Multiple sequence alignment - TraesCS7B01G437900

Loading Multiple Alignment...

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 TraesCS7B01G437900 chr7B 100.000 6097 0 0 1 6097 704151440 704157536 0.000000e+00 11260.0
1 TraesCS7B01G437900 chr7B 98.545 6118 53 13 2 6097 704086592 704092695 0.000000e+00 10772.0
2 TraesCS7B01G437900 chr7B 78.650 2356 364 79 1439 3735 639090322 639088047 0.000000e+00 1435.0
3 TraesCS7B01G437900 chr7B 100.000 532 0 0 6338 6869 704157777 704158308 0.000000e+00 983.0
4 TraesCS7B01G437900 chr7B 97.749 533 8 2 6338 6869 704092710 704093239 0.000000e+00 915.0
5 TraesCS7B01G437900 chr7B 80.234 1027 103 48 5098 6092 639086753 639085795 0.000000e+00 680.0
6 TraesCS7B01G437900 chr7B 82.729 689 88 19 3722 4399 639087892 639087224 9.930000e-163 584.0
7 TraesCS7B01G437900 chr7B 81.955 399 44 12 4541 4923 639087150 639086764 5.170000e-81 313.0
8 TraesCS7B01G437900 chr7B 73.062 787 139 45 628 1393 639091066 639090332 1.940000e-50 211.0
9 TraesCS7B01G437900 chr7A 92.621 5014 260 47 719 5685 705135130 705140080 0.000000e+00 7108.0
10 TraesCS7B01G437900 chr7A 80.592 2839 423 74 1593 4392 667481019 667478270 0.000000e+00 2073.0
11 TraesCS7B01G437900 chr7A 87.079 743 56 18 2 727 705132941 705133660 0.000000e+00 804.0
12 TraesCS7B01G437900 chr7A 94.340 424 13 4 5675 6092 705141577 705141995 2.090000e-179 640.0
13 TraesCS7B01G437900 chr7A 80.205 586 56 28 5531 6092 667478230 667477681 1.080000e-102 385.0
14 TraesCS7B01G437900 chr7A 91.866 209 16 1 6338 6546 705141980 705142187 2.420000e-74 291.0
15 TraesCS7B01G437900 chr7D 80.079 3032 442 92 1439 4399 576340137 576337197 0.000000e+00 2104.0
16 TraesCS7B01G437900 chr7D 80.507 1026 103 46 5098 6092 576336664 576335705 0.000000e+00 697.0
17 TraesCS7B01G437900 chr7D 82.544 401 40 15 4541 4923 576337121 576336733 6.640000e-85 326.0
18 TraesCS7B01G437900 chr3D 82.562 1015 117 41 3435 4423 181109635 181108655 0.000000e+00 839.0
19 TraesCS7B01G437900 chr3D 79.853 680 61 29 5359 6014 181107811 181107184 1.770000e-115 427.0
20 TraesCS7B01G437900 chr3D 84.527 349 40 11 4541 4885 181108587 181108249 3.970000e-87 333.0
21 TraesCS7B01G437900 chr3A 80.735 680 63 27 5359 6014 227919305 227919940 1.040000e-127 468.0
22 TraesCS7B01G437900 chr3A 80.401 449 64 16 3968 4402 227918107 227918545 3.090000e-83 320.0
23 TraesCS7B01G437900 chr3A 81.535 417 43 16 3542 3946 227917536 227917930 5.170000e-81 313.0
24 TraesCS7B01G437900 chr3A 82.857 350 44 10 4541 4885 227918613 227918951 4.030000e-77 300.0
25 TraesCS7B01G437900 chr3A 85.185 135 14 3 5360 5491 14856306 14856437 4.320000e-27 134.0
26 TraesCS7B01G437900 chr3A 84.270 89 14 0 5360 5448 227916230 227916318 3.410000e-13 87.9
27 TraesCS7B01G437900 chr3A 81.731 104 7 6 6506 6597 227920763 227920866 7.390000e-10 76.8


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 TraesCS7B01G437900 chr7B 704151440 704158308 6868 False 6121.500000 11260 100.000000 1 6869 2 chr7B.!!$F2 6868
1 TraesCS7B01G437900 chr7B 704086592 704093239 6647 False 5843.500000 10772 98.147000 2 6869 2 chr7B.!!$F1 6867
2 TraesCS7B01G437900 chr7B 639085795 639091066 5271 True 644.600000 1435 79.326000 628 6092 5 chr7B.!!$R1 5464
3 TraesCS7B01G437900 chr7A 705132941 705142187 9246 False 2210.750000 7108 91.476500 2 6546 4 chr7A.!!$F1 6544
4 TraesCS7B01G437900 chr7A 667477681 667481019 3338 True 1229.000000 2073 80.398500 1593 6092 2 chr7A.!!$R1 4499
5 TraesCS7B01G437900 chr7D 576335705 576340137 4432 True 1042.333333 2104 81.043333 1439 6092 3 chr7D.!!$R1 4653
6 TraesCS7B01G437900 chr3D 181107184 181109635 2451 True 533.000000 839 82.314000 3435 6014 3 chr3D.!!$R1 2579
7 TraesCS7B01G437900 chr3A 227916230 227920866 4636 False 260.950000 468 81.921500 3542 6597 6 chr3A.!!$F2 3055

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
564 588 2.238521 GTTTGGTCAGATTCCCTTGCA 58.761 47.619 0.0 0.00 0.0 4.08 F
2819 4392 4.697352 GGAATGCGGCATATCAATAGTTCT 59.303 41.667 17.0 0.00 0.0 3.01 F
2924 4497 0.033366 ATGCGTACTGACACTGTGCA 59.967 50.000 7.9 6.25 35.1 4.57 F
4046 5992 5.411361 CCAACCGATAATTTTCTGACTCACA 59.589 40.000 0.0 0.00 0.0 3.58 F
5722 9370 2.102252 CTCTCAGTTGCTCCCATCTACC 59.898 54.545 0.0 0.00 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 4063 3.648339 AACATGGAAATGAGCACACAC 57.352 42.857 0.00 0.00 0.00 3.82 R
4046 5992 3.770046 AGGTAAAAGCCAAAATACCGGT 58.230 40.909 13.98 13.98 42.10 5.28 R
4052 6002 6.740944 AACAACCTAGGTAAAAGCCAAAAT 57.259 33.333 16.67 0.00 0.00 1.82 R
5857 9505 0.172352 GGGACGACTCAGCAGAAGAG 59.828 60.000 0.00 0.00 39.04 2.85 R
6822 11123 0.178990 ACAAGGTTGGGCTTCAGGTC 60.179 55.000 0.00 0.00 0.00 3.85 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
175 178 2.746269 TCGATCGTTTCCTTGTTTCGT 58.254 42.857 15.94 0.00 0.00 3.85
281 298 3.922910 ACGAGCAGAACCCTTACTTAAC 58.077 45.455 0.00 0.00 0.00 2.01
564 588 2.238521 GTTTGGTCAGATTCCCTTGCA 58.761 47.619 0.00 0.00 0.00 4.08
2819 4392 4.697352 GGAATGCGGCATATCAATAGTTCT 59.303 41.667 17.00 0.00 0.00 3.01
2913 4486 1.535462 GGCTGTTTGTGAATGCGTACT 59.465 47.619 0.00 0.00 0.00 2.73
2915 4488 2.223144 GCTGTTTGTGAATGCGTACTGA 59.777 45.455 0.00 0.00 0.00 3.41
2917 4490 3.198872 TGTTTGTGAATGCGTACTGACA 58.801 40.909 0.00 0.00 0.00 3.58
2918 4491 3.001838 TGTTTGTGAATGCGTACTGACAC 59.998 43.478 0.00 0.00 0.00 3.67
2924 4497 0.033366 ATGCGTACTGACACTGTGCA 59.967 50.000 7.90 6.25 35.10 4.57
4046 5992 5.411361 CCAACCGATAATTTTCTGACTCACA 59.589 40.000 0.00 0.00 0.00 3.58
4052 6002 4.345859 AATTTTCTGACTCACACCGGTA 57.654 40.909 6.87 0.00 0.00 4.02
4784 6752 6.226052 TCTAATTGATACTACAGGCATGCAG 58.774 40.000 21.36 13.91 0.00 4.41
5053 7143 6.624710 TTCACACGAAATCAAAAACACTTG 57.375 33.333 0.00 0.00 0.00 3.16
5350 7481 6.798427 AATTAAGTCAGTCCTCTATGCTCA 57.202 37.500 0.00 0.00 0.00 4.26
5607 7746 2.766263 CCACAGCCATCTCAGTAGGTAA 59.234 50.000 0.00 0.00 0.00 2.85
5608 7747 3.389329 CCACAGCCATCTCAGTAGGTAAT 59.611 47.826 0.00 0.00 0.00 1.89
5609 7748 4.588951 CCACAGCCATCTCAGTAGGTAATA 59.411 45.833 0.00 0.00 0.00 0.98
5610 7749 5.247110 CCACAGCCATCTCAGTAGGTAATAT 59.753 44.000 0.00 0.00 0.00 1.28
5611 7750 6.437477 CCACAGCCATCTCAGTAGGTAATATA 59.563 42.308 0.00 0.00 0.00 0.86
5654 7793 4.256110 ACTTGATTGATCTCGCAACATCA 58.744 39.130 0.00 0.00 0.00 3.07
5722 9370 2.102252 CTCTCAGTTGCTCCCATCTACC 59.898 54.545 0.00 0.00 0.00 3.18
6524 10812 5.195001 CTGCTTACAGGTTAGAGGAGATC 57.805 47.826 0.00 0.00 40.48 2.75
6534 10822 5.357596 AGGTTAGAGGAGATCGTAGTGAAAC 59.642 44.000 0.00 0.00 0.00 2.78
6799 11100 4.151883 TCTAGGCAATGAAGCAAACCTTT 58.848 39.130 0.00 0.00 32.78 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.639039 TGTTTCATCATCACTCACAAAGTTAC 58.361 34.615 0.00 0.00 35.45 2.50
4 5 6.309712 ACTGTTTCATCATCACTCACAAAG 57.690 37.500 0.00 0.00 0.00 2.77
175 178 4.577988 TCAGGAATCCGGAAACCATTAA 57.422 40.909 25.19 9.99 0.00 1.40
281 298 7.524717 TTCCCACAAAGAAATTAAGGAGAAG 57.475 36.000 0.00 0.00 0.00 2.85
564 588 7.715249 TGCTACTCATCTACAAAGAAAAACACT 59.285 33.333 0.00 0.00 34.73 3.55
2491 4063 3.648339 AACATGGAAATGAGCACACAC 57.352 42.857 0.00 0.00 0.00 3.82
2819 4392 3.178865 CCCTGAACCTGGGTAAAGTCTA 58.821 50.000 0.00 0.00 37.76 2.59
2913 4486 2.894879 GGCGTGTGCACAGTGTCA 60.895 61.111 22.40 0.00 45.35 3.58
2924 4497 0.385390 CAAAGCAGAAAAGGGCGTGT 59.615 50.000 0.00 0.00 34.54 4.49
3094 4673 1.512734 GTTACCACGTCGACGCGAT 60.513 57.895 35.92 23.15 44.43 4.58
4046 5992 3.770046 AGGTAAAAGCCAAAATACCGGT 58.230 40.909 13.98 13.98 42.10 5.28
4052 6002 6.740944 AACAACCTAGGTAAAAGCCAAAAT 57.259 33.333 16.67 0.00 0.00 1.82
5053 7143 7.519032 AGCTAGGTGTGTAGAGATTCTTATC 57.481 40.000 0.00 0.00 0.00 1.75
5170 7301 2.419667 CACAGTACCTAAACAACGGGG 58.580 52.381 0.00 0.00 0.00 5.73
5350 7481 4.538490 TGTAGTCCCCTGGAATTAACACAT 59.462 41.667 0.00 0.00 31.38 3.21
5654 7793 3.016031 TGCATGCCGTTTTGACTGATAT 58.984 40.909 16.68 0.00 0.00 1.63
5857 9505 0.172352 GGGACGACTCAGCAGAAGAG 59.828 60.000 0.00 0.00 39.04 2.85
6524 10812 6.985013 TGTTAGCATATTTCGTTTCACTACG 58.015 36.000 0.00 0.00 42.68 3.51
6716 11016 9.681692 TGCACTGATATGAATATTGCAAATTAC 57.318 29.630 1.71 0.00 33.51 1.89
6718 11018 9.602568 TTTGCACTGATATGAATATTGCAAATT 57.397 25.926 19.84 4.89 42.71 1.82
6799 11100 9.396022 GGTCTAAATTGGAGTCAAAATATGAGA 57.604 33.333 0.00 0.00 39.19 3.27
6822 11123 0.178990 ACAAGGTTGGGCTTCAGGTC 60.179 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.