Multiple sequence alignment - TraesCS6A01G152300

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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 TraesCS6A01G152300 chr6A 100.000 3240 0 0 1 3240 137336421 137339660 0.000000e+00 5984
1 TraesCS6A01G152300 chr6A 96.860 1624 46 4 859 2478 577735415 577737037 0.000000e+00 2712
2 TraesCS6A01G152300 chr6A 94.718 1382 67 2 1 1382 201757958 201759333 0.000000e+00 2143
3 TraesCS6A01G152300 chr6A 95.455 88 4 0 1413 1500 201759331 201759418 1.210000e-29 141
4 TraesCS6A01G152300 chr2A 97.848 2741 56 3 1 2740 468299916 468297178 0.000000e+00 4732
5 TraesCS6A01G152300 chr2B 95.885 2746 104 8 1 2743 289895687 289892948 0.000000e+00 4436
6 TraesCS6A01G152300 chr6B 94.681 2745 127 11 1 2739 144956100 144958831 0.000000e+00 4242
7 TraesCS6A01G152300 chr4A 94.647 2746 128 10 1 2740 583957308 583954576 0.000000e+00 4239
8 TraesCS6A01G152300 chr4A 94.246 2155 107 9 592 2740 583960985 583958842 0.000000e+00 3277
9 TraesCS6A01G152300 chr2D 93.392 2482 136 13 1 2478 465151790 465154247 0.000000e+00 3650
10 TraesCS6A01G152300 chr3D 98.228 1524 25 1 1 1524 18300480 18302001 0.000000e+00 2663
11 TraesCS6A01G152300 chr3D 98.187 1158 20 1 1587 2744 18302002 18303158 0.000000e+00 2021
12 TraesCS6A01G152300 chr7A 95.804 1430 51 2 1 1430 577210135 577211555 0.000000e+00 2300
13 TraesCS6A01G152300 chr7A 95.803 1382 55 2 1 1382 654304394 654305772 0.000000e+00 2228
14 TraesCS6A01G152300 chr7A 94.002 1167 63 6 1578 2739 577211951 577213115 0.000000e+00 1760
15 TraesCS6A01G152300 chr7A 92.829 502 35 1 2739 3240 351027752 351027252 0.000000e+00 726
16 TraesCS6A01G152300 chr1A 94.632 503 25 2 2739 3240 371278681 371278180 0.000000e+00 778
17 TraesCS6A01G152300 chr1A 93.439 503 32 1 2739 3240 82466701 82467203 0.000000e+00 745
18 TraesCS6A01G152300 chr3A 93.426 502 33 0 2739 3240 87086500 87085999 0.000000e+00 745
19 TraesCS6A01G152300 chr3A 93.227 502 34 0 2739 3240 562805530 562805029 0.000000e+00 739
20 TraesCS6A01G152300 chr3A 92.644 503 35 2 2739 3240 443511064 443510563 0.000000e+00 723
21 TraesCS6A01G152300 chr5A 93.227 502 34 0 2739 3240 113947207 113946706 0.000000e+00 739
22 TraesCS6A01G152300 chrUn 92.430 502 38 0 2739 3240 33910967 33911468 0.000000e+00 717
23 TraesCS6A01G152300 chrUn 92.231 502 39 0 2739 3240 33790551 33791052 0.000000e+00 712


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 TraesCS6A01G152300 chr6A 137336421 137339660 3239 False 5984 5984 100.0000 1 3240 1 chr6A.!!$F1 3239
1 TraesCS6A01G152300 chr6A 577735415 577737037 1622 False 2712 2712 96.8600 859 2478 1 chr6A.!!$F2 1619
2 TraesCS6A01G152300 chr6A 201757958 201759418 1460 False 1142 2143 95.0865 1 1500 2 chr6A.!!$F3 1499
3 TraesCS6A01G152300 chr2A 468297178 468299916 2738 True 4732 4732 97.8480 1 2740 1 chr2A.!!$R1 2739
4 TraesCS6A01G152300 chr2B 289892948 289895687 2739 True 4436 4436 95.8850 1 2743 1 chr2B.!!$R1 2742
5 TraesCS6A01G152300 chr6B 144956100 144958831 2731 False 4242 4242 94.6810 1 2739 1 chr6B.!!$F1 2738
6 TraesCS6A01G152300 chr4A 583954576 583960985 6409 True 3758 4239 94.4465 1 2740 2 chr4A.!!$R1 2739
7 TraesCS6A01G152300 chr2D 465151790 465154247 2457 False 3650 3650 93.3920 1 2478 1 chr2D.!!$F1 2477
8 TraesCS6A01G152300 chr3D 18300480 18303158 2678 False 2342 2663 98.2075 1 2744 2 chr3D.!!$F1 2743
9 TraesCS6A01G152300 chr7A 654304394 654305772 1378 False 2228 2228 95.8030 1 1382 1 chr7A.!!$F1 1381
10 TraesCS6A01G152300 chr7A 577210135 577213115 2980 False 2030 2300 94.9030 1 2739 2 chr7A.!!$F2 2738
11 TraesCS6A01G152300 chr7A 351027252 351027752 500 True 726 726 92.8290 2739 3240 1 chr7A.!!$R1 501
12 TraesCS6A01G152300 chr1A 371278180 371278681 501 True 778 778 94.6320 2739 3240 1 chr1A.!!$R1 501
13 TraesCS6A01G152300 chr1A 82466701 82467203 502 False 745 745 93.4390 2739 3240 1 chr1A.!!$F1 501
14 TraesCS6A01G152300 chr3A 87085999 87086500 501 True 745 745 93.4260 2739 3240 1 chr3A.!!$R1 501
15 TraesCS6A01G152300 chr3A 562805029 562805530 501 True 739 739 93.2270 2739 3240 1 chr3A.!!$R3 501
16 TraesCS6A01G152300 chr3A 443510563 443511064 501 True 723 723 92.6440 2739 3240 1 chr3A.!!$R2 501
17 TraesCS6A01G152300 chr5A 113946706 113947207 501 True 739 739 93.2270 2739 3240 1 chr5A.!!$R1 501
18 TraesCS6A01G152300 chrUn 33910967 33911468 501 False 717 717 92.4300 2739 3240 1 chrUn.!!$F2 501
19 TraesCS6A01G152300 chrUn 33790551 33791052 501 False 712 712 92.2310 2739 3240 1 chrUn.!!$F1 501

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
152 3830 2.003548 GCAGGGTGGGAGGGATCTT 61.004 63.158 0.00 0.0 0.00 2.40 F
950 4631 3.971245 TTGTTTGTGCTGAAACCCTTT 57.029 38.095 8.19 0.0 35.34 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 4783 1.801178 CTTGTCCCTTTGCTTCTCGAC 59.199 52.381 0.0 0.0 0.00 4.20 R
2749 6685 0.609662 GGTGGTCGCACCTTAGGTTA 59.390 55.000 0.0 0.0 41.84 2.85 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
54 3732 4.586421 TGTGCCTTCAAAATATGTGGACAA 59.414 37.500 0.00 0.00 0.00 3.18
63 3741 5.914898 AAATATGTGGACAAGTTTAGGGC 57.085 39.130 0.00 0.00 0.00 5.19
152 3830 2.003548 GCAGGGTGGGAGGGATCTT 61.004 63.158 0.00 0.00 0.00 2.40
485 4164 5.195940 AGCCTTTGCAGCTATTAAGAATCA 58.804 37.500 0.00 0.00 39.29 2.57
950 4631 3.971245 TTGTTTGTGCTGAAACCCTTT 57.029 38.095 8.19 0.00 35.34 3.11
984 4665 8.655092 GCTGACATAATAGCATATTGACTTCTC 58.345 37.037 0.00 0.00 39.67 2.87
1087 4768 6.957631 TGGAGTGATGATTGTACCAAGTATT 58.042 36.000 0.00 0.00 0.00 1.89
1102 4783 5.415701 ACCAAGTATTTGCTTGAGTGGTATG 59.584 40.000 9.60 0.00 46.34 2.39
1174 4857 6.484643 ACACCATCTACAATGTGCTAATGATC 59.515 38.462 0.00 0.00 0.00 2.92
1430 5113 8.807667 ATCATTCTTGTTTTTGCTAAACTGAG 57.192 30.769 13.57 11.57 0.00 3.35
1468 5151 4.439305 TGAAAATGGCATGCTAGTGTTC 57.561 40.909 18.92 15.71 0.00 3.18
1571 5256 8.877808 TTGTTTTATAATCATTGTTGTGCACA 57.122 26.923 17.42 17.42 0.00 4.57
1684 5615 8.206867 CACTCCATCAAGTTTTATCATCTCCTA 58.793 37.037 0.00 0.00 0.00 2.94
1848 5779 0.322816 ATGATTGCGCCCAACAGTCT 60.323 50.000 4.18 0.00 32.95 3.24
1979 5910 2.610433 CGAGCATTGTGAGTCTTGCTA 58.390 47.619 9.41 0.00 44.98 3.49
1994 5925 7.931407 TGAGTCTTGCTAAAACTGTGAAATCTA 59.069 33.333 0.00 0.00 0.00 1.98
1997 5928 9.204570 GTCTTGCTAAAACTGTGAAATCTACTA 57.795 33.333 0.00 0.00 0.00 1.82
2428 6362 4.842531 TTCCTGATGCTTGATGACCTTA 57.157 40.909 0.00 0.00 0.00 2.69
2749 6685 5.289510 ACCAATCAACCTCTTATACCCTCT 58.710 41.667 0.00 0.00 0.00 3.69
2798 6734 0.754472 GACCCGGATTATCAACCCGA 59.246 55.000 0.73 0.00 45.58 5.14
2946 6882 4.715792 TGGTGAAAACATGATATTGCCCAT 59.284 37.500 0.00 0.00 0.00 4.00
2951 6887 9.979578 GTGAAAACATGATATTGCCCATTATTA 57.020 29.630 0.00 0.00 0.00 0.98
2975 6911 1.486310 TGCTTCGGGTTGCTCTGATAT 59.514 47.619 0.00 0.00 0.00 1.63
2977 6913 2.483714 GCTTCGGGTTGCTCTGATATCA 60.484 50.000 5.07 5.07 0.00 2.15
3089 7026 2.023414 TAGAACCGCCACCGCCATAG 62.023 60.000 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 3732 2.361230 GCTTGCGGGCCCTAAACT 60.361 61.111 22.43 0.00 0.00 2.66
63 3741 1.898574 GTGGGATATGGCTTGCGGG 60.899 63.158 0.00 0.00 0.00 6.13
152 3830 4.773013 TGCAATACAGCAGAATCATGAGA 58.227 39.130 0.09 0.00 40.11 3.27
363 4042 3.057174 GGAACTCCTGTAGATGATAGCGG 60.057 52.174 0.00 0.00 0.00 5.52
692 4371 6.285224 CACATATGTTGGGCAATCAAATCAT 58.715 36.000 5.37 0.00 0.00 2.45
984 4665 6.016777 GCTCACCCATTCTATAAATGAAGGTG 60.017 42.308 14.78 14.78 39.35 4.00
1087 4768 2.560981 TCTCGACATACCACTCAAGCAA 59.439 45.455 0.00 0.00 0.00 3.91
1102 4783 1.801178 CTTGTCCCTTTGCTTCTCGAC 59.199 52.381 0.00 0.00 0.00 4.20
1174 4857 6.583806 GCTGTAATTCCAAACTTGTCATTCAG 59.416 38.462 0.00 0.00 0.00 3.02
1544 5229 9.190858 GTGCACAACAATGATTATAAAACAAGA 57.809 29.630 13.17 0.00 0.00 3.02
1571 5256 8.375506 TGTTTGAGTAGTCTGGTCAATCTAATT 58.624 33.333 0.00 0.00 30.50 1.40
1572 5257 7.907389 TGTTTGAGTAGTCTGGTCAATCTAAT 58.093 34.615 0.00 0.00 30.50 1.73
1684 5615 5.299782 AGACGAGTCACTAAACAGTTCTTCT 59.700 40.000 5.99 0.00 0.00 2.85
1848 5779 1.852633 TGAGCTAGTGCCTTCTGCTA 58.147 50.000 0.00 0.00 42.00 3.49
1979 5910 6.449830 AGGGGTAGTAGATTTCACAGTTTT 57.550 37.500 0.00 0.00 0.00 2.43
1994 5925 3.328050 GCTATTGGCTGAATAGGGGTAGT 59.672 47.826 14.20 0.00 42.77 2.73
1997 5928 2.107204 CTGCTATTGGCTGAATAGGGGT 59.893 50.000 14.20 0.00 42.77 4.95
2550 6485 5.036117 ACCAAATATGCATAACTCGTCCT 57.964 39.130 11.13 0.00 0.00 3.85
2643 6579 3.191078 CCAACATTTGGCAAGTTTGGA 57.809 42.857 22.52 0.74 45.17 3.53
2734 6670 6.163680 ACCTTAGGTTAGAGGGTATAAGAGGT 59.836 42.308 0.00 0.00 37.36 3.85
2749 6685 0.609662 GGTGGTCGCACCTTAGGTTA 59.390 55.000 0.00 0.00 41.84 2.85
2946 6882 4.076394 AGCAACCCGAAGCAGTTTAATAA 58.924 39.130 0.00 0.00 0.00 1.40
2951 6887 0.179018 AGAGCAACCCGAAGCAGTTT 60.179 50.000 0.00 0.00 0.00 2.66
2975 6911 1.672363 CAGCAGCAACAACAGTCTTGA 59.328 47.619 0.00 0.00 0.00 3.02
2977 6913 1.672881 GTCAGCAGCAACAACAGTCTT 59.327 47.619 0.00 0.00 0.00 3.01
3031 6968 8.706322 AGGAAATCAAGGTAATTACAACAACT 57.294 30.769 17.16 2.04 0.00 3.16
3089 7026 4.459089 GGCTCTCACGGTCTGGGC 62.459 72.222 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.