Multiple sequence alignment - TraesCS6B01G274000

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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 TraesCS6B01G274000 chr6B 100.000 2189 0 0 1 2189 494428888 494426700 0.000000e+00 4043
1 TraesCS6B01G274000 chr6A 91.532 2220 128 22 1 2189 465933096 465935286 0.000000e+00 3003
2 TraesCS6B01G274000 chr6D 92.596 2053 110 23 146 2189 327205222 327207241 0.000000e+00 2911
3 TraesCS6B01G274000 chr6D 90.090 111 9 1 1 111 327205110 327205218 2.270000e-30 143


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 TraesCS6B01G274000 chr6B 494426700 494428888 2188 True 4043 4043 100.000 1 2189 1 chr6B.!!$R1 2188
1 TraesCS6B01G274000 chr6A 465933096 465935286 2190 False 3003 3003 91.532 1 2189 1 chr6A.!!$F1 2188
2 TraesCS6B01G274000 chr6D 327205110 327207241 2131 False 1527 2911 91.343 1 2189 2 chr6D.!!$F1 2188

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
894 911 0.540923 AGTCTTCCAGAGATGCCTGC 59.459 55.0 0.0 0.0 36.61 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 1992 2.159114 AGCCTTGCTTTTTCTTGCGAAA 60.159 40.909 0.0 0.0 33.89 3.46 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
44 45 4.165779 CACCAGTTTGCACGGATAATTTC 58.834 43.478 0.00 0.00 0.00 2.17
48 49 5.868801 CCAGTTTGCACGGATAATTTCATTT 59.131 36.000 0.00 0.00 0.00 2.32
50 51 7.543868 CCAGTTTGCACGGATAATTTCATTTAA 59.456 33.333 0.00 0.00 0.00 1.52
52 53 9.651913 AGTTTGCACGGATAATTTCATTTAATT 57.348 25.926 0.00 0.00 0.00 1.40
106 108 2.249309 CGTGCACTGCGTTCCTTG 59.751 61.111 16.19 0.00 0.00 3.61
113 115 0.888619 ACTGCGTTCCTTGATCGAGA 59.111 50.000 11.89 0.00 0.00 4.04
118 120 1.202582 CGTTCCTTGATCGAGACCAGT 59.797 52.381 11.89 0.00 0.00 4.00
122 124 1.202200 CCTTGATCGAGACCAGTCGTC 60.202 57.143 11.89 0.00 40.93 4.20
187 195 0.893727 GGAAACCCCATGCGTCAAGT 60.894 55.000 0.00 0.00 34.14 3.16
201 209 3.496884 GCGTCAAGTAATGGTGAAACTCA 59.503 43.478 0.00 0.00 36.74 3.41
420 435 6.089249 TCTTATCGCATCATATCACAGTGT 57.911 37.500 0.00 0.00 0.00 3.55
422 437 7.657336 TCTTATCGCATCATATCACAGTGTTA 58.343 34.615 0.00 0.00 0.00 2.41
466 481 7.010738 CACAGGATATCCAAAACAAAATGATGC 59.989 37.037 23.81 0.00 38.89 3.91
469 484 6.019640 GGATATCCAAAACAAAATGATGCACG 60.020 38.462 17.34 0.00 35.64 5.34
470 485 2.799412 TCCAAAACAAAATGATGCACGC 59.201 40.909 0.00 0.00 0.00 5.34
480 495 1.753930 TGATGCACGCCTCAATGATT 58.246 45.000 0.00 0.00 0.00 2.57
535 550 7.841282 ATACTAGTAACATCACAGCCACTAT 57.159 36.000 6.70 0.00 0.00 2.12
537 552 6.574350 ACTAGTAACATCACAGCCACTATTC 58.426 40.000 0.00 0.00 0.00 1.75
591 607 8.230486 CACTCAGATGATAATAATTAAACCGGC 58.770 37.037 0.00 0.00 0.00 6.13
609 625 4.764823 ACCGGCAAATAACAGAATCTTTGA 59.235 37.500 0.00 0.00 31.76 2.69
617 633 4.861102 AACAGAATCTTTGAAGGCCAAG 57.139 40.909 5.01 0.00 35.94 3.61
620 636 3.192212 CAGAATCTTTGAAGGCCAAGGAC 59.808 47.826 5.01 0.00 42.52 3.85
634 651 2.416701 CCAAGGACTTGTTTTTGCACGT 60.417 45.455 10.81 0.00 38.85 4.49
646 663 9.309796 CTTGTTTTTGCACGTATTAGTACTAAC 57.690 33.333 17.45 6.10 0.00 2.34
647 664 8.592105 TGTTTTTGCACGTATTAGTACTAACT 57.408 30.769 17.45 9.52 39.91 2.24
648 665 8.489559 TGTTTTTGCACGTATTAGTACTAACTG 58.510 33.333 17.45 12.14 36.36 3.16
650 667 5.252969 TGCACGTATTAGTACTAACTGGG 57.747 43.478 17.45 11.96 36.36 4.45
727 744 0.681564 TGCCAACGGTCACAAAAGGT 60.682 50.000 0.00 0.00 0.00 3.50
822 839 2.762535 AGTAATAGTGCACCGCAACT 57.237 45.000 14.63 9.86 41.47 3.16
823 840 3.880047 AGTAATAGTGCACCGCAACTA 57.120 42.857 14.63 0.00 41.47 2.24
824 841 3.782046 AGTAATAGTGCACCGCAACTAG 58.218 45.455 14.63 0.00 41.47 2.57
866 883 2.851263 TATATGCACCCGGAATCCAC 57.149 50.000 0.73 0.00 0.00 4.02
869 886 3.124921 GCACCCGGAATCCACACG 61.125 66.667 0.73 0.00 0.00 4.49
870 887 2.435938 CACCCGGAATCCACACGG 60.436 66.667 0.73 0.00 46.79 4.94
894 911 0.540923 AGTCTTCCAGAGATGCCTGC 59.459 55.000 0.00 0.00 36.61 4.85
984 1006 4.202090 GCCATAGAATTTCAGAAGCCAAGG 60.202 45.833 0.00 0.00 0.00 3.61
1106 1128 1.130054 AACCTCCAGCAGCTGAAGGA 61.130 55.000 33.11 21.26 32.44 3.36
1128 1150 1.061411 CATCATGCGCACAAGGTCG 59.939 57.895 14.90 0.00 0.00 4.79
1141 1163 3.371063 GGTCGTCGTCTCCAGCCA 61.371 66.667 0.00 0.00 0.00 4.75
1152 1174 1.377202 TCCAGCCATTTGGAGTCGC 60.377 57.895 0.00 0.00 42.24 5.19
1197 1219 2.031157 CGTCACATTGTGAAGGAAACCC 60.031 50.000 20.57 5.52 44.49 4.11
1275 1297 2.097825 CTTGCTAGCATTTCCTTGCCT 58.902 47.619 20.13 0.00 43.83 4.75
1291 1313 1.566298 GCCTCTGGAGTGGGGTGAAT 61.566 60.000 0.00 0.00 0.00 2.57
1297 1319 2.571653 CTGGAGTGGGGTGAATAACTCA 59.428 50.000 4.27 0.00 40.67 3.41
1298 1320 3.189606 TGGAGTGGGGTGAATAACTCAT 58.810 45.455 4.27 0.00 40.67 2.90
1309 1331 7.054124 GGGTGAATAACTCATCTTGTCCATAA 58.946 38.462 0.00 0.00 35.28 1.90
1357 1379 4.457603 TGAAACCAAATGTATTGTCCCTCG 59.542 41.667 0.00 0.00 0.00 4.63
1380 1402 5.333645 CGCTGCATGTAAGATGGAGATAAAC 60.334 44.000 9.18 0.00 39.43 2.01
1385 1407 7.828717 TGCATGTAAGATGGAGATAAACAAAGA 59.171 33.333 0.00 0.00 0.00 2.52
1492 1515 5.947228 ACGCAAAATGATCGATATCCATT 57.053 34.783 0.00 1.06 0.00 3.16
1531 1554 3.251487 GTGCTCGTTTTAGCCCTTGTAAA 59.749 43.478 0.00 0.00 42.05 2.01
1567 1590 6.206243 CAGTCTCCTTTTCCTGCATATATTGG 59.794 42.308 0.00 0.00 0.00 3.16
1569 1592 6.772716 GTCTCCTTTTCCTGCATATATTGGAA 59.227 38.462 0.00 0.00 36.87 3.53
1598 1621 7.050377 AGACAATTGTACCGAATCAGAATCAT 58.950 34.615 11.95 0.00 0.00 2.45
1599 1622 7.225538 AGACAATTGTACCGAATCAGAATCATC 59.774 37.037 11.95 0.00 0.00 2.92
1671 1694 7.448748 TTCTCTATTTTTCACTAGCAAACCC 57.551 36.000 0.00 0.00 0.00 4.11
1672 1695 6.539173 TCTCTATTTTTCACTAGCAAACCCA 58.461 36.000 0.00 0.00 0.00 4.51
1673 1696 7.001674 TCTCTATTTTTCACTAGCAAACCCAA 58.998 34.615 0.00 0.00 0.00 4.12
1674 1697 7.174946 TCTCTATTTTTCACTAGCAAACCCAAG 59.825 37.037 0.00 0.00 0.00 3.61
1675 1698 5.869649 ATTTTTCACTAGCAAACCCAAGT 57.130 34.783 0.00 0.00 0.00 3.16
1676 1699 4.647424 TTTTCACTAGCAAACCCAAGTG 57.353 40.909 0.00 0.00 40.54 3.16
1678 1701 2.571212 TCACTAGCAAACCCAAGTGTG 58.429 47.619 0.00 0.00 40.18 3.82
1680 1703 3.149196 CACTAGCAAACCCAAGTGTGAT 58.851 45.455 0.00 0.00 32.34 3.06
1728 1754 8.145767 AGGTTAATAAAACAAACTAAAGTGGGC 58.854 33.333 0.00 0.00 0.00 5.36
1733 1759 1.336755 ACAAACTAAAGTGGGCGCAAG 59.663 47.619 10.83 1.26 43.44 4.01
1734 1760 1.336755 CAAACTAAAGTGGGCGCAAGT 59.663 47.619 10.83 2.01 41.68 3.16
1735 1761 2.550606 CAAACTAAAGTGGGCGCAAGTA 59.449 45.455 10.83 0.00 41.68 2.24
1756 1782 9.030301 CAAGTAAATTAGGTTGAAGTTGGTTTG 57.970 33.333 0.00 0.00 0.00 2.93
1759 1785 9.027129 GTAAATTAGGTTGAAGTTGGTTTGAAC 57.973 33.333 0.00 0.00 0.00 3.18
1805 1837 7.979115 GAGTTAACTCATCTGCTAACACTAG 57.021 40.000 27.12 0.00 42.42 2.57
1829 1861 7.428826 AGTCTCAAGATTTCACCATTTTGTTC 58.571 34.615 0.00 0.00 0.00 3.18
1840 1872 5.243730 TCACCATTTTGTTCCCTTTCATCTC 59.756 40.000 0.00 0.00 0.00 2.75
1862 1894 9.866798 ATCTCTTTTTCTTTTCAATTAGGATGC 57.133 29.630 0.00 0.00 0.00 3.91
1863 1895 9.082313 TCTCTTTTTCTTTTCAATTAGGATGCT 57.918 29.630 0.00 0.00 0.00 3.79
1872 1904 5.505173 TCAATTAGGATGCTAAGCAAAGC 57.495 39.130 12.50 3.50 43.62 3.51
1876 1908 3.199880 AGGATGCTAAGCAAAGCGTAT 57.800 42.857 5.13 0.00 45.85 3.06
1891 1923 7.767198 AGCAAAGCGTATAAATAACTTACAGGA 59.233 33.333 0.00 0.00 0.00 3.86
1939 1971 5.105997 GCAATAGTGTTCTGCTTCCTCAAAT 60.106 40.000 0.00 0.00 33.20 2.32
2002 2034 2.676748 TCAACAAAATTCTGGCCCTGT 58.323 42.857 0.00 0.00 0.00 4.00
2023 2055 5.308825 TGTCTTTCCTCAACTTCCATTCTC 58.691 41.667 0.00 0.00 0.00 2.87
2122 2154 4.940046 AGTGCTATTCCTTCAGTGTCATTG 59.060 41.667 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 7.270793 ACGACGACGAATATGCTCTTAATTATC 59.729 37.037 15.32 0.00 42.66 1.75
106 108 0.026544 GTCGACGACTGGTCTCGATC 59.973 60.000 20.52 13.28 43.79 3.69
113 115 2.037136 CGGTAGGTCGACGACTGGT 61.037 63.158 25.87 14.10 32.47 4.00
122 124 1.355971 CCATGTTTGTCGGTAGGTCG 58.644 55.000 0.00 0.00 0.00 4.79
139 141 3.842925 GAGGCAAGCAACCGTCCCA 62.843 63.158 0.00 0.00 0.00 4.37
169 177 1.816074 TACTTGACGCATGGGGTTTC 58.184 50.000 14.94 3.40 0.00 2.78
443 458 7.043565 GTGCATCATTTTGTTTTGGATATCCT 58.956 34.615 22.35 0.00 36.82 3.24
466 481 3.181507 CCAGTGTTAATCATTGAGGCGTG 60.182 47.826 0.00 0.00 36.12 5.34
469 484 3.758554 ACACCAGTGTTAATCATTGAGGC 59.241 43.478 0.00 0.00 41.83 4.70
470 485 5.300969 CACACCAGTGTTAATCATTGAGG 57.699 43.478 0.00 0.00 42.83 3.86
535 550 5.068067 CACGTTTTTCCCTTTCCCTTTAGAA 59.932 40.000 0.00 0.00 0.00 2.10
537 552 4.581409 TCACGTTTTTCCCTTTCCCTTTAG 59.419 41.667 0.00 0.00 0.00 1.85
591 607 6.690530 TGGCCTTCAAAGATTCTGTTATTTG 58.309 36.000 3.32 0.00 34.66 2.32
596 612 3.575687 CCTTGGCCTTCAAAGATTCTGTT 59.424 43.478 3.32 0.00 34.56 3.16
609 625 2.419990 GCAAAAACAAGTCCTTGGCCTT 60.420 45.455 3.32 0.00 44.45 4.35
617 633 5.754778 ACTAATACGTGCAAAAACAAGTCC 58.245 37.500 0.00 0.00 34.10 3.85
620 636 9.309796 GTTAGTACTAATACGTGCAAAAACAAG 57.690 33.333 18.03 0.00 36.33 3.16
646 663 5.800438 GCGACTTTAGCTTTAATTTTCCCAG 59.200 40.000 0.00 0.00 0.00 4.45
647 664 5.241949 TGCGACTTTAGCTTTAATTTTCCCA 59.758 36.000 0.00 0.00 35.28 4.37
648 665 5.705902 TGCGACTTTAGCTTTAATTTTCCC 58.294 37.500 0.00 0.00 35.28 3.97
650 667 7.252995 CGTGATGCGACTTTAGCTTTAATTTTC 60.253 37.037 0.00 0.00 44.77 2.29
727 744 2.042297 TGTTGATGTTTCATAGGCCCCA 59.958 45.455 0.00 0.00 0.00 4.96
736 753 4.370049 CCTTTGCATGTGTTGATGTTTCA 58.630 39.130 0.00 0.00 0.00 2.69
866 883 0.318441 TCTGGAAGACTTGCTCCGTG 59.682 55.000 8.27 0.00 38.67 4.94
869 886 2.903798 CATCTCTGGAAGACTTGCTCC 58.096 52.381 8.27 0.00 38.67 4.70
870 887 2.278854 GCATCTCTGGAAGACTTGCTC 58.721 52.381 8.27 0.00 38.67 4.26
984 1006 4.005650 TCAGCATTGTTGGTTGATCTCTC 58.994 43.478 0.40 0.00 0.00 3.20
1106 1128 1.374343 CCTTGTGCGCATGATGCTCT 61.374 55.000 15.91 0.00 42.25 4.09
1128 1150 0.036388 TCCAAATGGCTGGAGACGAC 60.036 55.000 0.00 0.00 40.71 4.34
1275 1297 2.838202 GAGTTATTCACCCCACTCCAGA 59.162 50.000 0.00 0.00 31.16 3.86
1327 1349 8.141268 GGACAATACATTTGGTTTCAAGAGAAA 58.859 33.333 0.00 0.00 41.26 2.52
1357 1379 5.528690 TGTTTATCTCCATCTTACATGCAGC 59.471 40.000 0.00 0.00 0.00 5.25
1380 1402 5.525378 AGAGTAGTGTCACTTGCTTTCTTTG 59.475 40.000 11.54 0.00 0.00 2.77
1385 1407 4.946478 AGAGAGTAGTGTCACTTGCTTT 57.054 40.909 11.54 5.50 0.00 3.51
1456 1478 5.689514 TCATTTTGCGTTGTAAATTGACCTG 59.310 36.000 0.00 0.00 28.48 4.00
1492 1515 1.545428 GCACAGTCTGGATTTCCACCA 60.545 52.381 4.53 0.00 42.01 4.17
1531 1554 6.551227 AGGAAAAGGAGACTGCAAAAAGTATT 59.449 34.615 0.00 0.00 42.68 1.89
1569 1592 7.504924 TCTGATTCGGTACAATTGTCTTTTT 57.495 32.000 15.85 0.00 0.00 1.94
1571 1594 7.390440 TGATTCTGATTCGGTACAATTGTCTTT 59.610 33.333 15.85 0.00 0.00 2.52
1574 1597 6.662414 TGATTCTGATTCGGTACAATTGTC 57.338 37.500 15.85 6.91 0.00 3.18
1586 1609 7.149569 TGTGTTTTCCTGATGATTCTGATTC 57.850 36.000 0.00 0.00 0.00 2.52
1598 1621 2.098614 TGCTTTGCTGTGTTTTCCTGA 58.901 42.857 0.00 0.00 0.00 3.86
1599 1622 2.582728 TGCTTTGCTGTGTTTTCCTG 57.417 45.000 0.00 0.00 0.00 3.86
1645 1668 9.174166 GGGTTTGCTAGTGAAAAATAGAGAATA 57.826 33.333 0.00 0.00 0.00 1.75
1646 1669 7.669722 TGGGTTTGCTAGTGAAAAATAGAGAAT 59.330 33.333 0.00 0.00 0.00 2.40
1647 1670 7.001674 TGGGTTTGCTAGTGAAAAATAGAGAA 58.998 34.615 0.00 0.00 0.00 2.87
1648 1671 6.539173 TGGGTTTGCTAGTGAAAAATAGAGA 58.461 36.000 0.00 0.00 0.00 3.10
1649 1672 6.817765 TGGGTTTGCTAGTGAAAAATAGAG 57.182 37.500 0.00 0.00 0.00 2.43
1670 1693 3.340928 TGCTCAGATCAATCACACTTGG 58.659 45.455 0.00 0.00 0.00 3.61
1671 1694 5.366829 TTTGCTCAGATCAATCACACTTG 57.633 39.130 0.00 0.00 0.00 3.16
1672 1695 7.681304 GCATATTTGCTCAGATCAATCACACTT 60.681 37.037 0.35 0.00 45.77 3.16
1673 1696 6.238676 GCATATTTGCTCAGATCAATCACACT 60.239 38.462 0.35 0.00 45.77 3.55
1674 1697 5.913514 GCATATTTGCTCAGATCAATCACAC 59.086 40.000 0.35 0.00 45.77 3.82
1675 1698 6.068473 GCATATTTGCTCAGATCAATCACA 57.932 37.500 0.35 0.00 45.77 3.58
1703 1729 7.115236 CGCCCACTTTAGTTTGTTTTATTAACC 59.885 37.037 0.00 0.00 0.00 2.85
1728 1754 5.856455 CCAACTTCAACCTAATTTACTTGCG 59.144 40.000 0.00 0.00 0.00 4.85
1733 1759 9.027129 GTTCAAACCAACTTCAACCTAATTTAC 57.973 33.333 0.00 0.00 0.00 2.01
1734 1760 8.973182 AGTTCAAACCAACTTCAACCTAATTTA 58.027 29.630 0.00 0.00 32.34 1.40
1735 1761 7.763985 CAGTTCAAACCAACTTCAACCTAATTT 59.236 33.333 0.00 0.00 34.17 1.82
1793 1825 7.062839 GTGAAATCTTGAGACTAGTGTTAGCAG 59.937 40.741 0.00 0.00 0.00 4.24
1801 1833 7.721399 ACAAAATGGTGAAATCTTGAGACTAGT 59.279 33.333 0.00 0.00 0.00 2.57
1803 1835 8.463930 AACAAAATGGTGAAATCTTGAGACTA 57.536 30.769 0.00 0.00 0.00 2.59
1804 1836 6.966534 ACAAAATGGTGAAATCTTGAGACT 57.033 33.333 0.00 0.00 0.00 3.24
1805 1837 6.642540 GGAACAAAATGGTGAAATCTTGAGAC 59.357 38.462 0.00 0.00 0.00 3.36
1829 1861 9.551734 AATTGAAAAGAAAAAGAGATGAAAGGG 57.448 29.630 0.00 0.00 0.00 3.95
1859 1891 8.154649 AGTTATTTATACGCTTTGCTTAGCAT 57.845 30.769 8.05 0.00 41.28 3.79
1872 1904 7.977853 ACACTGGTCCTGTAAGTTATTTATACG 59.022 37.037 0.37 0.00 0.00 3.06
1876 1908 9.880157 GATTACACTGGTCCTGTAAGTTATTTA 57.120 33.333 9.03 0.00 37.48 1.40
1888 1920 3.515901 GACTCTTGGATTACACTGGTCCT 59.484 47.826 0.00 0.00 33.15 3.85
1891 1923 4.348168 ACAAGACTCTTGGATTACACTGGT 59.652 41.667 20.58 0.00 0.00 4.00
1960 1992 2.159114 AGCCTTGCTTTTTCTTGCGAAA 60.159 40.909 0.00 0.00 33.89 3.46
2002 2034 5.545723 AGAGAGAATGGAAGTTGAGGAAAGA 59.454 40.000 0.00 0.00 0.00 2.52
2091 2123 4.072131 TGAAGGAATAGCACTTCACCAAC 58.928 43.478 3.23 0.00 45.76 3.77
2122 2154 2.355010 ATGAGAGGGCTGCAAATACC 57.645 50.000 0.50 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.