Multiple sequence alignment - TraesCS3B01G296800

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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 TraesCS3B01G296800 chr3B 100.000 2390 0 0 1 2390 476037726 476035337 0.000000e+00 4414
1 TraesCS3B01G296800 chr3D 92.002 2413 123 29 20 2390 365527661 365525277 0.000000e+00 3323
2 TraesCS3B01G296800 chr3A 96.721 671 21 1 20 689 487444761 487444091 0.000000e+00 1116
3 TraesCS3B01G296800 chr3A 92.328 756 31 11 675 1418 487444053 487443313 0.000000e+00 1050
4 TraesCS3B01G296800 chr3A 91.743 218 15 3 1492 1708 487443285 487443070 1.390000e-77 300
5 TraesCS3B01G296800 chr3A 87.444 223 21 6 2172 2390 487442248 487442029 1.420000e-62 250


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 TraesCS3B01G296800 chr3B 476035337 476037726 2389 True 4414 4414 100.000 1 2390 1 chr3B.!!$R1 2389
1 TraesCS3B01G296800 chr3D 365525277 365527661 2384 True 3323 3323 92.002 20 2390 1 chr3D.!!$R1 2370
2 TraesCS3B01G296800 chr3A 487442029 487444761 2732 True 679 1116 92.059 20 2390 4 chr3A.!!$R1 2370

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
639 640 0.105778 CTTCTCTTCCTCCATCCCGC 59.894 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1809 0.105964 TGCGGTGGTGATACTATGCC 59.894 55.0 0.0 0.0 0.0 4.4 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
83 84 4.081142 TCGTATCCTTCAATGAGCCTTGAA 60.081 41.667 6.55 6.55 41.56 2.69
86 87 6.483307 CGTATCCTTCAATGAGCCTTGAATAA 59.517 38.462 7.04 1.19 42.54 1.40
180 181 4.415150 CCCCATGCCTGTCACGCT 62.415 66.667 0.00 0.00 0.00 5.07
501 502 1.950973 GAACGAGGAGGAGGAGGTGC 61.951 65.000 0.00 0.00 0.00 5.01
517 518 2.044650 GCTGCTGGGCTTGGATGA 60.045 61.111 0.00 0.00 0.00 2.92
536 537 3.268032 AAGGAGGCAGGTTGGGGG 61.268 66.667 0.00 0.00 0.00 5.40
638 639 0.755686 CCTTCTCTTCCTCCATCCCG 59.244 60.000 0.00 0.00 0.00 5.14
639 640 0.105778 CTTCTCTTCCTCCATCCCGC 59.894 60.000 0.00 0.00 0.00 6.13
640 641 0.325671 TTCTCTTCCTCCATCCCGCT 60.326 55.000 0.00 0.00 0.00 5.52
641 642 1.045350 TCTCTTCCTCCATCCCGCTG 61.045 60.000 0.00 0.00 0.00 5.18
643 644 2.285368 TTCCTCCATCCCGCTGGT 60.285 61.111 0.00 0.00 37.57 4.00
644 645 2.317149 CTTCCTCCATCCCGCTGGTC 62.317 65.000 0.00 0.00 37.57 4.02
687 690 7.630728 GCTGGGTTTACTCTTTGTTCTTTTCTT 60.631 37.037 0.00 0.00 0.00 2.52
688 691 7.768240 TGGGTTTACTCTTTGTTCTTTTCTTC 58.232 34.615 0.00 0.00 0.00 2.87
695 756 8.024145 ACTCTTTGTTCTTTTCTTCTCCTAGA 57.976 34.615 0.00 0.00 0.00 2.43
721 782 1.232792 TTGGGCTGGGCTCAAAACT 59.767 52.632 2.08 0.00 46.67 2.66
725 786 1.546029 GGGCTGGGCTCAAAACTAAAG 59.454 52.381 0.00 0.00 0.00 1.85
776 845 4.537015 CTGGGTTTACTCTTTGCTTTTCG 58.463 43.478 0.00 0.00 0.00 3.46
839 908 0.946528 TCGTCTCCGAGTCGAACAAA 59.053 50.000 15.64 0.00 38.40 2.83
842 911 1.000496 GTCTCCGAGTCGAACAAAGGT 60.000 52.381 15.64 0.00 0.00 3.50
853 922 2.784347 GAACAAAGGTCAGGGAGAAGG 58.216 52.381 0.00 0.00 0.00 3.46
1361 1459 5.659463 GGGAGGAGATGATCAAGATTATCG 58.341 45.833 0.00 0.00 38.42 2.92
1371 1469 2.079158 CAAGATTATCGCCGGCATCAT 58.921 47.619 28.98 17.11 0.00 2.45
1415 1513 1.202891 AGCGGCCCTTGTTCTTTTAGT 60.203 47.619 0.00 0.00 0.00 2.24
1416 1514 1.611977 GCGGCCCTTGTTCTTTTAGTT 59.388 47.619 0.00 0.00 0.00 2.24
1417 1515 2.815503 GCGGCCCTTGTTCTTTTAGTTA 59.184 45.455 0.00 0.00 0.00 2.24
1418 1516 3.119955 GCGGCCCTTGTTCTTTTAGTTAG 60.120 47.826 0.00 0.00 0.00 2.34
1419 1517 3.119955 CGGCCCTTGTTCTTTTAGTTAGC 60.120 47.826 0.00 0.00 0.00 3.09
1420 1518 4.079970 GGCCCTTGTTCTTTTAGTTAGCT 58.920 43.478 0.00 0.00 0.00 3.32
1421 1519 4.523173 GGCCCTTGTTCTTTTAGTTAGCTT 59.477 41.667 0.00 0.00 0.00 3.74
1422 1520 5.708697 GGCCCTTGTTCTTTTAGTTAGCTTA 59.291 40.000 0.00 0.00 0.00 3.09
1423 1521 6.208007 GGCCCTTGTTCTTTTAGTTAGCTTAA 59.792 38.462 0.00 0.00 0.00 1.85
1424 1522 7.082602 GCCCTTGTTCTTTTAGTTAGCTTAAC 58.917 38.462 0.00 0.00 38.94 2.01
1425 1523 7.591165 CCCTTGTTCTTTTAGTTAGCTTAACC 58.409 38.462 0.00 0.00 39.47 2.85
1426 1524 7.229907 CCCTTGTTCTTTTAGTTAGCTTAACCA 59.770 37.037 0.00 0.00 39.47 3.67
1427 1525 8.793592 CCTTGTTCTTTTAGTTAGCTTAACCAT 58.206 33.333 0.00 0.00 39.47 3.55
1443 1541 9.052759 AGCTTAACCATATTACGTTAATCAAGG 57.947 33.333 0.00 0.00 34.76 3.61
1474 1573 4.223255 AGCAAGAGGAAGAGTTTAGGTACC 59.777 45.833 2.73 2.73 0.00 3.34
1481 1580 4.465305 GGAAGAGTTTAGGTACCTGCTACA 59.535 45.833 25.33 0.00 0.00 2.74
1552 1651 9.515226 AATACTCCTGTAATTCAAGCAAAGTAA 57.485 29.630 0.00 0.00 31.80 2.24
1563 1662 6.801539 TCAAGCAAAGTAATACCTCTGTTG 57.198 37.500 0.00 0.00 0.00 3.33
1568 1667 6.940298 AGCAAAGTAATACCTCTGTTGCTAAA 59.060 34.615 6.22 0.00 46.07 1.85
1710 1810 9.681062 TTTGAATGGATTACTAGAGGTTAAAGG 57.319 33.333 0.00 0.00 0.00 3.11
1720 2313 9.650714 TTACTAGAGGTTAAAGGCATAGTATCA 57.349 33.333 0.00 0.00 0.00 2.15
1796 2389 6.017440 GCTATGGTTGGATTTGTAATTAGCGA 60.017 38.462 0.00 0.00 0.00 4.93
1805 2398 7.608761 TGGATTTGTAATTAGCGAAAGGTTAGT 59.391 33.333 0.00 0.00 44.26 2.24
1847 2440 7.776969 TGTGTAACCCGAGACTAATATAAGAGT 59.223 37.037 0.00 0.00 34.36 3.24
1893 2488 6.868622 AGGCATAAGTTGTAGACTAAGACAG 58.131 40.000 0.00 0.00 37.72 3.51
1969 2565 2.029623 GGGTTGTCGGAGCATAGTCTA 58.970 52.381 0.00 0.00 0.00 2.59
1979 2575 1.954382 AGCATAGTCTAACGGCATCGA 59.046 47.619 0.00 0.00 40.11 3.59
1990 2586 0.852777 CGGCATCGACAGGTTTATCG 59.147 55.000 0.00 0.00 39.00 2.92
1991 2587 0.582005 GGCATCGACAGGTTTATCGC 59.418 55.000 0.00 0.00 38.24 4.58
1994 2590 0.742505 ATCGACAGGTTTATCGCCGA 59.257 50.000 0.00 0.00 38.24 5.54
2015 2611 7.345192 GCCGATTGTACTATGTTGATTTAGTG 58.655 38.462 0.00 0.00 31.37 2.74
2031 2627 5.435686 TTTAGTGGTACATGAGGAGCATT 57.564 39.130 0.00 0.00 44.52 3.56
2049 2645 0.468226 TTCATAGTCATGCCCGGGAC 59.532 55.000 29.31 16.95 31.73 4.46
2076 2672 7.860872 GGATTCACGTTAACAAATTTCACTCTT 59.139 33.333 6.39 0.00 0.00 2.85
2106 2702 5.825679 TGTACTTGTGTTATTGCTTGTCCTT 59.174 36.000 0.00 0.00 0.00 3.36
2109 2705 4.829064 TGTGTTATTGCTTGTCCTTGAC 57.171 40.909 0.00 0.00 0.00 3.18
2116 2712 1.084370 GCTTGTCCTTGACGGATCGG 61.084 60.000 0.00 0.00 45.44 4.18
2265 2868 7.501225 AGGATATTTGGTTAACCGATAAACCTG 59.499 37.037 26.42 0.00 44.55 4.00
2267 2870 2.713877 TGGTTAACCGATAAACCTGCC 58.286 47.619 19.65 0.00 44.55 4.85
2268 2871 2.040012 TGGTTAACCGATAAACCTGCCA 59.960 45.455 19.65 0.00 44.55 4.92
2270 2873 4.080469 TGGTTAACCGATAAACCTGCCATA 60.080 41.667 19.65 0.00 44.55 2.74
2303 2906 9.883142 ATTTCCAAAAATGTAAAGTTTCACTCA 57.117 25.926 0.00 0.00 33.78 3.41
2320 2923 6.101650 TCACTCACAGACATCATGTTACTT 57.898 37.500 0.00 0.00 0.00 2.24
2368 2971 5.596268 TGATCGTGTTCATTTTCAGAGTG 57.404 39.130 0.00 0.00 0.00 3.51
2374 2977 5.848036 CGTGTTCATTTTCAGAGTGTCAATC 59.152 40.000 0.00 0.00 0.00 2.67
2381 2986 7.922278 TCATTTTCAGAGTGTCAATCTTTTTGG 59.078 33.333 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.865978 TCGTAACTTAATACTACTGTGCAATTG 58.134 33.333 0.00 0.00 0.00 2.32
1 2 8.991243 TCGTAACTTAATACTACTGTGCAATT 57.009 30.769 0.00 0.00 0.00 2.32
2 3 7.705325 CCTCGTAACTTAATACTACTGTGCAAT 59.295 37.037 0.00 0.00 0.00 3.56
3 4 7.031372 CCTCGTAACTTAATACTACTGTGCAA 58.969 38.462 0.00 0.00 0.00 4.08
4 5 6.558009 CCTCGTAACTTAATACTACTGTGCA 58.442 40.000 0.00 0.00 0.00 4.57
5 6 5.458126 GCCTCGTAACTTAATACTACTGTGC 59.542 44.000 0.00 0.00 0.00 4.57
6 7 6.558009 TGCCTCGTAACTTAATACTACTGTG 58.442 40.000 0.00 0.00 0.00 3.66
7 8 6.376581 ACTGCCTCGTAACTTAATACTACTGT 59.623 38.462 0.00 0.00 0.00 3.55
8 9 6.793349 ACTGCCTCGTAACTTAATACTACTG 58.207 40.000 0.00 0.00 0.00 2.74
9 10 8.511604 TTACTGCCTCGTAACTTAATACTACT 57.488 34.615 0.00 0.00 0.00 2.57
10 11 9.741647 AATTACTGCCTCGTAACTTAATACTAC 57.258 33.333 0.00 0.00 32.67 2.73
11 12 9.740239 CAATTACTGCCTCGTAACTTAATACTA 57.260 33.333 0.00 0.00 32.67 1.82
12 13 8.472413 TCAATTACTGCCTCGTAACTTAATACT 58.528 33.333 0.00 0.00 32.67 2.12
13 14 8.638685 TCAATTACTGCCTCGTAACTTAATAC 57.361 34.615 0.00 0.00 32.67 1.89
14 15 9.656040 TTTCAATTACTGCCTCGTAACTTAATA 57.344 29.630 0.00 0.00 32.67 0.98
15 16 8.556213 TTTCAATTACTGCCTCGTAACTTAAT 57.444 30.769 0.00 0.00 32.67 1.40
16 17 7.874016 TCTTTCAATTACTGCCTCGTAACTTAA 59.126 33.333 0.00 0.00 32.67 1.85
17 18 7.380536 TCTTTCAATTACTGCCTCGTAACTTA 58.619 34.615 0.00 0.00 32.67 2.24
18 19 6.228258 TCTTTCAATTACTGCCTCGTAACTT 58.772 36.000 0.00 0.00 32.67 2.66
56 57 5.080337 AGGCTCATTGAAGGATACGATAGA 58.920 41.667 0.00 0.00 46.39 1.98
83 84 3.751518 GGATGGCGGTAAAGTGGATTAT 58.248 45.455 0.00 0.00 0.00 1.28
86 87 0.179056 CGGATGGCGGTAAAGTGGAT 60.179 55.000 0.00 0.00 0.00 3.41
185 186 0.879400 GCAGGATCTCACATGCCGAG 60.879 60.000 6.43 6.43 40.88 4.63
266 267 2.947785 AGGTCGAGGGAGAGGGGT 60.948 66.667 0.00 0.00 0.00 4.95
501 502 0.034767 TTCTCATCCAAGCCCAGCAG 60.035 55.000 0.00 0.00 0.00 4.24
517 518 2.234296 CCCCAACCTGCCTCCTTCT 61.234 63.158 0.00 0.00 0.00 2.85
536 537 2.490685 GGCTTCTCCTCCGACGAC 59.509 66.667 0.00 0.00 0.00 4.34
658 661 1.780919 ACAAAGAGTAAACCCAGCCCT 59.219 47.619 0.00 0.00 0.00 5.19
687 690 5.303320 AGCCCAAGCATCTCTCTAGGAGA 62.303 52.174 11.77 11.77 45.31 3.71
688 691 1.344114 GCCCAAGCATCTCTCTAGGAG 59.656 57.143 2.70 2.70 40.18 3.69
695 756 3.004951 CCCAGCCCAAGCATCTCT 58.995 61.111 0.00 0.00 43.56 3.10
721 782 0.472471 CCCAAGCCCTATCGCCTTTA 59.528 55.000 0.00 0.00 0.00 1.85
776 845 1.447945 GAGCTGGGCTTTGAGTCTTC 58.552 55.000 0.00 0.00 39.88 2.87
839 908 0.338120 CCTCTCCTTCTCCCTGACCT 59.662 60.000 0.00 0.00 0.00 3.85
842 911 1.388174 ACTCCTCTCCTTCTCCCTGA 58.612 55.000 0.00 0.00 0.00 3.86
853 922 1.143277 TGTCCCGATCCTACTCCTCTC 59.857 57.143 0.00 0.00 0.00 3.20
941 1037 2.607750 ACCGGAGATGCCACCAGT 60.608 61.111 9.46 0.00 35.94 4.00
1050 1146 1.821936 CATCTGCGCCTCCTCTTCT 59.178 57.895 4.18 0.00 0.00 2.85
1122 1218 2.024846 CACCTCCTCCTCTAGGTTCTCA 60.025 54.545 0.00 0.00 43.77 3.27
1361 1459 2.106938 TGTCTCGATGATGCCGGC 59.893 61.111 22.73 22.73 0.00 6.13
1371 1469 1.303091 TTCATCGCTCGGTGTCTCGA 61.303 55.000 2.29 0.00 37.60 4.04
1417 1515 9.052759 CCTTGATTAACGTAATATGGTTAAGCT 57.947 33.333 16.64 0.00 42.43 3.74
1418 1516 8.833493 ACCTTGATTAACGTAATATGGTTAAGC 58.167 33.333 12.18 12.18 42.34 3.09
1421 1519 8.614346 GCAACCTTGATTAACGTAATATGGTTA 58.386 33.333 0.00 0.00 35.40 2.85
1422 1520 7.338449 AGCAACCTTGATTAACGTAATATGGTT 59.662 33.333 0.00 0.00 36.46 3.67
1423 1521 6.826741 AGCAACCTTGATTAACGTAATATGGT 59.173 34.615 0.00 0.00 31.19 3.55
1424 1522 7.259290 AGCAACCTTGATTAACGTAATATGG 57.741 36.000 0.00 0.00 0.00 2.74
1427 1525 8.392612 GCTTTAGCAACCTTGATTAACGTAATA 58.607 33.333 0.00 0.00 41.59 0.98
1428 1526 7.248437 GCTTTAGCAACCTTGATTAACGTAAT 58.752 34.615 0.00 0.00 41.59 1.89
1429 1527 6.604930 GCTTTAGCAACCTTGATTAACGTAA 58.395 36.000 0.00 0.00 41.59 3.18
1430 1528 6.173191 GCTTTAGCAACCTTGATTAACGTA 57.827 37.500 0.00 0.00 41.59 3.57
1431 1529 5.043189 GCTTTAGCAACCTTGATTAACGT 57.957 39.130 0.00 0.00 41.59 3.99
1474 1573 2.159240 TGTCTGAAGCCGTATGTAGCAG 60.159 50.000 0.00 0.00 0.00 4.24
1481 1580 4.833380 AGTATACCATGTCTGAAGCCGTAT 59.167 41.667 0.00 0.00 0.00 3.06
1523 1622 9.696917 CTTTGCTTGAATTACAGGAGTATTTTT 57.303 29.630 0.00 0.00 0.00 1.94
1606 1705 8.403236 ACCCTTTGTTCGTAAATATTAAGATGC 58.597 33.333 0.00 0.00 0.00 3.91
1613 1712 6.243148 AGTCCACCCTTTGTTCGTAAATATT 58.757 36.000 0.00 0.00 0.00 1.28
1708 1808 0.393077 GCGGTGGTGATACTATGCCT 59.607 55.000 0.00 0.00 0.00 4.75
1709 1809 0.105964 TGCGGTGGTGATACTATGCC 59.894 55.000 0.00 0.00 0.00 4.40
1710 1810 1.948104 TTGCGGTGGTGATACTATGC 58.052 50.000 0.00 0.00 0.00 3.14
1719 2312 5.665381 AATTTTAACATTTTGCGGTGGTG 57.335 34.783 0.00 0.00 0.00 4.17
1720 2313 6.931840 ACATAATTTTAACATTTTGCGGTGGT 59.068 30.769 5.13 0.00 0.00 4.16
1760 2353 4.343231 TCCAACCATAGCACAATTCACAT 58.657 39.130 0.00 0.00 0.00 3.21
1796 2389 5.644636 TGTTCGACTCAAACAACTAACCTTT 59.355 36.000 0.00 0.00 33.86 3.11
1805 2398 5.220700 GGTTACACATGTTCGACTCAAACAA 60.221 40.000 0.00 0.00 39.84 2.83
1847 2440 1.184322 TCACTTGGTTACCCGCGGTA 61.184 55.000 26.12 13.74 37.09 4.02
1893 2488 1.403814 TGGATCGTCCTCTGGTGATC 58.596 55.000 5.77 10.70 37.46 2.92
1962 2558 2.293677 CCTGTCGATGCCGTTAGACTAT 59.706 50.000 0.00 0.00 37.05 2.12
1969 2565 2.277084 GATAAACCTGTCGATGCCGTT 58.723 47.619 0.00 0.00 37.05 4.44
1979 2575 2.396590 ACAATCGGCGATAAACCTGT 57.603 45.000 24.28 19.58 0.00 4.00
1990 2586 7.345192 CACTAAATCAACATAGTACAATCGGC 58.655 38.462 0.00 0.00 31.35 5.54
1991 2587 7.494625 ACCACTAAATCAACATAGTACAATCGG 59.505 37.037 0.00 0.00 31.35 4.18
2015 2611 5.220710 ACTATGAATGCTCCTCATGTACC 57.779 43.478 0.00 0.00 35.21 3.34
2031 2627 1.744320 CGTCCCGGGCATGACTATGA 61.744 60.000 18.49 0.00 36.36 2.15
2049 2645 6.140110 AGTGAAATTTGTTAACGTGAATCCG 58.860 36.000 0.00 0.00 0.00 4.18
2054 2650 7.079182 ACAAGAGTGAAATTTGTTAACGTGA 57.921 32.000 0.00 0.00 31.38 4.35
2076 2672 4.578516 AGCAATAACACAAGTACAAGCACA 59.421 37.500 0.00 0.00 0.00 4.57
2116 2712 0.739813 AATAGTTCGAGGGTGCACGC 60.740 55.000 25.22 25.22 0.00 5.34
2190 2789 4.103627 TCCTCCGGAACCTAGTTTTCTTTT 59.896 41.667 5.23 0.00 0.00 2.27
2194 2793 3.908643 ATCCTCCGGAACCTAGTTTTC 57.091 47.619 5.23 0.00 34.34 2.29
2246 2849 3.083293 GGCAGGTTTATCGGTTAACCAA 58.917 45.455 24.14 6.59 44.99 3.67
2302 2905 8.251026 TCTAGGTAAAGTAACATGATGTCTGTG 58.749 37.037 0.00 0.00 0.00 3.66
2303 2906 8.362464 TCTAGGTAAAGTAACATGATGTCTGT 57.638 34.615 0.00 0.00 0.00 3.41
2368 2971 1.000274 AGGCGTGCCAAAAAGATTGAC 60.000 47.619 14.29 0.00 38.92 3.18


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

AutoCloner maintained by Alex Coulton.