGA 58.923 45.455 0.00 0.00 44.12 4.26
658 659 3.079578 AGACAATGAATGTGACTGGCTG 58.920 45.455 0.00 0.00 44.12 4.85
659 660 3.430042 AGACAATGAATGTGACTGGCT 57.570 42.857 0.00 0.00 44.12 4.75
660 661 3.503363 TGAAGACAATGAATGTGACTGGC 59.497 43.478 0.00 0.00 44.12 4.85
661 662 5.694231 TTGAAGACAATGAATGTGACTGG 57.306 39.130 0.00 0.00 44.12 4.00
756 757 8.738645 ACCATTTTGGAATTAGTAGAAGCTAG 57.261 34.615 0.00 0.00 40.96 3.42
759 760 7.556635 AGGTACCATTTTGGAATTAGTAGAAGC 59.443 37.037 15.94 0.00 40.96 3.86
903 921 8.310382 AGTAAGCCTGCTAGATCATTTATGTAG 58.690 37.037 0.00 0.00 35.11 2.74
912 930 4.898265 AGATTGAGTAAGCCTGCTAGATCA 59.102 41.667 0.00 0.00 0.00 2.92
915 933 3.316588 CGAGATTGAGTAAGCCTGCTAGA 59.683 47.826 0.00 0.00 0.00 2.43
917 935 3.288092 TCGAGATTGAGTAAGCCTGCTA 58.712 45.455 0.00 0.00 0.00 3.49
921 939 6.203723 GCAAATAATCGAGATTGAGTAAGCCT 59.796 38.462 8.46 0.00 32.50 4.58
931 949 6.855836 ACACAACATGCAAATAATCGAGATT 58.144 32.000 3.67 3.67 34.93 2.40
984 1002 2.828549 ATGGGAAATGTCGGGCGC 60.829 61.111 0.00 0.00 0.00 6.53
1021 1039 0.385974 GCATGCAAACACCAGTCGTC 60.386 55.000 14.21 0.00 0.00 4.20
1108 1126 7.815383 TCCATCCACAAAAGATATACCTCAAT 58.185 34.615 0.00 0.00 0.00 2.57
1109 1127 7.206789 TCCATCCACAAAAGATATACCTCAA 57.793 36.000 0.00 0.00 0.00 3.02
1147 1165 3.818210 ACAGCCATGTGACGTAATTTTGA 59.182 39.130 0.00 0.00 38.57 2.69
1235 1253 7.658575 CAGATGAAAATGTTCCTTCCAACAAAT 59.341 33.333 0.00 0.00 39.69 2.32
1360 1378 5.620206 TGTATTGGCTTGTCGGATATTGAT 58.380 37.500 0.00 0.00 0.00 2.57
1419 1437 5.333798 GCGTAAACAGAAGAAGCATACACAA 60.334 40.000 0.00 0.00 0.00 3.33
1453 1471 6.622549 CCCCGTTTATAAGTAAAACATGCAA 58.377 36.000 0.00 0.00 36.78 4.08
1516 1534 9.513906 TCTATGTTTCTTCCACATACATTCAAA 57.486 29.630 0.00 0.00 36.28 2.69
1517 1535 9.513906 TTCTATGTTTCTTCCACATACATTCAA 57.486 29.630 0.00 0.00 36.28 2.69
1518 1536 9.513906 TTTCTATGTTTCTTCCACATACATTCA 57.486 29.630 0.00 0.00 36.28 2.57
1573 1591 3.081804 CTCTTTTGCCCCGTTCATAAGT 58.918 45.455 0.00 0.00 0.00 2.24
1579 1597 0.596577 GGTTCTCTTTTGCCCCGTTC 59.403 55.000 0.00 0.00 0.00 3.95
1586 1604 5.248870 TCAAGTTTGAGGTTCTCTTTTGC 57.751 39.130 0.00 0.00 32.50 3.68
1647 1665 9.052759 ACTGTTTTTCACGAATGTAGTTTCTAT 57.947 29.630 0.00 0.00 0.00 1.98
1812 1830 8.477256 CCAAACTGATATGGTGTAATTTTGGAT 58.523 33.333 3.65 0.00 41.94 3.41
1823 1841 9.581099 GTAAATTTAACCCAAACTGATATGGTG 57.419 33.333 0.00 0.00 34.79 4.17
1857 1875 6.073440 GCAGCAAATTCAATCAAAATGAGTGT 60.073 34.615 7.56 0.00 42.45 3.55
1868 1886 2.861935 CCGAATGGCAGCAAATTCAATC 59.138 45.455 16.33 0.00 33.27 2.67
1893 1911 4.927425 TCAGACGGTAGTTTTCATAAGTGC 59.073 41.667 0.00 0.00 0.00 4.40
1909 1927 8.759641 CAAGTGAAGAATAAGATATTCAGACGG 58.240 37.037 11.50 2.12 32.64 4.79
1917 1935 9.941325 CCATAGCTCAAGTGAAGAATAAGATAT 57.059 33.333 0.00 0.00 0.00 1.63
1969 1992 8.620116 ACATAAAAATGGAAAGTTTTCATGGG 57.380 30.769 10.23 0.42 38.92 4.00
1994 2017 4.265904 TCGACCATCAGACAGCTTTTTA 57.734 40.909 0.00 0.00 0.00 1.52
1995 2018 3.126001 TCGACCATCAGACAGCTTTTT 57.874 42.857 0.00 0.00 0.00 1.94
2054 2077 2.117137 CAACTCGGGACATCGTTATCG 58.883 52.381 0.00 0.00 38.55 2.92
2060 2083 1.660607 CACAATCAACTCGGGACATCG 59.339 52.381 0.00 0.00 0.00 3.84
2061 2084 2.699954 ACACAATCAACTCGGGACATC 58.300 47.619 0.00 0.00 0.00 3.06
2062 2085 2.813754 CAACACAATCAACTCGGGACAT 59.186 45.455 0.00 0.00 0.00 3.06
2063 2086 2.217750 CAACACAATCAACTCGGGACA 58.782 47.619 0.00 0.00 0.00 4.02
2064 2087 2.218603 ACAACACAATCAACTCGGGAC 58.781 47.619 0.00 0.00 0.00 4.46
2095 2118 6.646653 TGTGCACACAAAATTTGAACTTGTAA 59.353 30.769 17.42 0.00 38.56 2.41
2105 2128 3.055530 TGGAACCTGTGCACACAAAATTT 60.056 39.130 17.42 2.55 41.33 1.82
2130 2153 7.004555 TCACATCTTCTTACCTTTAGCTGAA 57.995 36.000 0.00 0.00 0.00 3.02
2198 2221 4.278170 TGCCCATAATAAAGCTTTGATCGG 59.722 41.667 22.02 14.05 0.00 4.18
2246 2269 6.264292 AGTTATCTTGCACAACCATTAACACA 59.736 34.615 0.00 0.00 0.00 3.72
2301 2324 9.461312 TCAAACAATTAGGTGCATTATAAGAGT 57.539 29.630 0.00 0.00 0.00 3.24
2356 2379 3.505680 TGGTACCACAAGCAAACATGATC 59.494 43.478 11.60 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.