Multiple sequence alignment - TraesCS6B01G409000

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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 TraesCS6B01G409000 chr6B 100.000 2871 0 0 1 2871 682743764 682740894 0.000000e+00 5302
1 TraesCS6B01G409000 chr6B 85.374 1805 229 18 184 1979 682712816 682711038 0.000000e+00 1838
2 TraesCS6B01G409000 chr6B 84.652 1466 188 16 520 1979 682676407 682674973 0.000000e+00 1426
3 TraesCS6B01G409000 chr6B 78.367 1396 274 19 982 2368 682662139 682660763 0.000000e+00 880
4 TraesCS6B01G409000 chr6B 98.526 475 7 0 1894 2368 682707930 682707456 0.000000e+00 839
5 TraesCS6B01G409000 chr6B 94.819 386 10 1 2365 2740 682707171 682706786 6.850000e-166 593
6 TraesCS6B01G409000 chr6B 96.324 136 5 0 2736 2871 682697184 682697049 1.040000e-54 224
7 TraesCS6B01G409000 chr6B 84.615 104 14 1 2264 2367 704860852 704860751 5.060000e-18 102
8 TraesCS6B01G409000 chr6D 93.708 2384 107 13 1 2368 450213521 450211165 0.000000e+00 3531
9 TraesCS6B01G409000 chr6D 96.325 517 9 1 2365 2871 450210880 450210364 0.000000e+00 841
10 TraesCS6B01G409000 chr6D 79.317 498 90 8 1874 2368 450168347 450167860 1.270000e-88 337
11 TraesCS6B01G409000 chr6D 83.810 105 15 1 2264 2368 452081555 452081453 6.550000e-17 99
12 TraesCS6B01G409000 chr6A 78.434 1456 276 28 927 2368 595664933 595663502 0.000000e+00 915
13 TraesCS6B01G409000 chr6A 88.102 664 75 4 166 826 595679602 595678940 0.000000e+00 785
14 TraesCS6B01G409000 chr6A 90.909 99 9 0 2773 2871 595678536 595678438 1.790000e-27 134
15 TraesCS6B01G409000 chr6A 83.810 105 15 1 2264 2368 609162218 609162116 6.550000e-17 99


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 TraesCS6B01G409000 chr6B 682740894 682743764 2870 True 5302.0 5302 100.000000 1 2871 1 chr6B.!!$R4 2870
1 TraesCS6B01G409000 chr6B 682674973 682676407 1434 True 1426.0 1426 84.652000 520 1979 1 chr6B.!!$R2 1459
2 TraesCS6B01G409000 chr6B 682706786 682712816 6030 True 1090.0 1838 92.906333 184 2740 3 chr6B.!!$R6 2556
3 TraesCS6B01G409000 chr6B 682660763 682662139 1376 True 880.0 880 78.367000 982 2368 1 chr6B.!!$R1 1386
4 TraesCS6B01G409000 chr6D 450210364 450213521 3157 True 2186.0 3531 95.016500 1 2871 2 chr6D.!!$R3 2870
5 TraesCS6B01G409000 chr6A 595663502 595664933 1431 True 915.0 915 78.434000 927 2368 1 chr6A.!!$R1 1441
6 TraesCS6B01G409000 chr6A 595678438 595679602 1164 True 459.5 785 89.505500 166 2871 2 chr6A.!!$R3 2705

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
801 822 0.035881 TGCTGCTTGGAGAACTGAGG 59.964 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2743 6281 1.352083 AAGCTCCCTACTCTTGTGCA 58.648 50.0 0.0 0.0 0.0 4.57 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
33 34 0.604780 CAGCAGTGGTTGGAGGTCAG 60.605 60.000 0.00 0.00 0.00 3.51
59 60 2.922234 GCCCCTGATAGCCTTGCT 59.078 61.111 0.00 0.00 43.41 3.91
65 66 2.945668 CCCTGATAGCCTTGCTTGTTAC 59.054 50.000 0.00 0.00 40.44 2.50
105 106 2.802816 GCCACTATTAGTCATTCCTGCG 59.197 50.000 0.00 0.00 0.00 5.18
127 128 0.247736 AGTGACTCCTTCGATGGCAC 59.752 55.000 12.42 13.78 0.00 5.01
150 151 3.755905 AGTTGTTTCATCACACACACACA 59.244 39.130 0.00 0.00 0.00 3.72
152 153 3.077359 TGTTTCATCACACACACACACA 58.923 40.909 0.00 0.00 0.00 3.72
182 195 1.429021 GCACACACACACACACCTG 59.571 57.895 0.00 0.00 0.00 4.00
214 228 1.762522 ATCCAATCGCATCCGCCTCT 61.763 55.000 0.00 0.00 33.11 3.69
399 416 3.694072 CCTTCACCTCGGCATTCATTAAA 59.306 43.478 0.00 0.00 0.00 1.52
422 439 4.960938 ACGCCTATGACATAATGTGATGT 58.039 39.130 10.56 0.00 42.82 3.06
455 473 7.148573 CCATCTATCAGTTATAAACCATGACGC 60.149 40.741 0.00 0.00 0.00 5.19
480 500 7.906527 GCGTATTCGGTGTTGTATTTTCTAATT 59.093 33.333 0.00 0.00 37.56 1.40
481 501 9.763465 CGTATTCGGTGTTGTATTTTCTAATTT 57.237 29.630 0.00 0.00 0.00 1.82
490 510 9.077885 TGTTGTATTTTCTAATTTGGCTCTCTT 57.922 29.630 0.00 0.00 0.00 2.85
529 549 4.745125 CACATATCCCGTGATACAGTGAAC 59.255 45.833 13.49 0.00 41.14 3.18
652 673 8.322905 ACCCTTCCGGTATTAAATAGAAGTTA 57.677 34.615 0.00 0.00 45.97 2.24
703 724 5.656416 TCAAACACCCATCACTTTCTCTTTT 59.344 36.000 0.00 0.00 0.00 2.27
735 756 5.828299 TCGACATTCTTTGTTTTCCTGTT 57.172 34.783 0.00 0.00 39.18 3.16
743 764 4.528596 TCTTTGTTTTCCTGTTCCACCAAA 59.471 37.500 0.00 0.00 0.00 3.28
749 770 6.325028 TGTTTTCCTGTTCCACCAAATTATGA 59.675 34.615 0.00 0.00 0.00 2.15
801 822 0.035881 TGCTGCTTGGAGAACTGAGG 59.964 55.000 0.00 0.00 0.00 3.86
805 826 0.687354 GCTTGGAGAACTGAGGACCA 59.313 55.000 0.00 0.00 0.00 4.02
826 862 0.777446 CTAGGAGGAGGAGGAGGAGG 59.223 65.000 0.00 0.00 0.00 4.30
828 864 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
831 867 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
832 868 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
833 869 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
834 870 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
835 871 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
836 872 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
837 873 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
838 874 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
839 875 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
840 876 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
841 877 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
842 878 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
843 879 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
844 880 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
859 895 0.533032 GGAGGTAGAGGAGCACACAC 59.467 60.000 0.00 0.00 0.00 3.82
917 953 7.361799 CCGGTGAGATCGTGATTATTGTCTATA 60.362 40.741 0.00 0.00 0.00 1.31
925 961 9.862371 ATCGTGATTATTGTCTATATTCTCCAC 57.138 33.333 0.00 0.00 0.00 4.02
941 977 0.319040 CCACGTGACTGGTCTCACTG 60.319 60.000 19.30 0.00 38.79 3.66
965 1001 1.539496 GGCTCACCACGTCTAACAACA 60.539 52.381 0.00 0.00 35.26 3.33
1043 1079 2.105821 AGGAAACCATGGAAACGACTCA 59.894 45.455 21.47 0.00 0.00 3.41
1090 1127 2.843701 CCCTCCCAAATGATCTTCTCG 58.156 52.381 0.00 0.00 0.00 4.04
1110 1147 4.392047 TCGGCTATCTTATGTCGTTCCTA 58.608 43.478 0.00 0.00 0.00 2.94
1116 1153 6.238953 GCTATCTTATGTCGTTCCTACCTTCA 60.239 42.308 0.00 0.00 0.00 3.02
1118 1155 4.768448 TCTTATGTCGTTCCTACCTTCACA 59.232 41.667 0.00 0.00 0.00 3.58
1130 1167 0.249447 CCTTCACACGACTCTGTGCA 60.249 55.000 0.00 0.00 43.74 4.57
1214 1251 0.882042 GACCCCGATAGCTACGACGA 60.882 60.000 14.62 0.00 0.00 4.20
1431 1468 2.904905 CCCTGGCGGGTAATCGAA 59.095 61.111 12.30 0.00 46.12 3.71
1438 1475 3.023119 TGGCGGGTAATCGAAACTACTA 58.977 45.455 0.00 0.00 0.00 1.82
1497 1536 0.322816 TGCACTTTGAGGGATGCTCC 60.323 55.000 0.00 0.00 38.90 4.70
1527 1566 9.095065 GATTTTTCGAGTTATAAGGTGCTAGAA 57.905 33.333 0.00 0.00 0.00 2.10
1567 1606 8.668510 AAGTTGTGACATCTATGTGAATATCC 57.331 34.615 0.00 0.00 41.95 2.59
1569 1608 9.147732 AGTTGTGACATCTATGTGAATATCCTA 57.852 33.333 0.00 0.00 41.95 2.94
1661 1700 3.036091 CCCCAAATCTCATTGGCTTCAT 58.964 45.455 0.49 0.00 46.97 2.57
1695 1735 1.382629 GGGTTGGGCTCCTTTGCTA 59.617 57.895 0.00 0.00 0.00 3.49
1696 1736 0.033109 GGGTTGGGCTCCTTTGCTAT 60.033 55.000 0.00 0.00 0.00 2.97
1784 1827 5.178096 ACTGTGGTAATCCATCATGTGAA 57.822 39.130 0.00 0.00 46.20 3.18
1844 1887 0.875059 CTCTGGAAAGTTTGTCGGGC 59.125 55.000 0.00 0.00 0.00 6.13
1845 1888 0.181587 TCTGGAAAGTTTGTCGGGCA 59.818 50.000 0.00 0.00 0.00 5.36
1847 1890 0.394488 TGGAAAGTTTGTCGGGCACA 60.394 50.000 0.00 0.00 0.00 4.57
1856 1899 2.969628 TGTCGGGCACAACAAATTTT 57.030 40.000 0.00 0.00 29.30 1.82
1919 1966 2.556622 CGCCACCTCCTATTGTTGTTTT 59.443 45.455 0.00 0.00 0.00 2.43
2187 5427 7.651027 ATTGCTATACAAAAAGAGAGCCATT 57.349 32.000 0.00 0.00 42.86 3.16
2383 5911 3.380954 TGGTGTGATAGTTCGCCGTATTA 59.619 43.478 0.00 0.00 37.07 0.98
2666 6204 1.285280 TAGGTGTGGATGGAACCCAG 58.715 55.000 0.00 0.00 36.75 4.45
2866 6404 9.025425 GACTAATGTAGGTAGTACCGAAGGCAA 62.025 44.444 13.76 0.00 44.90 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.034053 CGAAAAAGCCCAGCAGTAACAA 59.966 45.455 0.00 0.00 0.00 2.83
65 66 0.449388 CTAGCGAAAAAGCCCAGCAG 59.551 55.000 0.00 0.00 38.01 4.24
105 106 1.202428 GCCATCGAAGGAGTCACTACC 60.202 57.143 11.67 0.00 0.00 3.18
127 128 4.097714 GTGTGTGTGTGATGAAACAACTG 58.902 43.478 0.00 0.00 0.00 3.16
128 129 3.755905 TGTGTGTGTGTGATGAAACAACT 59.244 39.130 0.00 0.00 0.00 3.16
182 195 3.488489 CGATTGGATCCACGTTTGTTTC 58.512 45.455 15.91 1.01 0.00 2.78
214 228 9.455144 TGAGGGGTTACATATTTCCTTATTCTA 57.545 33.333 0.00 0.00 0.00 2.10
399 416 5.368145 ACATCACATTATGTCATAGGCGTT 58.632 37.500 0.00 0.00 35.08 4.84
422 439 7.420913 GGTTTATAACTGATAGATGGGTGGGAA 60.421 40.741 0.00 0.00 0.00 3.97
455 473 9.763465 AAATTAGAAAATACAACACCGAATACG 57.237 29.630 0.00 0.00 39.43 3.06
490 510 1.361204 TGTGCCATCCTCTCTTCCAA 58.639 50.000 0.00 0.00 0.00 3.53
529 549 8.420945 CGACAAATAGTCTAGATTATCTTTGCG 58.579 37.037 15.76 15.41 45.32 4.85
563 584 1.320344 ATGTGAGAGCGGGCGAACTA 61.320 55.000 0.00 0.00 0.00 2.24
564 585 2.172483 AATGTGAGAGCGGGCGAACT 62.172 55.000 0.00 0.00 0.00 3.01
652 673 5.789574 TGTGGGTGGGTCTTATAGAAAAT 57.210 39.130 0.00 0.00 0.00 1.82
703 724 4.072131 CAAAGAATGTCGAAGGAAGGGAA 58.928 43.478 0.00 0.00 0.00 3.97
735 756 3.904800 TCTCGCTCATAATTTGGTGGA 57.095 42.857 0.00 0.00 0.00 4.02
743 764 1.409064 TCACGCCTTCTCGCTCATAAT 59.591 47.619 0.00 0.00 0.00 1.28
749 770 1.244697 TTCTCTCACGCCTTCTCGCT 61.245 55.000 0.00 0.00 0.00 4.93
781 802 1.544093 CCTCAGTTCTCCAAGCAGCAA 60.544 52.381 0.00 0.00 0.00 3.91
801 822 1.783979 TCCTCCTCCTCCTAGATGGTC 59.216 57.143 0.00 0.00 37.07 4.02
805 826 2.358258 CTCCTCCTCCTCCTCCTAGAT 58.642 57.143 0.00 0.00 0.00 1.98
826 862 1.293683 ACCTCCTCCTCCTCCTCCTC 61.294 65.000 0.00 0.00 0.00 3.71
828 864 0.481128 CTACCTCCTCCTCCTCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
831 867 0.481128 CCTCTACCTCCTCCTCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
832 868 1.423921 CTCCTCTACCTCCTCCTCCTC 59.576 61.905 0.00 0.00 0.00 3.71
833 869 1.529744 CTCCTCTACCTCCTCCTCCT 58.470 60.000 0.00 0.00 0.00 3.69
834 870 0.178973 GCTCCTCTACCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
835 871 0.553819 TGCTCCTCTACCTCCTCCTC 59.446 60.000 0.00 0.00 0.00 3.71
836 872 0.260523 GTGCTCCTCTACCTCCTCCT 59.739 60.000 0.00 0.00 0.00 3.69
837 873 0.033011 TGTGCTCCTCTACCTCCTCC 60.033 60.000 0.00 0.00 0.00 4.30
838 874 1.107945 GTGTGCTCCTCTACCTCCTC 58.892 60.000 0.00 0.00 0.00 3.71
839 875 0.409876 TGTGTGCTCCTCTACCTCCT 59.590 55.000 0.00 0.00 0.00 3.69
840 876 0.533032 GTGTGTGCTCCTCTACCTCC 59.467 60.000 0.00 0.00 0.00 4.30
841 877 0.171455 CGTGTGTGCTCCTCTACCTC 59.829 60.000 0.00 0.00 0.00 3.85
842 878 0.539901 ACGTGTGTGCTCCTCTACCT 60.540 55.000 0.00 0.00 0.00 3.08
843 879 0.109226 GACGTGTGTGCTCCTCTACC 60.109 60.000 0.00 0.00 0.00 3.18
844 880 0.596577 TGACGTGTGTGCTCCTCTAC 59.403 55.000 0.00 0.00 0.00 2.59
859 895 4.271816 AGCCGCCGCTAGATGACG 62.272 66.667 0.00 0.00 46.08 4.35
917 953 1.546476 GAGACCAGTCACGTGGAGAAT 59.454 52.381 17.00 0.00 40.44 2.40
941 977 1.870055 TTAGACGTGGTGAGCCGGTC 61.870 60.000 1.90 0.00 39.60 4.79
965 1001 0.105039 GCCTATGCCGAAGCTGTAGT 59.895 55.000 0.00 0.00 40.80 2.73
1090 1127 4.523558 AGGTAGGAACGACATAAGATAGCC 59.476 45.833 0.00 0.00 35.02 3.93
1116 1153 0.676184 ATGTCTGCACAGAGTCGTGT 59.324 50.000 0.00 3.88 38.27 4.49
1118 1155 3.504021 CATGTCTGCACAGAGTCGT 57.496 52.632 0.00 0.00 38.27 4.34
1130 1167 1.736032 GCTTACCGAGAACGCATGTCT 60.736 52.381 0.00 0.00 38.29 3.41
1192 1229 1.612463 GTCGTAGCTATCGGGGTCATT 59.388 52.381 13.32 0.00 0.00 2.57
1214 1251 1.227556 GTGTTGGAGCCACTGACGT 60.228 57.895 0.00 0.00 0.00 4.34
1218 1255 1.682854 ACAAATGTGTTGGAGCCACTG 59.317 47.619 0.00 0.00 32.58 3.66
1253 1290 2.654877 GAGTTGGGTCGCGAAGGA 59.345 61.111 12.06 0.00 0.00 3.36
1338 1375 3.306225 GCTTCATTTGTTGGAATGCCTCA 60.306 43.478 0.00 0.00 37.03 3.86
1372 1409 4.424626 TGAACTTGACACGATAGAGCATC 58.575 43.478 0.00 0.00 41.38 3.91
1431 1468 6.374613 TCAAGTGTGACGAGATGATAGTAGTT 59.625 38.462 0.00 0.00 0.00 2.24
1438 1475 4.790765 TCTTCAAGTGTGACGAGATGAT 57.209 40.909 0.00 0.00 31.90 2.45
1514 1553 7.561722 TCATCTCTAACACTTCTAGCACCTTAT 59.438 37.037 0.00 0.00 0.00 1.73
1527 1566 7.896811 TGTCACAACTTATCATCTCTAACACT 58.103 34.615 0.00 0.00 0.00 3.55
1567 1606 8.657074 TTAAGATGTCGTAATGTTTGGGATAG 57.343 34.615 0.00 0.00 0.00 2.08
1569 1608 7.931578 TTTAAGATGTCGTAATGTTTGGGAT 57.068 32.000 0.00 0.00 0.00 3.85
1661 1700 2.304761 CAACCCCAAAGTGGAGCTAGTA 59.695 50.000 0.00 0.00 40.96 1.82
1703 1743 9.772973 TTACAGATGTTGTTACAAGTAATGACT 57.227 29.630 0.00 0.00 41.29 3.41
1709 1751 8.556194 CAAGCTTTACAGATGTTGTTACAAGTA 58.444 33.333 0.00 0.00 41.29 2.24
1856 1899 8.974408 CGTGTCGGATCATATATTTTCAACTTA 58.026 33.333 0.00 0.00 0.00 2.24
1919 1966 7.829706 AGACATACATAGAATCTAGCGGATGTA 59.170 37.037 16.03 11.13 35.05 2.29
2109 5349 7.220030 ACCCAAGCTGTACTATAATCTCAATG 58.780 38.462 0.00 0.00 0.00 2.82
2383 5911 6.183361 ACTCCATGGGCACATAGAATCTTTAT 60.183 38.462 13.02 0.00 34.99 1.40
2523 6061 5.711036 GGTGTGGATATATCGTCCTACTCTT 59.289 44.000 6.64 0.00 36.68 2.85
2666 6204 1.515081 TGTTTAGCCAGTGTTACCGC 58.485 50.000 0.00 0.00 0.00 5.68
2743 6281 1.352083 AAGCTCCCTACTCTTGTGCA 58.648 50.000 0.00 0.00 0.00 4.57
2784 6322 8.181904 TCAGTTGAGGAAAATAATGCTTTCTT 57.818 30.769 0.00 0.00 33.99 2.52
2796 6334 6.409524 AATCAAGCATTCAGTTGAGGAAAA 57.590 33.333 0.00 0.00 36.16 2.29


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

AutoCloner maintained by Alex Coulton.