Multiple sequence alignment - TraesCS6D01G154300

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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 TraesCS6D01G154300 chr6D 100.000 4393 0 0 1 4393 129483145 129487537 0.000000e+00 8113
1 TraesCS6D01G154300 chr6A 96.005 2603 57 12 1813 4393 166980848 166983425 0.000000e+00 4187
2 TraesCS6D01G154300 chr6A 92.064 1676 95 18 1 1650 166979008 166980671 0.000000e+00 2324
3 TraesCS6D01G154300 chr6A 91.724 145 11 1 1691 1835 166980659 166980802 2.680000e-47 200
4 TraesCS6D01G154300 chr6B 94.947 1504 64 5 1 1493 227638327 227639829 0.000000e+00 2346
5 TraesCS6D01G154300 chr6B 95.144 1318 44 8 1558 2870 227639826 227641128 0.000000e+00 2061
6 TraesCS6D01G154300 chr6B 91.150 904 34 16 3000 3870 227641251 227642141 0.000000e+00 1184
7 TraesCS6D01G154300 chr6B 91.841 527 26 8 3884 4393 227642262 227642788 0.000000e+00 719


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 TraesCS6D01G154300 chr6D 129483145 129487537 4392 False 8113.0 8113 100.000000 1 4393 1 chr6D.!!$F1 4392
1 TraesCS6D01G154300 chr6A 166979008 166983425 4417 False 2237.0 4187 93.264333 1 4393 3 chr6A.!!$F1 4392
2 TraesCS6D01G154300 chr6B 227638327 227642788 4461 False 1577.5 2346 93.270500 1 4393 4 chr6B.!!$F1 4392

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
509 546 0.554792 CTGGATTCCTGGCCTGGATT 59.445 55.000 29.96 25.74 35.83 3.01 F
1270 1308 0.729116 CCGGACAACATGTGATGAGC 59.271 55.000 0.00 0.00 0.00 4.26 F
1299 1337 0.917533 ATGCATTGCCTCCTGAGAGT 59.082 50.000 6.12 0.00 38.58 3.24 F
1681 1727 1.535860 GGAAAACGCAAGAGCTTTGCA 60.536 47.619 23.83 0.00 45.14 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1574 0.250901 CTGAAGTCTGGTGGGTTGGG 60.251 60.000 0.00 0.0 0.0 4.12 R
2092 2208 2.554893 TCGACAAAAATGCAAGGTACCC 59.445 45.455 8.74 0.0 0.0 3.69 R
3183 3346 4.333926 GCTGGAACCAAGCTTCAATAGTAG 59.666 45.833 0.00 0.0 0.0 2.57 R
3472 3646 4.080695 TGTGCCATATCTCAGCTCTCTTTT 60.081 41.667 0.00 0.0 0.0 2.27 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
91 98 6.127451 ACCAAAAAGAACTCGTTCCAAATCTT 60.127 34.615 6.20 0.00 40.33 2.40
93 100 6.693315 AAAAGAACTCGTTCCAAATCTTCA 57.307 33.333 6.20 0.00 40.33 3.02
105 112 1.961180 AATCTTCAGCCTCCGTCCCG 61.961 60.000 0.00 0.00 0.00 5.14
109 116 4.473520 CAGCCTCCGTCCCGCAAT 62.474 66.667 0.00 0.00 0.00 3.56
131 138 4.798682 ACCCGGCGAGAATCCCCT 62.799 66.667 9.30 0.00 0.00 4.79
235 258 1.120795 CCTCCTCCTCCTCCATCTGC 61.121 65.000 0.00 0.00 0.00 4.26
484 521 2.126346 GACATTGCAGCGTTGGCC 60.126 61.111 0.16 0.00 41.24 5.36
509 546 0.554792 CTGGATTCCTGGCCTGGATT 59.445 55.000 29.96 25.74 35.83 3.01
526 563 5.928839 CCTGGATTCTTATTAGATGTGACGG 59.071 44.000 0.00 0.00 0.00 4.79
569 606 3.499737 CATTGGGCGTCGTCAGGC 61.500 66.667 0.00 0.00 0.00 4.85
582 619 2.262915 CAGGCGTCTGTCCTGTCC 59.737 66.667 9.39 0.00 44.62 4.02
585 622 1.668151 GGCGTCTGTCCTGTCCAAC 60.668 63.158 0.00 0.00 0.00 3.77
604 641 6.476053 GTCCAACACCTCGAGTAATTATCTTC 59.524 42.308 12.31 0.00 0.00 2.87
634 671 2.223758 CCTCGATTAGGTCCGTTTCCTC 60.224 54.545 0.00 0.00 40.94 3.71
673 710 4.909696 TTAGTTGATGTGGGTTTGTGTG 57.090 40.909 0.00 0.00 0.00 3.82
726 763 1.594293 GGCATGATGCTGCATTGCC 60.594 57.895 31.32 31.32 44.28 4.52
732 769 3.305619 ATGCTGCATTGCCCTGGGA 62.306 57.895 19.27 0.00 0.00 4.37
738 775 0.903942 GCATTGCCCTGGGAAATTCA 59.096 50.000 16.84 0.55 0.00 2.57
901 938 2.103094 TCTCGGAATATGCTGACTTGGG 59.897 50.000 0.00 0.00 0.00 4.12
958 996 5.518487 CCAGTGTTTGTGGTTGTAATTTGTC 59.482 40.000 0.00 0.00 0.00 3.18
968 1006 7.067728 GTGGTTGTAATTTGTCGTAAAGTCTC 58.932 38.462 0.00 0.00 0.00 3.36
1029 1067 5.302360 TCAGTGAATGTTGGGTTAGTACAC 58.698 41.667 0.00 0.00 0.00 2.90
1083 1121 2.601314 TCATCGCACGAAATTAGGAACG 59.399 45.455 0.00 0.00 0.00 3.95
1245 1283 2.572733 CTCTTGTCTGCGAGAGGGA 58.427 57.895 4.39 0.00 45.37 4.20
1270 1308 0.729116 CCGGACAACATGTGATGAGC 59.271 55.000 0.00 0.00 0.00 4.26
1299 1337 0.917533 ATGCATTGCCTCCTGAGAGT 59.082 50.000 6.12 0.00 38.58 3.24
1326 1364 2.475111 TGCAAGAGTCGCTTTTCTTACG 59.525 45.455 0.00 0.00 33.60 3.18
1519 1558 7.902387 ACTCATATCATATGCAGTGAATCAC 57.098 36.000 5.02 5.02 34.10 3.06
1522 1561 7.399634 TCATATCATATGCAGTGAATCACCAT 58.600 34.615 10.12 9.72 34.49 3.55
1524 1563 6.570672 ATCATATGCAGTGAATCACCATTC 57.429 37.500 10.12 0.00 39.24 2.67
1533 1572 6.127647 GCAGTGAATCACCATTCCAGATTTTA 60.128 38.462 10.12 0.00 38.14 1.52
1535 1574 8.133627 CAGTGAATCACCATTCCAGATTTTATC 58.866 37.037 10.12 0.00 38.14 1.75
1540 1579 5.656416 TCACCATTCCAGATTTTATCCCAAC 59.344 40.000 0.00 0.00 0.00 3.77
1558 1597 3.490348 CAACCCACCAGACTTCAGAAAT 58.510 45.455 0.00 0.00 0.00 2.17
1559 1598 4.506625 CCAACCCACCAGACTTCAGAAATA 60.507 45.833 0.00 0.00 0.00 1.40
1560 1599 4.559862 ACCCACCAGACTTCAGAAATAG 57.440 45.455 0.00 0.00 0.00 1.73
1601 1643 9.952030 TGACATTTAGATATTACTGGTTGAACA 57.048 29.630 0.00 0.00 0.00 3.18
1681 1727 1.535860 GGAAAACGCAAGAGCTTTGCA 60.536 47.619 23.83 0.00 45.14 4.08
1688 1734 2.056577 GCAAGAGCTTTGCATGTTGAC 58.943 47.619 21.23 0.00 44.34 3.18
1715 1761 6.707440 TTTAGCTTTGTCACCTCATTTCAA 57.293 33.333 0.00 0.00 0.00 2.69
1756 1803 7.620806 GCTTCTAAAATGCAGCAATTCAACTTC 60.621 37.037 0.00 0.00 32.17 3.01
1850 1965 5.468746 TGTGTTTTCTACTAACAGGCATGAC 59.531 40.000 4.84 0.00 36.27 3.06
2092 2208 3.139077 GAGGTGAGGTTTGTACAACAGG 58.861 50.000 8.07 0.00 0.00 4.00
2870 3023 8.213679 ACTCACTTGTTCTGTGCCATATATATT 58.786 33.333 0.00 0.00 35.58 1.28
3206 3369 3.084786 ACTATTGAAGCTTGGTTCCAGC 58.915 45.455 2.10 5.56 0.00 4.85
4036 4339 2.037367 AGGCGCTGGGAGTAGTCA 59.963 61.111 7.64 0.00 0.00 3.41
4156 4471 4.843147 TCACATAGCAAACGAAACAGTTG 58.157 39.130 0.00 0.00 34.14 3.16
4162 4477 2.450160 CAAACGAAACAGTTGTCAGGC 58.550 47.619 0.00 0.00 34.14 4.85
4163 4478 1.745232 AACGAAACAGTTGTCAGGCA 58.255 45.000 0.00 0.00 32.39 4.75
4197 4512 1.252015 CGCGTAAATCACTCGTGTAGC 59.748 52.381 0.00 0.00 30.74 3.58
4198 4513 2.256174 GCGTAAATCACTCGTGTAGCA 58.744 47.619 0.00 0.00 0.00 3.49
4200 4515 2.852413 CGTAAATCACTCGTGTAGCAGG 59.148 50.000 0.00 0.00 0.00 4.85
4201 4516 3.672511 CGTAAATCACTCGTGTAGCAGGT 60.673 47.826 0.00 0.00 0.00 4.00
4204 4519 0.313987 TCACTCGTGTAGCAGGTGTG 59.686 55.000 14.06 14.06 41.73 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.628657 CGAGGGGGAGAAAGGTATAGTG 59.371 54.545 0.00 0.00 0.00 2.74
109 116 3.000819 ATTCTCGCCGGGTGTGGA 61.001 61.111 2.18 0.00 0.00 4.02
170 190 2.534349 CGTGAATTACCTCGTTGGATCG 59.466 50.000 4.38 0.00 39.71 3.69
396 433 2.358737 ACAGCGCACCTGCCTAAC 60.359 61.111 11.47 0.00 45.78 2.34
463 500 1.133253 CAACGCTGCAATGTCCGAG 59.867 57.895 0.00 0.00 0.00 4.63
468 505 4.041917 CGGCCAACGCTGCAATGT 62.042 61.111 2.24 0.00 33.74 2.71
484 521 2.587194 CCAGGAATCCAGCTCGCG 60.587 66.667 0.00 0.00 0.00 5.87
509 546 4.818005 TCTACGCCGTCACATCTAATAAGA 59.182 41.667 0.00 0.00 35.80 2.10
569 606 0.600255 GGTGTTGGACAGGACAGACG 60.600 60.000 0.00 0.00 0.00 4.18
575 612 0.469331 ACTCGAGGTGTTGGACAGGA 60.469 55.000 18.41 0.00 0.00 3.86
582 619 6.338146 TGGAAGATAATTACTCGAGGTGTTG 58.662 40.000 18.41 0.00 0.00 3.33
585 622 6.392625 TCTGGAAGATAATTACTCGAGGTG 57.607 41.667 18.41 0.00 38.67 4.00
604 641 2.739885 CCTAATCGAGGCAGATCTGG 57.260 55.000 23.89 7.57 38.96 3.86
630 667 2.042537 AGCATCTCCGCCAGAGGA 60.043 61.111 0.00 0.00 43.44 3.71
634 671 1.310933 AAAAGCAGCATCTCCGCCAG 61.311 55.000 0.00 0.00 0.00 4.85
673 710 2.270352 TCAAGGACCACAACCACATC 57.730 50.000 0.00 0.00 0.00 3.06
738 775 6.180472 CCCACTAGAAACACAACTATGGAAT 58.820 40.000 0.00 0.00 0.00 3.01
1083 1121 3.369787 CCCATCCCTTTGAGAAAAATGGC 60.370 47.826 0.00 0.00 32.61 4.40
1245 1283 2.925724 TCACATGTTGTCCGGAAAACT 58.074 42.857 32.38 18.36 0.00 2.66
1270 1308 1.674441 AGGCAATGCATCAATGAGTCG 59.326 47.619 7.79 0.00 0.00 4.18
1299 1337 1.882912 AAGCGACTCTTGCATTGTGA 58.117 45.000 0.00 0.00 32.79 3.58
1326 1364 0.393537 CTGGTGAGACATCCTTGGGC 60.394 60.000 0.00 0.00 0.00 5.36
1410 1448 8.200024 ATCTAACTAGATGATAATGGCACACT 57.800 34.615 0.00 0.00 41.05 3.55
1446 1484 5.226396 CCGCCAAACATTAATTCAAAGACA 58.774 37.500 0.00 0.00 0.00 3.41
1502 1541 4.823442 GGAATGGTGATTCACTGCATATGA 59.177 41.667 16.02 0.00 39.98 2.15
1512 1551 6.550854 GGGATAAAATCTGGAATGGTGATTCA 59.449 38.462 0.00 0.00 39.98 2.57
1519 1558 4.344968 GGGTTGGGATAAAATCTGGAATGG 59.655 45.833 0.00 0.00 0.00 3.16
1522 1561 4.349365 GTGGGTTGGGATAAAATCTGGAA 58.651 43.478 0.00 0.00 0.00 3.53
1524 1563 3.031013 GGTGGGTTGGGATAAAATCTGG 58.969 50.000 0.00 0.00 0.00 3.86
1533 1572 0.698818 GAAGTCTGGTGGGTTGGGAT 59.301 55.000 0.00 0.00 0.00 3.85
1535 1574 0.250901 CTGAAGTCTGGTGGGTTGGG 60.251 60.000 0.00 0.00 0.00 4.12
1540 1579 4.559862 ACTATTTCTGAAGTCTGGTGGG 57.440 45.455 0.00 0.00 0.00 4.61
1558 1597 9.832445 CTAAATGTCAAAGGCCTATAAGAACTA 57.168 33.333 5.16 0.00 0.00 2.24
1559 1598 8.548877 TCTAAATGTCAAAGGCCTATAAGAACT 58.451 33.333 5.16 0.00 0.00 3.01
1560 1599 8.732746 TCTAAATGTCAAAGGCCTATAAGAAC 57.267 34.615 5.16 0.00 0.00 3.01
1656 1702 2.508526 AGCTCTTGCGTTTTCCAGATT 58.491 42.857 0.00 0.00 45.42 2.40
1660 1706 1.535860 GCAAAGCTCTTGCGTTTTCCA 60.536 47.619 14.80 0.00 45.42 3.53
1669 1715 3.004002 TGAGTCAACATGCAAAGCTCTTG 59.996 43.478 0.00 0.00 0.00 3.02
1670 1716 3.216800 TGAGTCAACATGCAAAGCTCTT 58.783 40.909 0.00 0.00 0.00 2.85
1681 1727 6.294176 GGTGACAAAGCTAAATGAGTCAACAT 60.294 38.462 0.00 0.00 41.85 2.71
1688 1734 6.506500 AATGAGGTGACAAAGCTAAATGAG 57.493 37.500 0.00 0.00 36.52 2.90
1715 1761 8.734386 CATTTTAGAAGCCTACTGATTCTGTTT 58.266 33.333 3.16 0.00 35.09 2.83
1826 1873 5.468746 GTCATGCCTGTTAGTAGAAAACACA 59.531 40.000 0.00 0.00 33.45 3.72
1843 1958 1.171308 AGCATCAACACAGTCATGCC 58.829 50.000 9.26 0.00 42.26 4.40
1850 1965 6.364165 CCAAGAAAAACATAGCATCAACACAG 59.636 38.462 0.00 0.00 0.00 3.66
1990 2105 3.007940 TCTCAAATGAGTGATCACCGGTT 59.992 43.478 22.21 11.24 42.60 4.44
2092 2208 2.554893 TCGACAAAAATGCAAGGTACCC 59.445 45.455 8.74 0.00 0.00 3.69
2870 3023 7.122715 ACCCAGGTAGCATTAATCACATTTAA 58.877 34.615 0.00 0.00 0.00 1.52
3181 3344 5.488341 TGGAACCAAGCTTCAATAGTAGAC 58.512 41.667 0.00 0.00 0.00 2.59
3183 3346 4.333926 GCTGGAACCAAGCTTCAATAGTAG 59.666 45.833 0.00 0.00 0.00 2.57
3206 3369 4.526970 AGGACAACATACATGGCTTTAGG 58.473 43.478 0.00 0.00 0.00 2.69
3472 3646 4.080695 TGTGCCATATCTCAGCTCTCTTTT 60.081 41.667 0.00 0.00 0.00 2.27
3874 4070 3.511934 AGCTAGGCATATACAGTACAGCC 59.488 47.826 10.45 10.45 42.31 4.85
3880 4076 4.642885 GCTAGCTAGCTAGGCATATACAGT 59.357 45.833 39.60 10.66 45.62 3.55
3908 4211 1.330655 CCTGCCTACATCGTCACCCT 61.331 60.000 0.00 0.00 0.00 4.34
3909 4212 1.144057 CCTGCCTACATCGTCACCC 59.856 63.158 0.00 0.00 0.00 4.61
3965 4268 3.579302 CCAGGACCAGCCCAACCA 61.579 66.667 0.00 0.00 37.37 3.67
4162 4477 3.771491 GCGCGCTCAGTCAGTGTG 61.771 66.667 26.67 0.00 44.70 3.82
4200 4515 1.598130 GTCAGACAGGTGCCCACAC 60.598 63.158 0.00 0.00 46.66 3.82
4201 4516 2.828868 GTCAGACAGGTGCCCACA 59.171 61.111 0.00 0.00 0.00 4.17
4204 4519 1.374758 CTTCGTCAGACAGGTGCCC 60.375 63.158 0.41 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.