Multiple sequence alignment - TraesCS1B01G372700

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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 TraesCS1B01G372700 chr1B 100.000 2519 0 0 1 2519 603224524 603227042 0 4652
1 TraesCS1B01G372700 chr1B 94.881 2305 110 7 1 2299 39833636 39835938 0 3596
2 TraesCS1B01G372700 chr2B 97.023 2519 74 1 1 2519 731624895 731622378 0 4235
3 TraesCS1B01G372700 chr3B 95.317 2520 109 9 1 2519 637643462 637640951 0 3991
4 TraesCS1B01G372700 chr3B 93.434 2528 129 22 1 2519 84776753 84774254 0 3714
5 TraesCS1B01G372700 chr3B 97.686 778 17 1 1 777 1649066 1649843 0 1336
6 TraesCS1B01G372700 chr3B 87.722 676 73 8 1 674 469810290 469809623 0 780
7 TraesCS1B01G372700 chr5B 95.159 2520 117 5 1 2519 701869129 701866614 0 3973
8 TraesCS1B01G372700 chr5B 94.643 2520 124 7 1 2517 697910857 697908346 0 3895
9 TraesCS1B01G372700 chrUn 94.806 2522 121 7 1 2519 8324585 8322071 0 3923
10 TraesCS1B01G372700 chr6B 93.508 2526 128 22 1 2519 257366249 257363753 0 3723
11 TraesCS1B01G372700 chr7B 93.502 2524 127 22 1 2519 465822596 465825087 0 3718


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 TraesCS1B01G372700 chr1B 603224524 603227042 2518 False 4652 4652 100.000 1 2519 1 chr1B.!!$F2 2518
1 TraesCS1B01G372700 chr1B 39833636 39835938 2302 False 3596 3596 94.881 1 2299 1 chr1B.!!$F1 2298
2 TraesCS1B01G372700 chr2B 731622378 731624895 2517 True 4235 4235 97.023 1 2519 1 chr2B.!!$R1 2518
3 TraesCS1B01G372700 chr3B 637640951 637643462 2511 True 3991 3991 95.317 1 2519 1 chr3B.!!$R3 2518
4 TraesCS1B01G372700 chr3B 84774254 84776753 2499 True 3714 3714 93.434 1 2519 1 chr3B.!!$R1 2518
5 TraesCS1B01G372700 chr3B 1649066 1649843 777 False 1336 1336 97.686 1 777 1 chr3B.!!$F1 776
6 TraesCS1B01G372700 chr3B 469809623 469810290 667 True 780 780 87.722 1 674 1 chr3B.!!$R2 673
7 TraesCS1B01G372700 chr5B 701866614 701869129 2515 True 3973 3973 95.159 1 2519 1 chr5B.!!$R2 2518
8 TraesCS1B01G372700 chr5B 697908346 697910857 2511 True 3895 3895 94.643 1 2517 1 chr5B.!!$R1 2516
9 TraesCS1B01G372700 chrUn 8322071 8324585 2514 True 3923 3923 94.806 1 2519 1 chrUn.!!$R1 2518
10 TraesCS1B01G372700 chr6B 257363753 257366249 2496 True 3723 3723 93.508 1 2519 1 chr6B.!!$R1 2518
11 TraesCS1B01G372700 chr7B 465822596 465825087 2491 False 3718 3718 93.502 1 2519 1 chr7B.!!$F1 2518

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
87 88 2.119801 AATGGTTCATCAGCGAGCTT 57.88 45.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1648 0.868406 CACTCTTGGAACCGTGCTTC 59.132 55.0 0.0 0.0 0.0 3.86 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
87 88 2.119801 AATGGTTCATCAGCGAGCTT 57.880 45.000 0.00 0.00 0.00 3.74
400 406 2.146342 GCACACTCACTACAGCAACAT 58.854 47.619 0.00 0.00 0.00 2.71
567 574 3.003068 CCAAAATGCCGAAAAACATGCAA 59.997 39.130 0.00 0.00 37.27 4.08
714 725 6.268847 AGGTATGGTTTTTGGCTGTTAAATCA 59.731 34.615 0.00 0.00 0.00 2.57
966 979 5.277857 AGGACGAGGTAATTCGAATTGAT 57.722 39.130 29.20 16.51 43.03 2.57
1157 1173 5.453480 GGAGGAAGGTTTGCTACGAGAATAT 60.453 44.000 0.00 0.00 0.00 1.28
1168 1184 7.689446 TGCTACGAGAATATAGCAGATTACT 57.311 36.000 1.90 0.00 46.82 2.24
1340 1356 6.151144 GCTCCTACCACAAGTTTGAACATATT 59.849 38.462 0.00 0.00 0.00 1.28
1355 1371 3.757270 ACATATTCCCACGGTGTTTTCA 58.243 40.909 7.45 0.00 0.00 2.69
1369 1385 5.468592 GGTGTTTTCATGTTGTGATGCATA 58.531 37.500 0.00 0.00 36.54 3.14
1423 1439 8.699749 GCCAGTTTGTAGTTGATCAATTAAAAC 58.300 33.333 23.00 23.00 0.00 2.43
1437 1453 0.606944 TAAAACTGGCATTCGCGGGT 60.607 50.000 6.13 0.00 39.92 5.28
1453 1469 1.883275 CGGGTGCAGGTGATAAAAACA 59.117 47.619 0.00 0.00 0.00 2.83
1589 1607 5.781210 TGTGTTTGATTTGCCTCATGTAA 57.219 34.783 0.00 0.00 0.00 2.41
1668 1686 3.517901 AGTGTCGGTTTGGGATTCTGATA 59.482 43.478 0.00 0.00 0.00 2.15
1873 1894 8.491134 ACTATCATTAACTAGGCAACCACATTA 58.509 33.333 0.00 0.00 37.17 1.90
2409 2437 5.588648 GGAATTGGGAAACTTGACGATGATA 59.411 40.000 0.00 0.00 0.00 2.15
2412 2440 3.055458 TGGGAAACTTGACGATGATAGCA 60.055 43.478 0.00 0.00 0.00 3.49
2418 2446 1.926561 TGACGATGATAGCAGCACAC 58.073 50.000 0.00 0.00 0.00 3.82
2451 2479 2.068519 CAGCTGACAATGTTGCTCGTA 58.931 47.619 8.42 0.00 33.03 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
470 476 2.751259 CACTGGCATTGCTGTCTATGTT 59.249 45.455 8.82 0.0 0.00 2.71
825 837 9.997482 GTTAAACTTTGTGTGACAGAAATTAGA 57.003 29.630 8.39 0.0 0.00 2.10
966 979 2.727123 TCTGCAACAGACCTCCAAAA 57.273 45.000 0.00 0.0 35.39 2.44
1157 1173 8.264347 TGTACATTTTGGATGAGTAATCTGCTA 58.736 33.333 0.00 0.0 35.43 3.49
1168 1184 9.695526 CTTGAAGATTTTGTACATTTTGGATGA 57.304 29.630 0.00 0.0 0.00 2.92
1305 1321 2.375174 TGTGGTAGGAGCAAGGAAACAT 59.625 45.455 0.00 0.0 0.00 2.71
1340 1356 1.678627 CAACATGAAAACACCGTGGGA 59.321 47.619 0.00 0.0 0.00 4.37
1369 1385 1.335964 CGTCTCCGTTATCGCATCCAT 60.336 52.381 0.00 0.0 35.54 3.41
1437 1453 4.275689 CAGACTGTGTTTTTATCACCTGCA 59.724 41.667 0.00 0.0 35.25 4.41
1561 1577 4.159321 TGAGGCAAATCAAACACAAACAGA 59.841 37.500 0.00 0.0 0.00 3.41
1564 1580 4.810491 ACATGAGGCAAATCAAACACAAAC 59.190 37.500 0.00 0.0 31.76 2.93
1589 1607 9.373450 ACATCTAATGAGTCCAGATATAACAGT 57.627 33.333 0.00 0.0 0.00 3.55
1630 1648 0.868406 CACTCTTGGAACCGTGCTTC 59.132 55.000 0.00 0.0 0.00 3.86
1668 1686 9.190317 GTCCTTCTTAATGACCTTGGAAATAAT 57.810 33.333 0.00 0.0 0.00 1.28
1873 1894 7.398024 ACATCTAGTGAGTTGCTTAGGAAAAT 58.602 34.615 0.00 0.0 0.00 1.82
2083 2109 8.721478 GTCTTGAGCTATAATTTGAAGTGTGAA 58.279 33.333 0.00 0.0 0.00 3.18
2266 2292 2.122768 GAGAGAGGACATTGGGGTCAT 58.877 52.381 0.00 0.0 39.59 3.06
2369 2397 2.501223 TTCCCTGTACGAGCTTGCCG 62.501 60.000 0.00 0.0 0.00 5.69
2409 2437 1.374758 GAACGCTAGGTGTGCTGCT 60.375 57.895 0.00 0.0 0.00 4.24
2412 2440 1.293498 CTGGAACGCTAGGTGTGCT 59.707 57.895 0.00 0.0 0.00 4.40
2418 2446 1.812922 CAGCTGCTGGAACGCTAGG 60.813 63.158 21.71 0.0 31.80 3.02
2451 2479 1.670811 CCTTGAACGTGAACTGCTTGT 59.329 47.619 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.