Multiple sequence alignment - TraesCS1B01G457800

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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 TraesCS1B01G457800 chr1B 100.000 2534 0 0 1 2534 672472791 672475324 0.000000 4680.0
1 TraesCS1B01G457800 chr1B 98.455 2007 26 3 533 2534 668811003 668808997 0.000000 3530.0
2 TraesCS1B01G457800 chr7B 98.952 2004 19 2 533 2534 644461603 644463606 0.000000 3583.0
3 TraesCS1B01G457800 chr7B 99.601 501 2 0 1 501 644460823 644461323 0.000000 915.0
4 TraesCS1B01G457800 chr3A 98.752 2003 24 1 533 2534 633105416 633107418 0.000000 3559.0
5 TraesCS1B01G457800 chr3A 99.202 501 4 0 1 501 633104637 633105137 0.000000 904.0
6 TraesCS1B01G457800 chr7D 98.702 2003 25 1 533 2534 382062838 382064840 0.000000 3554.0
7 TraesCS1B01G457800 chr7D 98.652 2003 26 1 533 2534 381961001 381958999 0.000000 3548.0
8 TraesCS1B01G457800 chr7D 98.502 2003 29 1 533 2534 626685075 626683073 0.000000 3531.0
9 TraesCS1B01G457800 chr7D 99.202 501 4 0 1 501 382062058 382062558 0.000000 904.0
10 TraesCS1B01G457800 chr7D 100.000 31 0 0 499 529 106357495 106357525 0.000098 58.4
11 TraesCS1B01G457800 chr7D 100.000 31 0 0 499 529 381960911 381960881 0.000098 58.4
12 TraesCS1B01G457800 chr7D 100.000 31 0 0 499 529 382062928 382062958 0.000098 58.4
13 TraesCS1B01G457800 chr6D 98.652 2003 26 1 533 2534 124530282 124532284 0.000000 3548.0
14 TraesCS1B01G457800 chr6D 99.401 501 3 0 1 501 458910158 458910658 0.000000 909.0
15 TraesCS1B01G457800 chr6D 99.202 501 4 0 1 501 124529502 124530002 0.000000 904.0
16 TraesCS1B01G457800 chr6D 100.000 31 0 0 499 529 124530372 124530402 0.000098 58.4
17 TraesCS1B01G457800 chr6D 100.000 31 0 0 499 529 283219982 283220012 0.000098 58.4
18 TraesCS1B01G457800 chr6D 100.000 31 0 0 499 529 458911028 458911058 0.000098 58.4
19 TraesCS1B01G457800 chrUn 98.603 2005 25 2 533 2534 189405242 189407246 0.000000 3544.0
20 TraesCS1B01G457800 chrUn 99.401 501 3 0 1 501 395660854 395661354 0.000000 909.0
21 TraesCS1B01G457800 chrUn 99.202 501 4 0 1 501 189404462 189404962 0.000000 904.0
22 TraesCS1B01G457800 chrUn 99.002 501 5 0 1 501 251412090 251411590 0.000000 898.0
23 TraesCS1B01G457800 chrUn 100.000 31 0 0 499 529 189405332 189405362 0.000098 58.4
24 TraesCS1B01G457800 chrUn 100.000 31 0 0 499 529 251411220 251411190 0.000098 58.4
25 TraesCS1B01G457800 chrUn 100.000 31 0 0 499 529 413812156 413812186 0.000098 58.4
26 TraesCS1B01G457800 chr1D 98.602 2003 26 2 533 2534 141318974 141316973 0.000000 3542.0
27 TraesCS1B01G457800 chr6B 99.202 501 4 0 1 501 307002600 307002100 0.000000 904.0


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 TraesCS1B01G457800 chr1B 672472791 672475324 2533 False 4680.000000 4680 100.000000 1 2534 1 chr1B.!!$F1 2533
1 TraesCS1B01G457800 chr1B 668808997 668811003 2006 True 3530.000000 3530 98.455000 533 2534 1 chr1B.!!$R1 2001
2 TraesCS1B01G457800 chr7B 644460823 644463606 2783 False 2249.000000 3583 99.276500 1 2534 2 chr7B.!!$F1 2533
3 TraesCS1B01G457800 chr3A 633104637 633107418 2781 False 2231.500000 3559 98.977000 1 2534 2 chr3A.!!$F1 2533
4 TraesCS1B01G457800 chr7D 626683073 626685075 2002 True 3531.000000 3531 98.502000 533 2534 1 chr7D.!!$R1 2001
5 TraesCS1B01G457800 chr7D 381958999 381961001 2002 True 1803.200000 3548 99.326000 499 2534 2 chr7D.!!$R2 2035
6 TraesCS1B01G457800 chr7D 382062058 382064840 2782 False 1505.466667 3554 99.301333 1 2534 3 chr7D.!!$F2 2533
7 TraesCS1B01G457800 chr6D 124529502 124532284 2782 False 1503.466667 3548 99.284667 1 2534 3 chr6D.!!$F2 2533
8 TraesCS1B01G457800 chr6D 458910158 458911058 900 False 483.700000 909 99.700500 1 529 2 chr6D.!!$F3 528
9 TraesCS1B01G457800 chrUn 189404462 189407246 2784 False 1502.133333 3544 99.268333 1 2534 3 chrUn.!!$F3 2533
10 TraesCS1B01G457800 chrUn 395660854 395661354 500 False 909.000000 909 99.401000 1 501 1 chrUn.!!$F1 500
11 TraesCS1B01G457800 chrUn 251411190 251412090 900 True 478.200000 898 99.501000 1 529 2 chrUn.!!$R1 528
12 TraesCS1B01G457800 chr1D 141316973 141318974 2001 True 3542.000000 3542 98.602000 533 2534 1 chr1D.!!$R1 2001
13 TraesCS1B01G457800 chr6B 307002100 307002600 500 True 904.000000 904 99.202000 1 501 1 chr6B.!!$R1 500

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
899 1151 0.532573 CTTCCTTGCCGCTGAGACTA 59.467 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2068 1.873591 GCGACATCTCCGGCATAAATT 59.126 47.619 0.0 0.0 0.0 1.82 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
313 314 2.360165 TCGCGAATAGGGAGTTAAGGAC 59.640 50.000 6.20 0.00 36.85 3.85
405 406 1.378646 GGTTGAAGCAGCCCCTACC 60.379 63.158 0.00 0.00 0.00 3.18
501 502 4.705507 AGCTTATGAGTTGAGTTCGTCCTA 59.294 41.667 0.00 0.00 0.00 2.94
502 503 4.799428 GCTTATGAGTTGAGTTCGTCCTAC 59.201 45.833 0.00 0.00 0.00 3.18
503 504 5.393243 GCTTATGAGTTGAGTTCGTCCTACT 60.393 44.000 0.00 0.00 0.00 2.57
504 505 6.585695 TTATGAGTTGAGTTCGTCCTACTT 57.414 37.500 0.00 0.00 0.00 2.24
505 506 4.238761 TGAGTTGAGTTCGTCCTACTTG 57.761 45.455 0.00 0.00 0.00 3.16
506 507 2.987821 GAGTTGAGTTCGTCCTACTTGC 59.012 50.000 0.00 0.00 0.00 4.01
507 508 2.628657 AGTTGAGTTCGTCCTACTTGCT 59.371 45.455 0.00 0.00 0.00 3.91
508 509 3.069729 AGTTGAGTTCGTCCTACTTGCTT 59.930 43.478 0.00 0.00 0.00 3.91
509 510 4.280174 AGTTGAGTTCGTCCTACTTGCTTA 59.720 41.667 0.00 0.00 0.00 3.09
510 511 4.170292 TGAGTTCGTCCTACTTGCTTAC 57.830 45.455 0.00 0.00 0.00 2.34
511 512 3.570975 TGAGTTCGTCCTACTTGCTTACA 59.429 43.478 0.00 0.00 0.00 2.41
512 513 4.167268 GAGTTCGTCCTACTTGCTTACAG 58.833 47.826 0.00 0.00 0.00 2.74
514 515 2.799017 TCGTCCTACTTGCTTACAGGA 58.201 47.619 0.00 0.00 34.79 3.86
515 516 3.362706 TCGTCCTACTTGCTTACAGGAT 58.637 45.455 0.00 0.00 39.33 3.24
516 517 3.380637 TCGTCCTACTTGCTTACAGGATC 59.619 47.826 0.00 0.00 39.33 3.36
517 518 3.491104 CGTCCTACTTGCTTACAGGATCC 60.491 52.174 2.48 2.48 39.33 3.36
518 519 3.707102 GTCCTACTTGCTTACAGGATCCT 59.293 47.826 9.02 9.02 39.33 3.24
519 520 4.162509 GTCCTACTTGCTTACAGGATCCTT 59.837 45.833 13.00 6.61 39.33 3.36
520 521 5.363005 GTCCTACTTGCTTACAGGATCCTTA 59.637 44.000 13.00 5.56 39.33 2.69
521 522 5.962031 TCCTACTTGCTTACAGGATCCTTAA 59.038 40.000 13.00 12.87 32.20 1.85
522 523 6.098409 TCCTACTTGCTTACAGGATCCTTAAG 59.902 42.308 24.76 24.76 32.20 1.85
523 524 6.098409 CCTACTTGCTTACAGGATCCTTAAGA 59.902 42.308 29.09 18.94 0.00 2.10
524 525 6.374417 ACTTGCTTACAGGATCCTTAAGAA 57.626 37.500 29.09 22.71 0.00 2.52
525 526 6.779860 ACTTGCTTACAGGATCCTTAAGAAA 58.220 36.000 29.09 25.88 0.00 2.52
526 527 6.655425 ACTTGCTTACAGGATCCTTAAGAAAC 59.345 38.462 29.09 19.36 0.00 2.78
527 528 6.374417 TGCTTACAGGATCCTTAAGAAACT 57.626 37.500 29.09 3.86 0.00 2.66
528 529 6.173339 TGCTTACAGGATCCTTAAGAAACTG 58.827 40.000 29.09 15.30 37.94 3.16
529 530 6.013725 TGCTTACAGGATCCTTAAGAAACTGA 60.014 38.462 29.09 13.69 36.39 3.41
531 532 7.065204 GCTTACAGGATCCTTAAGAAACTGAAG 59.935 40.741 29.09 13.59 36.39 3.02
899 1151 0.532573 CTTCCTTGCCGCTGAGACTA 59.467 55.000 0.00 0.00 0.00 2.59
1557 1814 1.457604 AGCTTTGCTCTTCTGGGCA 59.542 52.632 0.00 0.00 30.62 5.36
1708 1965 7.079451 TGTTTTTCTCTCCTTTCCTATCAGT 57.921 36.000 0.00 0.00 0.00 3.41
1725 1982 3.926616 TCAGTGAGTTCCGATCCTTTTC 58.073 45.455 0.00 0.00 0.00 2.29
1811 2068 7.782168 CCTATATCAGCTATACATCCTCCTTGA 59.218 40.741 0.00 0.00 0.00 3.02
1958 2215 2.816958 CGCTCTGCTGGATGCGTT 60.817 61.111 14.38 0.00 46.63 4.84
2035 2292 1.647545 GCGCCTGCTCTATTGTTGCA 61.648 55.000 0.00 0.00 38.39 4.08
2195 2452 3.361977 CTTTGTTGGACCGCCGGG 61.362 66.667 8.57 0.00 36.79 5.73
2502 2759 1.075226 TCCGGATTGCTAGCTCCCT 60.075 57.895 17.23 0.00 0.00 4.20
2530 2787 1.741528 TCCGCTACAGACGATACACA 58.258 50.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
405 406 2.369394 GCTGGAACAACCCATAGAAGG 58.631 52.381 0.00 0.00 38.70 3.46
501 502 6.374417 TTCTTAAGGATCCTGTAAGCAAGT 57.626 37.500 24.52 9.41 0.00 3.16
502 503 6.881602 AGTTTCTTAAGGATCCTGTAAGCAAG 59.118 38.462 24.52 17.26 0.00 4.01
503 504 6.655003 CAGTTTCTTAAGGATCCTGTAAGCAA 59.345 38.462 24.52 20.69 0.00 3.91
504 505 6.013725 TCAGTTTCTTAAGGATCCTGTAAGCA 60.014 38.462 24.52 17.73 0.00 3.91
505 506 6.407202 TCAGTTTCTTAAGGATCCTGTAAGC 58.593 40.000 24.52 15.86 0.00 3.09
506 507 8.314751 TCTTCAGTTTCTTAAGGATCCTGTAAG 58.685 37.037 17.02 21.76 0.00 2.34
507 508 8.202461 TCTTCAGTTTCTTAAGGATCCTGTAA 57.798 34.615 17.02 14.25 0.00 2.41
508 509 7.093289 CCTCTTCAGTTTCTTAAGGATCCTGTA 60.093 40.741 17.02 7.28 0.00 2.74
509 510 6.296145 CCTCTTCAGTTTCTTAAGGATCCTGT 60.296 42.308 17.02 8.32 0.00 4.00
510 511 6.112058 CCTCTTCAGTTTCTTAAGGATCCTG 58.888 44.000 17.02 2.64 0.00 3.86
511 512 5.788014 ACCTCTTCAGTTTCTTAAGGATCCT 59.212 40.000 9.02 9.02 0.00 3.24
512 513 6.056090 ACCTCTTCAGTTTCTTAAGGATCC 57.944 41.667 2.48 2.48 0.00 3.36
514 515 5.337652 CCGACCTCTTCAGTTTCTTAAGGAT 60.338 44.000 1.85 0.00 0.00 3.24
515 516 4.021368 CCGACCTCTTCAGTTTCTTAAGGA 60.021 45.833 1.85 0.00 0.00 3.36
516 517 4.021368 TCCGACCTCTTCAGTTTCTTAAGG 60.021 45.833 1.85 0.00 0.00 2.69
517 518 5.135508 TCCGACCTCTTCAGTTTCTTAAG 57.864 43.478 0.00 0.00 0.00 1.85
518 519 4.587684 ACTCCGACCTCTTCAGTTTCTTAA 59.412 41.667 0.00 0.00 0.00 1.85
519 520 4.150359 ACTCCGACCTCTTCAGTTTCTTA 58.850 43.478 0.00 0.00 0.00 2.10
520 521 2.966516 ACTCCGACCTCTTCAGTTTCTT 59.033 45.455 0.00 0.00 0.00 2.52
521 522 2.599677 ACTCCGACCTCTTCAGTTTCT 58.400 47.619 0.00 0.00 0.00 2.52
522 523 3.506844 ACTACTCCGACCTCTTCAGTTTC 59.493 47.826 0.00 0.00 0.00 2.78
523 524 3.498334 ACTACTCCGACCTCTTCAGTTT 58.502 45.455 0.00 0.00 0.00 2.66
524 525 3.157750 ACTACTCCGACCTCTTCAGTT 57.842 47.619 0.00 0.00 0.00 3.16
525 526 2.883122 ACTACTCCGACCTCTTCAGT 57.117 50.000 0.00 0.00 0.00 3.41
526 527 3.118334 TCCTACTACTCCGACCTCTTCAG 60.118 52.174 0.00 0.00 0.00 3.02
527 528 2.842496 TCCTACTACTCCGACCTCTTCA 59.158 50.000 0.00 0.00 0.00 3.02
528 529 3.557228 TCCTACTACTCCGACCTCTTC 57.443 52.381 0.00 0.00 0.00 2.87
529 530 4.313020 TTTCCTACTACTCCGACCTCTT 57.687 45.455 0.00 0.00 0.00 2.85
531 532 5.591877 TGTATTTTCCTACTACTCCGACCTC 59.408 44.000 0.00 0.00 0.00 3.85
1027 1279 2.738314 CGAAAAGACCCGGAAATAACGT 59.262 45.455 0.73 0.00 0.00 3.99
1424 1681 1.749634 CTCCGAACGAAGGGAGTGTAT 59.250 52.381 10.77 0.00 43.91 2.29
1708 1965 4.968259 TCAAAGAAAAGGATCGGAACTCA 58.032 39.130 0.00 0.00 0.00 3.41
1725 1982 6.890360 GGTACGAACGAAGAAATTTCAAAG 57.110 37.500 19.99 11.99 0.00 2.77
1811 2068 1.873591 GCGACATCTCCGGCATAAATT 59.126 47.619 0.00 0.00 0.00 1.82
1958 2215 3.055819 GCGAGCTTCTTATATGGGATCCA 60.056 47.826 15.23 0.00 38.19 3.41
2195 2452 2.737376 GAGACCACCGTGTTCGCC 60.737 66.667 0.00 0.00 35.54 5.54
2502 2759 3.441222 TCGTCTGTAGCGGAACTATGAAA 59.559 43.478 0.00 0.00 32.15 2.69


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

AutoCloner maintained by Alex Coulton.