Multiple sequence alignment - TraesCS6A01G113200

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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 TraesCS6A01G113200 chr6A 100.000 2867 0 0 1 2867 83268358 83265492 0.000000e+00 5295
1 TraesCS6A01G113200 chr6B 92.036 2662 158 27 2 2645 140587885 140590510 0.000000e+00 3692
2 TraesCS6A01G113200 chr6B 87.251 251 12 6 2634 2867 140591007 140591254 4.710000e-68 268
3 TraesCS6A01G113200 chr6B 82.456 228 32 6 2464 2687 21817572 21817795 2.920000e-45 193
4 TraesCS6A01G113200 chr6D 93.580 2134 117 13 1 2128 65476505 65478624 0.000000e+00 3164
5 TraesCS6A01G113200 chr6D 92.435 727 29 11 2160 2867 65484460 65485179 0.000000e+00 1014


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 TraesCS6A01G113200 chr6A 83265492 83268358 2866 True 5295 5295 100.0000 1 2867 1 chr6A.!!$R1 2866
1 TraesCS6A01G113200 chr6B 140587885 140591254 3369 False 1980 3692 89.6435 2 2867 2 chr6B.!!$F2 2865
2 TraesCS6A01G113200 chr6D 65476505 65478624 2119 False 3164 3164 93.5800 1 2128 1 chr6D.!!$F1 2127
3 TraesCS6A01G113200 chr6D 65484460 65485179 719 False 1014 1014 92.4350 2160 2867 1 chr6D.!!$F2 707

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
710 713 0.320073 TCGTTCCACCGCTAACAAGG 60.320 55.0 0.0 0.0 0.0 3.61 F
1357 1360 0.044092 TGGGAGGCCCTTCTCATACA 59.956 55.0 0.0 0.0 45.7 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1667 1.304713 CAAGCATGCCTGGGGAAGT 60.305 57.895 15.66 0.0 0.0 3.01 R
2268 2290 1.608283 GCAACTAGACGGCTGAAACCT 60.608 52.381 0.00 0.0 0.0 3.50 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
50 51 9.575783 TTTTTACATCAAGTTAGTTCAACCAAC 57.424 29.630 0.00 0.00 37.93 3.77
52 53 9.616156 TTTACATCAAGTTAGTTCAACCAACTA 57.384 29.630 1.48 0.00 44.13 2.24
155 156 4.515191 AGCAAGCGAAGTTTATCACAAGAA 59.485 37.500 0.00 0.00 0.00 2.52
189 190 2.857748 CCCGTTTTCTTTGAGCAACAAC 59.142 45.455 0.00 0.00 38.29 3.32
204 205 3.670055 GCAACAACTGATATGTGCACAAC 59.330 43.478 25.72 17.90 0.00 3.32
263 264 4.577693 ACGCTTGCATGATGATTGAAGTAT 59.422 37.500 3.33 0.00 0.00 2.12
390 392 0.423544 AAATCACCCTCCCTCCTCCT 59.576 55.000 0.00 0.00 0.00 3.69
470 472 8.944029 CATATTTAAGATCATCTCCATGACCAC 58.056 37.037 0.00 0.00 42.05 4.16
580 582 1.509548 CCTTCCAACCCCATCCCACT 61.510 60.000 0.00 0.00 0.00 4.00
598 601 3.838903 CCACTCACCTACCCTATTATCCC 59.161 52.174 0.00 0.00 0.00 3.85
600 603 3.473621 ACTCACCTACCCTATTATCCCCA 59.526 47.826 0.00 0.00 0.00 4.96
641 644 4.142790 TCTATGTCTTCTAGCCCTAACCG 58.857 47.826 0.00 0.00 0.00 4.44
642 645 2.519771 TGTCTTCTAGCCCTAACCGA 57.480 50.000 0.00 0.00 0.00 4.69
710 713 0.320073 TCGTTCCACCGCTAACAAGG 60.320 55.000 0.00 0.00 0.00 3.61
784 787 2.978010 CTCTTTTGCCGCCACCGT 60.978 61.111 0.00 0.00 0.00 4.83
818 821 5.332280 CGCTTAGATTGCAATTAATCGTCGA 60.332 40.000 14.33 0.00 40.99 4.20
821 824 7.267177 GCTTAGATTGCAATTAATCGTCGATTC 59.733 37.037 23.11 9.81 40.99 2.52
854 857 8.916628 ATTGGTACCTATTTTGCAACAATTTT 57.083 26.923 14.36 0.00 0.00 1.82
865 868 4.440880 TGCAACAATTTTCAACAAGGAGG 58.559 39.130 0.00 0.00 0.00 4.30
957 960 6.273730 TCTCTCCCCAAAAACCTTGATAACTA 59.726 38.462 0.00 0.00 0.00 2.24
1059 1062 2.983030 GCCGGTGATGGTTGCACA 60.983 61.111 1.90 0.00 37.99 4.57
1069 1072 3.070576 GTTGCACATCTGGCCCCC 61.071 66.667 0.00 0.00 0.00 5.40
1113 1116 2.281070 CACCAAGGCGTGCTCTGT 60.281 61.111 0.00 0.00 0.00 3.41
1309 1312 2.438434 CCCCCAGCGATGTGTTCC 60.438 66.667 0.00 0.00 0.00 3.62
1357 1360 0.044092 TGGGAGGCCCTTCTCATACA 59.956 55.000 0.00 0.00 45.70 2.29
1358 1361 1.345422 TGGGAGGCCCTTCTCATACAT 60.345 52.381 0.00 0.00 45.70 2.29
1393 1396 3.320823 TTGCTCGACATGCAAGGAA 57.679 47.368 6.48 0.00 44.24 3.36
1397 1400 1.511850 CTCGACATGCAAGGAACACA 58.488 50.000 0.00 0.00 0.00 3.72
1435 1438 2.761208 ACTAAGATAGCGCTCCAACTGT 59.239 45.455 16.34 5.06 0.00 3.55
1650 1660 0.905337 AGCTGGACCTAAACGAGCCT 60.905 55.000 0.00 0.00 39.30 4.58
1657 1667 0.323629 CCTAAACGAGCCTCCACCAA 59.676 55.000 0.00 0.00 0.00 3.67
1670 1680 1.077265 CACCAACTTCCCCAGGCAT 59.923 57.895 0.00 0.00 0.00 4.40
1753 1763 2.104967 CATTGTCTTCCATGGCCATGT 58.895 47.619 37.30 18.53 37.11 3.21
2054 2076 0.178995 TGTTCATCTTGTGCAGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
2087 2109 1.824230 GGGCATGCCATGTTTCAGTTA 59.176 47.619 36.56 0.00 37.98 2.24
2267 2289 3.429684 GGAAGGAAGATTCGAGGTGAGAC 60.430 52.174 0.00 0.00 0.00 3.36
2268 2290 2.808919 AGGAAGATTCGAGGTGAGACA 58.191 47.619 0.00 0.00 0.00 3.41
2384 2406 1.478137 GCATCACGTCGTAGCTTAGG 58.522 55.000 0.00 0.00 0.00 2.69
2474 2498 5.581874 GGCAGTAATTTGCAACAAAGCATAT 59.418 36.000 0.00 0.00 45.86 1.78
2493 2517 8.859236 AGCATATTATACTTTGAGCATGATGT 57.141 30.769 0.00 0.00 0.00 3.06
2536 2560 6.749923 ACTTATGAAATCCTGAGAGTTTGC 57.250 37.500 0.00 0.00 28.55 3.68
2554 2578 2.517959 TGCTTGTGCTTCTAGCCAAAT 58.482 42.857 11.38 0.00 41.51 2.32
2637 2662 9.783081 ATACACATAAGCATACATGATCAAGAA 57.217 29.630 4.68 0.00 0.00 2.52
2657 3189 5.251764 AGAATCAGTGGTCTTTCATTCCAG 58.748 41.667 0.00 0.00 31.54 3.86
2704 3253 6.861055 TCCACGAGATAAAAATTCAGCAAAAC 59.139 34.615 0.00 0.00 0.00 2.43
2771 3320 7.907389 AGACCAACATGTAGATTTTGAGAGTA 58.093 34.615 0.00 0.00 0.00 2.59
2859 3408 8.073768 GTCTACATTCGAAAACAGAAAATGGAA 58.926 33.333 0.00 0.00 32.83 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.340122 TCTTACTGTCAGATGACCAATCTAG 57.660 40.000 6.91 2.88 44.24 2.43
58 59 4.193826 TGCCTTCTTACTGTCAGATGAC 57.806 45.455 6.91 6.01 44.97 3.06
119 120 1.802960 CGCTTGCTATGCTATCCCAAG 59.197 52.381 0.00 0.00 36.78 3.61
128 129 4.201812 TGTGATAAACTTCGCTTGCTATGC 60.202 41.667 0.00 0.00 0.00 3.14
155 156 4.765273 AGAAAACGGGAAAAGCAACATTT 58.235 34.783 0.00 0.00 0.00 2.32
263 264 6.778834 ATCTATCAAACATGCCAAATGTGA 57.221 33.333 0.00 0.00 31.80 3.58
390 392 5.487433 AGTATTGTGACATTTCGATGGTGA 58.513 37.500 0.00 0.00 0.00 4.02
451 453 4.849813 TTGTGGTCATGGAGATGATCTT 57.150 40.909 0.00 0.00 40.05 2.40
453 455 4.521146 AGTTTGTGGTCATGGAGATGATC 58.479 43.478 0.00 0.00 40.78 2.92
470 472 9.994432 TTTATTTTTGGCACACATTTAAGTTTG 57.006 25.926 0.00 0.00 39.29 2.93
580 582 3.473621 ACTGGGGATAATAGGGTAGGTGA 59.526 47.826 0.00 0.00 0.00 4.02
641 644 4.038642 GGATCTAGAGGATGGACAAGTGTC 59.961 50.000 2.69 2.69 38.32 3.67
642 645 3.964031 GGATCTAGAGGATGGACAAGTGT 59.036 47.826 0.00 0.00 34.33 3.55
710 713 6.010219 AGATCTAGATCTACCTCTTTGGAGC 58.990 44.000 29.92 1.50 45.69 4.70
784 787 0.108992 AATCTAAGCGGCGACAACGA 60.109 50.000 12.98 0.00 42.66 3.85
788 791 0.672091 TTGCAATCTAAGCGGCGACA 60.672 50.000 12.98 0.00 33.85 4.35
794 797 4.835463 CGACGATTAATTGCAATCTAAGCG 59.165 41.667 29.09 29.09 39.58 4.68
854 857 5.832539 ATTCTTCTTCTCCTCCTTGTTGA 57.167 39.130 0.00 0.00 0.00 3.18
929 932 1.529744 AGGTTTTTGGGGAGAGACCA 58.470 50.000 0.00 0.00 41.20 4.02
1069 1072 2.866523 TACTGTAGGGGCCAGGTCCG 62.867 65.000 3.21 0.00 34.16 4.79
1341 1344 1.544314 GGCATGTATGAGAAGGGCCTC 60.544 57.143 6.46 0.00 37.00 4.70
1357 1360 4.552365 CGCCATGGAGGACGGCAT 62.552 66.667 18.40 0.00 46.60 4.40
1393 1396 4.072131 GTGGACAACAATATGACCTGTGT 58.928 43.478 0.00 0.00 36.32 3.72
1397 1400 6.620877 TCTTAGTGGACAACAATATGACCT 57.379 37.500 0.00 0.00 36.32 3.85
1435 1438 2.584608 GCTAGCCTCCGCCTTCAA 59.415 61.111 2.29 0.00 34.57 2.69
1456 1459 2.034066 CTCCCCCAACACACGCAT 59.966 61.111 0.00 0.00 0.00 4.73
1463 1466 3.727258 CCATCCGCTCCCCCAACA 61.727 66.667 0.00 0.00 0.00 3.33
1613 1623 3.086282 AGCTTCATCATGTCAATGTGCA 58.914 40.909 12.25 0.00 35.15 4.57
1650 1660 2.840753 GCCTGGGGAAGTTGGTGGA 61.841 63.158 0.00 0.00 0.00 4.02
1657 1667 1.304713 CAAGCATGCCTGGGGAAGT 60.305 57.895 15.66 0.00 0.00 3.01
1686 1696 2.603473 CCTCCGTGGACACCCTCA 60.603 66.667 0.00 0.00 38.35 3.86
1753 1763 3.880490 ACATTCTCGTTGCCAAGTGTAAA 59.120 39.130 0.00 0.00 0.00 2.01
1954 1976 6.307800 CCGCAATACTTGAATAAAAACCACTG 59.692 38.462 0.00 0.00 0.00 3.66
2054 2076 2.965147 GGCATGCCCATATTGTAAACCT 59.035 45.455 27.24 0.00 0.00 3.50
2208 2230 4.752604 TGCACGCTAACATTTTAGAGAACA 59.247 37.500 9.05 4.34 37.31 3.18
2267 2289 2.069273 CAACTAGACGGCTGAAACCTG 58.931 52.381 0.00 0.00 0.00 4.00
2268 2290 1.608283 GCAACTAGACGGCTGAAACCT 60.608 52.381 0.00 0.00 0.00 3.50
2310 2332 3.606687 CGGCCCTACTTATGTCAAAACT 58.393 45.455 0.00 0.00 0.00 2.66
2358 2380 2.607038 GCTACGACGTGATGCCATATCA 60.607 50.000 11.56 0.00 0.00 2.15
2428 2450 6.427853 TGCCATTCTATCGTCAAAATAGATGG 59.572 38.462 12.41 12.41 36.03 3.51
2480 2504 8.680039 TTGATCATGTATACATCATGCTCAAA 57.320 30.769 15.60 3.49 46.04 2.69
2481 2505 7.935210 AGTTGATCATGTATACATCATGCTCAA 59.065 33.333 15.60 15.41 46.42 3.02
2522 2546 2.157738 GCACAAGCAAACTCTCAGGAT 58.842 47.619 0.00 0.00 41.58 3.24
2531 2555 1.608590 TGGCTAGAAGCACAAGCAAAC 59.391 47.619 0.00 0.00 44.75 2.93
2536 2560 6.199937 ACATTATTTGGCTAGAAGCACAAG 57.800 37.500 0.00 0.00 44.75 3.16
2554 2578 9.658475 CACGAAAAGTGTTATCTTGAAACATTA 57.342 29.630 0.00 0.00 45.51 1.90
2588 2613 2.357009 AGACTTTGCAAGTTGTGAGCAG 59.643 45.455 4.48 0.00 43.03 4.24
2616 2641 9.000486 ACTGATTCTTGATCATGTATGCTTATG 58.000 33.333 8.33 0.00 43.59 1.90
2617 2642 9.000486 CACTGATTCTTGATCATGTATGCTTAT 58.000 33.333 8.33 0.00 43.59 1.73
2620 2645 5.763698 CCACTGATTCTTGATCATGTATGCT 59.236 40.000 8.33 0.00 43.59 3.79
2637 2662 4.841422 CTCTGGAATGAAAGACCACTGAT 58.159 43.478 0.00 0.00 0.00 2.90
2644 3176 3.620821 GTGCTAGCTCTGGAATGAAAGAC 59.379 47.826 17.23 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.