Multiple sequence alignment - TraesCS1B01G172100

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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 TraesCS1B01G172100 chr1B 100.000 2621 0 0 1 2621 307005661 307003041 0.000000e+00 4841.0
1 TraesCS1B01G172100 chr1B 80.000 125 19 6 27 148 15377493 15377614 1.290000e-13 87.9
2 TraesCS1B01G172100 chr1D 96.075 2650 56 15 1 2621 214069446 214066816 0.000000e+00 4274.0
3 TraesCS1B01G172100 chr1A 95.606 2253 63 15 278 2508 271621082 271618844 0.000000e+00 3579.0
4 TraesCS1B01G172100 chr2D 86.408 412 54 2 1107 1517 483256320 483255910 1.430000e-122 449.0
5 TraesCS1B01G172100 chr2D 84.071 113 18 0 41 153 174456489 174456377 2.760000e-20 110.0
6 TraesCS1B01G172100 chr2A 86.441 413 52 4 1107 1517 626589676 626589266 1.430000e-122 449.0
7 TraesCS1B01G172100 chr2B 86.165 412 55 2 1107 1517 568275143 568275553 6.660000e-121 444.0
8 TraesCS1B01G172100 chr6D 85.000 420 54 9 1102 1516 452722177 452721762 4.030000e-113 418.0
9 TraesCS1B01G172100 chr6D 84.653 404 62 0 1113 1516 296348047 296347644 1.130000e-108 403.0
10 TraesCS1B01G172100 chr6A 84.964 419 56 7 1102 1516 598619737 598619322 4.030000e-113 418.0
11 TraesCS1B01G172100 chr6A 84.901 404 61 0 1113 1516 422328668 422328265 2.430000e-110 409.0
12 TraesCS1B01G172100 chr3A 78.313 166 33 3 23 187 703210719 703210882 1.280000e-18 104.0
13 TraesCS1B01G172100 chr4A 83.168 101 16 1 41 140 646840640 646840740 9.990000e-15 91.6
14 TraesCS1B01G172100 chr4A 82.178 101 17 1 41 140 646973485 646973585 4.650000e-13 86.1
15 TraesCS1B01G172100 chr6B 83.333 60 10 0 71 130 21457782 21457723 3.640000e-04 56.5
16 TraesCS1B01G172100 chr6B 100.000 28 0 0 76 103 15116591 15116618 5.000000e-03 52.8


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 TraesCS1B01G172100 chr1B 307003041 307005661 2620 True 4841 4841 100.000 1 2621 1 chr1B.!!$R1 2620
1 TraesCS1B01G172100 chr1D 214066816 214069446 2630 True 4274 4274 96.075 1 2621 1 chr1D.!!$R1 2620
2 TraesCS1B01G172100 chr1A 271618844 271621082 2238 True 3579 3579 95.606 278 2508 1 chr1A.!!$R1 2230

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
686 691 1.063764 GTTCTCCGCTACACTCCTACG 59.936 57.143 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2137 0.456824 CTGACATGACTCCACGACCG 60.457 60.0 0.0 0.0 0.0 4.79 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
72 76 6.375455 AGTTCGAATATTGGCTTTGACTGAAT 59.625 34.615 0.00 0.00 0.00 2.57
82 86 7.249186 TGGCTTTGACTGAATTCAAATTTTG 57.751 32.000 9.88 2.59 43.03 2.44
300 304 2.436646 CGTGCGCCATTCCTCCTT 60.437 61.111 4.18 0.00 0.00 3.36
491 496 2.825264 GCTAGGTAGCCAGCCAGG 59.175 66.667 0.42 0.00 43.39 4.45
646 651 6.208797 TGGTTTCGGATAGTGATATCTCGATT 59.791 38.462 3.98 0.00 33.04 3.34
679 684 2.452105 GAGATTCGTTCTCCGCTACAC 58.548 52.381 6.82 0.00 44.46 2.90
686 691 1.063764 GTTCTCCGCTACACTCCTACG 59.936 57.143 0.00 0.00 0.00 3.51
882 887 2.347490 GCTCCCCAAGAAGCGTCA 59.653 61.111 1.61 0.00 0.00 4.35
1272 1277 1.893808 CAAGACCAAGGTGCACGCT 60.894 57.895 11.45 6.38 0.00 5.07
1299 1304 2.677228 CCATTCTTCGGCCACCCT 59.323 61.111 2.24 0.00 0.00 4.34
1666 1671 1.884235 AGCTAGCTGCAACGACTTTT 58.116 45.000 18.57 0.00 45.94 2.27
1769 1780 3.418995 AGTCTCGTCCTACTAGTGCAAA 58.581 45.455 5.39 0.00 0.00 3.68
1830 1841 6.782494 ACCCCTACTAGTCTAGTACTACTCTC 59.218 46.154 14.62 0.00 39.80 3.20
1977 1992 1.181741 TAGCTAGCTCCATGGCTCGG 61.182 60.000 23.26 0.10 42.97 4.63
2049 2064 3.325870 TGTAACCTCTCGCATCTTGTTG 58.674 45.455 0.00 0.00 0.00 3.33
2121 2137 1.375523 CTTGTGAGGGGTACGGTGC 60.376 63.158 0.00 0.00 0.00 5.01
2152 2168 1.681264 TCATGTCAGTGTGTGTCGTCT 59.319 47.619 0.00 0.00 0.00 4.18
2469 2505 7.787725 CTGAGTTTTCAGTGGTTACTTAAGT 57.212 36.000 13.68 13.68 44.74 2.24
2531 2567 5.466728 AGTGTACTATGAGTGCAGTTTTGTG 59.533 40.000 0.00 0.00 40.79 3.33
2532 2568 3.904136 ACTATGAGTGCAGTTTTGTGC 57.096 42.857 0.00 0.00 44.27 4.57
2580 2616 3.510388 TCACTCGTTGATGCTTAGGAG 57.490 47.619 0.00 0.00 33.65 3.69
2611 2647 3.620488 TGCATCTCCTTTTCCACATACC 58.380 45.455 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
300 304 1.999648 AAATGTTGAGCTGAAGGGCA 58.000 45.000 0.00 0.00 34.17 5.36
486 491 1.044790 ATTAATGGTGGCTGCCTGGC 61.045 55.000 21.03 12.87 42.18 4.85
487 492 1.956477 GTATTAATGGTGGCTGCCTGG 59.044 52.381 21.03 0.00 0.00 4.45
488 493 2.880890 GAGTATTAATGGTGGCTGCCTG 59.119 50.000 21.03 0.00 0.00 4.85
489 494 2.509548 TGAGTATTAATGGTGGCTGCCT 59.490 45.455 21.03 0.83 0.00 4.75
490 495 2.618709 GTGAGTATTAATGGTGGCTGCC 59.381 50.000 12.87 12.87 0.00 4.85
491 496 2.618709 GGTGAGTATTAATGGTGGCTGC 59.381 50.000 0.00 0.00 0.00 5.25
492 497 3.214328 GGGTGAGTATTAATGGTGGCTG 58.786 50.000 0.00 0.00 0.00 4.85
493 498 2.174854 GGGGTGAGTATTAATGGTGGCT 59.825 50.000 0.00 0.00 0.00 4.75
591 596 2.751731 CCGGTGTGGGATATGGCCA 61.752 63.158 8.56 8.56 0.00 5.36
646 651 1.486310 CGAATCTCACCCCCAAGATCA 59.514 52.381 0.00 0.00 31.03 2.92
686 691 2.359531 AGAACAGGAGATACGCAGCTAC 59.640 50.000 0.00 0.00 0.00 3.58
1533 1538 4.731853 TGGGAGGGGATGTCGGCA 62.732 66.667 0.00 0.00 0.00 5.69
1666 1671 5.948162 GTGGGAATACATAGGATACGTAGGA 59.052 44.000 0.08 0.00 46.39 2.94
1747 1758 3.900966 TGCACTAGTAGGACGAGACTA 57.099 47.619 1.45 0.00 0.00 2.59
1748 1759 2.783609 TGCACTAGTAGGACGAGACT 57.216 50.000 1.45 0.00 0.00 3.24
1749 1760 3.500014 GTTTGCACTAGTAGGACGAGAC 58.500 50.000 1.45 0.00 0.00 3.36
1754 1765 0.989890 CGCGTTTGCACTAGTAGGAC 59.010 55.000 0.00 0.00 42.97 3.85
1769 1780 2.702592 TGGAGGAATTTAATCCGCGT 57.297 45.000 4.92 0.00 44.60 6.01
2049 2064 7.792374 TTGCAATACCAAGAGATAGATCAAC 57.208 36.000 0.00 0.00 0.00 3.18
2121 2137 0.456824 CTGACATGACTCCACGACCG 60.457 60.000 0.00 0.00 0.00 4.79
2152 2168 2.661176 AGATTCCCCAACTGGACCTA 57.339 50.000 0.00 0.00 37.39 3.08
2244 2260 4.396519 CATAAAAAGCAATGCAAAAGCGG 58.603 39.130 8.35 0.00 0.00 5.52
2362 2378 6.296026 TGCTACCATTTCTGTATACATTCCC 58.704 40.000 5.91 0.00 0.00 3.97
2531 2567 2.092838 GCAGAGACAGAAACATGTACGC 59.907 50.000 0.00 0.00 32.25 4.42
2532 2568 3.317150 TGCAGAGACAGAAACATGTACG 58.683 45.455 0.00 0.00 32.25 3.67


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

AutoCloner maintained by Alex Coulton.