Multiple sequence alignment - TraesCS6B01G436500

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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 TraesCS6B01G436500 chr6B 100.000 3070 0 0 1 3070 704101311 704104380 0.000000e+00 5670.0
1 TraesCS6B01G436500 chr6B 86.863 510 61 2 311 814 704140461 704139952 1.600000e-157 566.0
2 TraesCS6B01G436500 chr6B 85.153 458 68 0 1501 1958 704138691 704138234 1.290000e-128 470.0
3 TraesCS6B01G436500 chr6B 80.105 573 110 4 327 897 704109240 704108670 1.020000e-114 424.0
4 TraesCS6B01G436500 chr6B 82.500 480 78 5 1502 1978 704108279 704107803 1.700000e-112 416.0
5 TraesCS6B01G436500 chr6B 80.083 482 90 6 1498 1976 704373336 704373814 1.350000e-93 353.0
6 TraesCS6B01G436500 chr6B 83.442 308 30 16 20 308 704147603 704147298 1.810000e-67 267.0
7 TraesCS6B01G436500 chr6A 89.286 2380 172 36 123 2447 608647674 608650025 0.000000e+00 2905.0
8 TraesCS6B01G436500 chr6A 98.885 628 1 1 2449 3070 46768022 46767395 0.000000e+00 1116.0
9 TraesCS6B01G436500 chr6A 81.481 1215 163 28 20 1183 608662899 608661696 0.000000e+00 941.0
10 TraesCS6B01G436500 chr6A 91.486 646 45 5 122 766 608787151 608786515 0.000000e+00 880.0
11 TraesCS6B01G436500 chr6A 88.658 529 49 4 764 1287 608738390 608737868 4.320000e-178 634.0
12 TraesCS6B01G436500 chr6A 88.250 400 27 3 2068 2447 608725390 608724991 7.760000e-126 460.0
13 TraesCS6B01G436500 chr6A 82.680 485 77 6 1498 1978 608654123 608653642 1.020000e-114 424.0
14 TraesCS6B01G436500 chr6A 80.389 566 100 9 337 897 608655064 608654505 1.320000e-113 420.0
15 TraesCS6B01G436500 chr6A 81.497 481 85 4 1498 1976 608979393 608979871 2.870000e-105 392.0
16 TraesCS6B01G436500 chr6D 92.946 1290 59 12 153 1415 461735772 461737056 0.000000e+00 1849.0
17 TraesCS6B01G436500 chr6D 93.120 1061 49 5 1409 2447 461764462 461765520 0.000000e+00 1533.0
18 TraesCS6B01G436500 chr6D 84.981 1072 146 14 124 1184 461815322 461814255 0.000000e+00 1074.0
19 TraesCS6B01G436500 chr6D 84.934 458 69 0 1501 1958 461813939 461813482 6.000000e-127 464.0
20 TraesCS6B01G436500 chr6D 78.313 747 128 21 172 897 461797608 461796875 4.670000e-123 451.0
21 TraesCS6B01G436500 chr6D 82.536 481 78 5 1501 1978 461796489 461796012 4.730000e-113 418.0
22 TraesCS6B01G436500 chr3B 99.839 621 1 0 2450 3070 187356835 187357455 0.000000e+00 1142.0
23 TraesCS6B01G436500 chr3B 98.887 629 1 1 2448 3070 27504773 27504145 0.000000e+00 1118.0
24 TraesCS6B01G436500 chr3B 99.252 401 2 1 2671 3070 747722424 747722824 0.000000e+00 723.0
25 TraesCS6B01G436500 chr5A 99.678 621 1 1 2450 3070 10558546 10557927 0.000000e+00 1134.0
26 TraesCS6B01G436500 chr5A 98.433 638 2 3 2441 3070 38823732 38824369 0.000000e+00 1116.0
27 TraesCS6B01G436500 chr4A 99.678 621 1 1 2450 3070 742584226 742584845 0.000000e+00 1134.0
28 TraesCS6B01G436500 chr1A 99.519 624 1 2 2448 3070 278664716 278664094 0.000000e+00 1134.0
29 TraesCS6B01G436500 chr4B 98.884 627 1 1 2450 3070 583065348 583064722 0.000000e+00 1114.0
30 TraesCS6B01G436500 chr2B 98.884 627 1 1 2450 3070 72755730 72756356 0.000000e+00 1114.0
31 TraesCS6B01G436500 chr7A 80.682 88 11 4 2293 2380 457849291 457849210 2.560000e-06 63.9


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 TraesCS6B01G436500 chr6B 704101311 704104380 3069 False 5670.0 5670 100.0000 1 3070 1 chr6B.!!$F1 3069
1 TraesCS6B01G436500 chr6B 704138234 704140461 2227 True 518.0 566 86.0080 311 1958 2 chr6B.!!$R3 1647
2 TraesCS6B01G436500 chr6B 704107803 704109240 1437 True 420.0 424 81.3025 327 1978 2 chr6B.!!$R2 1651
3 TraesCS6B01G436500 chr6A 608647674 608650025 2351 False 2905.0 2905 89.2860 123 2447 1 chr6A.!!$F1 2324
4 TraesCS6B01G436500 chr6A 46767395 46768022 627 True 1116.0 1116 98.8850 2449 3070 1 chr6A.!!$R1 621
5 TraesCS6B01G436500 chr6A 608661696 608662899 1203 True 941.0 941 81.4810 20 1183 1 chr6A.!!$R2 1163
6 TraesCS6B01G436500 chr6A 608786515 608787151 636 True 880.0 880 91.4860 122 766 1 chr6A.!!$R5 644
7 TraesCS6B01G436500 chr6A 608737868 608738390 522 True 634.0 634 88.6580 764 1287 1 chr6A.!!$R4 523
8 TraesCS6B01G436500 chr6A 608653642 608655064 1422 True 422.0 424 81.5345 337 1978 2 chr6A.!!$R6 1641
9 TraesCS6B01G436500 chr6D 461735772 461737056 1284 False 1849.0 1849 92.9460 153 1415 1 chr6D.!!$F1 1262
10 TraesCS6B01G436500 chr6D 461764462 461765520 1058 False 1533.0 1533 93.1200 1409 2447 1 chr6D.!!$F2 1038
11 TraesCS6B01G436500 chr6D 461813482 461815322 1840 True 769.0 1074 84.9575 124 1958 2 chr6D.!!$R2 1834
12 TraesCS6B01G436500 chr6D 461796012 461797608 1596 True 434.5 451 80.4245 172 1978 2 chr6D.!!$R1 1806
13 TraesCS6B01G436500 chr3B 187356835 187357455 620 False 1142.0 1142 99.8390 2450 3070 1 chr3B.!!$F1 620
14 TraesCS6B01G436500 chr3B 27504145 27504773 628 True 1118.0 1118 98.8870 2448 3070 1 chr3B.!!$R1 622
15 TraesCS6B01G436500 chr5A 10557927 10558546 619 True 1134.0 1134 99.6780 2450 3070 1 chr5A.!!$R1 620
16 TraesCS6B01G436500 chr5A 38823732 38824369 637 False 1116.0 1116 98.4330 2441 3070 1 chr5A.!!$F1 629
17 TraesCS6B01G436500 chr4A 742584226 742584845 619 False 1134.0 1134 99.6780 2450 3070 1 chr4A.!!$F1 620
18 TraesCS6B01G436500 chr1A 278664094 278664716 622 True 1134.0 1134 99.5190 2448 3070 1 chr1A.!!$R1 622
19 TraesCS6B01G436500 chr4B 583064722 583065348 626 True 1114.0 1114 98.8840 2450 3070 1 chr4B.!!$R1 620
20 TraesCS6B01G436500 chr2B 72755730 72756356 626 False 1114.0 1114 98.8840 2450 3070 1 chr2B.!!$F1 620

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
609 682 0.101219 TCATCATGAGAGGCGACGTG 59.899 55.0 0.09 0.00 0.00 4.49 F
1094 1444 0.029035 AGCCTCACTAACGCGTATCG 59.971 55.0 14.46 6.48 45.38 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 2363 1.007387 GGCGCAACCAGTTTCTTGG 60.007 57.895 10.83 0.0 44.09 3.61 R
2071 2912 4.208746 AGTATAAGTTCTCGAGTCCAGGG 58.791 47.826 13.13 0.0 0.00 4.45 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
29 30 2.867368 TGTCGTGTTAATGCGTCTTGTT 59.133 40.909 2.45 0.00 0.00 2.83
30 31 4.049869 TGTCGTGTTAATGCGTCTTGTTA 58.950 39.130 2.45 0.00 0.00 2.41
31 32 4.687018 TGTCGTGTTAATGCGTCTTGTTAT 59.313 37.500 2.45 0.00 0.00 1.89
78 85 7.800300 ATCTTAACCTAGGTGGAATAGGATC 57.200 40.000 17.14 0.00 42.15 3.36
79 86 6.689561 TCTTAACCTAGGTGGAATAGGATCA 58.310 40.000 17.14 0.00 42.15 2.92
89 96 3.388024 TGGAATAGGATCAGGAAACCTCG 59.612 47.826 0.00 0.00 35.52 4.63
119 129 2.373502 AGAGGAGGCTGCCATATAAACC 59.626 50.000 22.65 11.44 0.00 3.27
122 132 2.784347 GAGGCTGCCATATAAACCTCC 58.216 52.381 22.65 0.00 38.18 4.30
608 681 0.817654 TTCATCATGAGAGGCGACGT 59.182 50.000 0.09 0.00 0.00 4.34
609 682 0.101219 TCATCATGAGAGGCGACGTG 59.899 55.000 0.09 0.00 0.00 4.49
800 873 2.969238 CCTCACGCGGATGCATCC 60.969 66.667 32.34 32.34 42.97 3.51
997 1335 3.258372 TCACAGTCTACCGAAGCTTCAAT 59.742 43.478 25.47 14.95 0.00 2.57
1026 1367 4.469227 ACCTTGCATAAATGGGCATACAAA 59.531 37.500 0.00 0.00 40.17 2.83
1094 1444 0.029035 AGCCTCACTAACGCGTATCG 59.971 55.000 14.46 6.48 45.38 2.92
1114 1464 3.692101 TCGTTCATCAAACAACCACAAGT 59.308 39.130 0.00 0.00 37.77 3.16
1128 1478 6.752170 CAACCACAAGTTAAGCCAATTGCTG 61.752 44.000 0.00 0.00 43.68 4.41
1153 1503 2.385803 ACGTCCCCTCGATAAGTGATT 58.614 47.619 0.00 0.00 34.70 2.57
1193 1543 4.868067 AGTGAAAAGGTACGTACTCACTG 58.132 43.478 31.42 0.00 39.92 3.66
1205 1555 4.201832 ACGTACTCACTGACGATCATCTTC 60.202 45.833 0.89 0.00 41.60 2.87
1207 1557 2.428890 ACTCACTGACGATCATCTTCCC 59.571 50.000 0.00 0.00 0.00 3.97
1256 1627 6.861065 TCATCTTTGTCTGGTTTTGTCTAC 57.139 37.500 0.00 0.00 0.00 2.59
1258 1629 3.558418 TCTTTGTCTGGTTTTGTCTACGC 59.442 43.478 0.00 0.00 0.00 4.42
1324 2006 6.322712 TCACAAAGGTAACAAGCCACTAAAAT 59.677 34.615 0.00 0.00 41.41 1.82
1337 2019 6.809869 AGCCACTAAAATAATGAATCCAAGC 58.190 36.000 0.00 0.00 0.00 4.01
1343 2025 5.712152 AAATAATGAATCCAAGCGATCCC 57.288 39.130 0.00 0.00 0.00 3.85
1358 2044 6.156748 AGCGATCCCGTTATATATATGCAA 57.843 37.500 5.44 0.00 38.24 4.08
1371 2057 1.748950 TATGCAAGCCATCGAAAGCA 58.251 45.000 12.01 6.13 35.34 3.91
1428 2130 5.304101 TGGTCAAAATAGCAAATCCTTGTGT 59.696 36.000 0.00 0.00 34.79 3.72
1435 2137 1.069049 GCAAATCCTTGTGTTGTGCCT 59.931 47.619 0.00 0.00 34.79 4.75
1463 2237 1.412343 GCCCATGGCCGATGTAATTTT 59.588 47.619 6.09 0.00 44.06 1.82
1522 2363 4.524328 ACAGATTTGGGTTCAACCAGAATC 59.476 41.667 19.36 19.36 42.47 2.52
1745 2586 4.775236 AGCCATCTACTCCTGATTTCAAC 58.225 43.478 0.00 0.00 0.00 3.18
1766 2607 2.224354 CCACAAAAATCTGGCAAGGCTT 60.224 45.455 0.00 0.00 0.00 4.35
1787 2628 6.467677 GCTTACTATCTATGGCTTCCAATCA 58.532 40.000 0.00 0.00 36.95 2.57
1803 2644 4.022935 TCCAATCAGACAACAACTTCATGC 60.023 41.667 0.00 0.00 0.00 4.06
1811 2652 3.120683 ACAACAACTTCATGCGATACGTG 60.121 43.478 0.00 0.00 36.55 4.49
2008 2849 2.953648 CCCATGCTATGATTCACTTGCA 59.046 45.455 10.90 10.90 34.88 4.08
2071 2912 0.861837 CAAGATGCGGCCGATTAGTC 59.138 55.000 33.48 17.63 0.00 2.59
2108 2949 8.848182 AGAACTTATACTAGTAGCTATTGCGTT 58.152 33.333 8.85 3.48 45.42 4.84
2228 3085 2.354821 ACGTTTGCTCTCTTTTGTGTCC 59.645 45.455 0.00 0.00 0.00 4.02
2353 3210 1.141019 GATGGCTACGAAGACGGCA 59.859 57.895 0.00 0.00 44.46 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.857665 CGCATTAACACGACACATCTAGT 59.142 43.478 0.00 0.00 0.00 2.57
5 6 2.683968 AGACGCATTAACACGACACAT 58.316 42.857 6.01 0.00 0.00 3.21
6 7 2.143008 AGACGCATTAACACGACACA 57.857 45.000 6.01 0.00 0.00 3.72
7 8 2.220133 ACAAGACGCATTAACACGACAC 59.780 45.455 6.01 0.00 0.00 3.67
8 9 2.475818 ACAAGACGCATTAACACGACA 58.524 42.857 6.01 0.00 0.00 4.35
10 11 6.947903 TTATAACAAGACGCATTAACACGA 57.052 33.333 6.01 0.00 0.00 4.35
11 12 7.010606 TGTTTATAACAAGACGCATTAACACG 58.989 34.615 0.00 0.00 38.72 4.49
12 13 8.716619 TTGTTTATAACAAGACGCATTAACAC 57.283 30.769 1.10 0.00 45.79 3.32
48 49 4.481072 TCCACCTAGGTTAAGATAGCCTC 58.519 47.826 13.15 0.00 40.17 4.70
54 57 7.313731 TGATCCTATTCCACCTAGGTTAAGAT 58.686 38.462 13.15 6.91 37.58 2.40
59 62 4.077982 TCCTGATCCTATTCCACCTAGGTT 60.078 45.833 13.15 0.00 37.58 3.50
78 85 0.875059 GGCTTGAACGAGGTTTCCTG 59.125 55.000 0.00 0.00 31.76 3.86
79 86 0.472471 TGGCTTGAACGAGGTTTCCT 59.528 50.000 0.00 0.00 36.03 3.36
119 129 0.543277 TGCATGCACCTTCCTAGGAG 59.457 55.000 18.46 3.85 45.05 3.69
122 132 1.099879 GCCTGCATGCACCTTCCTAG 61.100 60.000 18.46 4.12 0.00 3.02
320 387 4.433615 GACTTTCAACAGCTGGATCGATA 58.566 43.478 19.93 3.16 0.00 2.92
321 388 3.265791 GACTTTCAACAGCTGGATCGAT 58.734 45.455 19.93 0.00 0.00 3.59
324 391 2.413453 GTCGACTTTCAACAGCTGGATC 59.587 50.000 19.93 3.60 0.00 3.36
608 681 1.667236 CCTGCCGATCTTGTTATGCA 58.333 50.000 0.00 0.00 0.00 3.96
609 682 0.947244 CCCTGCCGATCTTGTTATGC 59.053 55.000 0.00 0.00 0.00 3.14
800 873 2.317609 CGGAACCTGAGGTTGTGCG 61.318 63.158 23.60 12.52 46.95 5.34
926 1264 2.987149 ACGAATGTAAGCTCAACGAGTG 59.013 45.455 10.55 0.00 31.39 3.51
997 1335 3.298619 CCCATTTATGCAAGGTCATCCA 58.701 45.455 0.00 0.00 35.89 3.41
1026 1367 4.832823 CCAAGGAACAAGGGATTGTTAGTT 59.167 41.667 6.36 1.46 44.37 2.24
1094 1444 6.019881 GCTTAACTTGTGGTTGTTTGATGAAC 60.020 38.462 0.00 0.00 38.75 3.18
1128 1478 2.428530 ACTTATCGAGGGGACGTTAACC 59.571 50.000 0.00 0.00 34.70 2.85
1134 1484 3.123804 CAAATCACTTATCGAGGGGACG 58.876 50.000 0.00 0.00 0.00 4.79
1153 1503 7.523293 TTTCACTTAGAAAATCCAGATGCAA 57.477 32.000 0.00 0.00 43.00 4.08
1288 1970 9.353999 CTTGTTACCTTTGTGATAATAAAAGCC 57.646 33.333 0.00 0.00 31.03 4.35
1291 1973 8.861086 TGGCTTGTTACCTTTGTGATAATAAAA 58.139 29.630 0.00 0.00 0.00 1.52
1307 1989 9.516314 GGATTCATTATTTTAGTGGCTTGTTAC 57.484 33.333 0.00 0.00 0.00 2.50
1324 2006 2.104111 ACGGGATCGCTTGGATTCATTA 59.896 45.455 8.28 0.00 40.63 1.90
1337 2019 5.405571 GGCTTGCATATATATAACGGGATCG 59.594 44.000 0.00 0.00 43.02 3.69
1343 2025 7.463469 TTCGATGGCTTGCATATATATAACG 57.537 36.000 0.00 0.00 0.00 3.18
1358 2044 2.369860 TGATATCCTGCTTTCGATGGCT 59.630 45.455 0.00 0.00 0.00 4.75
1371 2057 6.384015 TCAGTGTGGATTACAAGTGATATCCT 59.616 38.462 0.00 0.00 41.89 3.24
1522 2363 1.007387 GGCGCAACCAGTTTCTTGG 60.007 57.895 10.83 0.00 44.09 3.61
1745 2586 1.345415 AGCCTTGCCAGATTTTTGTGG 59.655 47.619 0.00 0.00 36.85 4.17
1766 2607 6.782494 TGTCTGATTGGAAGCCATAGATAGTA 59.218 38.462 0.00 0.00 31.53 1.82
1787 2628 3.367932 CGTATCGCATGAAGTTGTTGTCT 59.632 43.478 0.00 0.00 0.00 3.41
1811 2652 4.543084 GCTTGAATGGCGCGCCTC 62.543 66.667 45.79 36.23 36.94 4.70
2071 2912 4.208746 AGTATAAGTTCTCGAGTCCAGGG 58.791 47.826 13.13 0.00 0.00 4.45
2228 3085 5.407502 TCATACTGTATTCAACACGACCAG 58.592 41.667 0.00 0.00 33.45 4.00


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

AutoCloner maintained by Alex Coulton.