Multiple sequence alignment - TraesCS6A01G089700

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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 TraesCS6A01G089700 chr6A 100.000 2549 0 0 1 2549 57900572 57903120 0.000000e+00 4708
1 TraesCS6A01G089700 chr6A 96.548 1970 63 2 584 2549 203520916 203518948 0.000000e+00 3256
2 TraesCS6A01G089700 chr6A 96.646 1968 49 3 588 2539 617222869 617220903 0.000000e+00 3253
3 TraesCS6A01G089700 chr2A 96.843 1964 58 4 587 2549 233255260 233257220 0.000000e+00 3280
4 TraesCS6A01G089700 chr2A 96.506 1975 61 7 580 2549 611725146 611723175 0.000000e+00 3258
5 TraesCS6A01G089700 chr2A 94.870 1969 91 8 583 2548 674415066 674413105 0.000000e+00 3068
6 TraesCS6A01G089700 chr3A 96.614 1979 50 3 586 2549 735555339 735557315 0.000000e+00 3267
7 TraesCS6A01G089700 chr7B 96.328 1988 55 4 580 2549 552932152 552930165 0.000000e+00 3251
8 TraesCS6A01G089700 chr2D 95.369 1965 81 7 588 2549 498471644 498469687 0.000000e+00 3116
9 TraesCS6A01G089700 chr2D 94.555 1965 72 11 588 2549 547242743 547240811 0.000000e+00 3003
10 TraesCS6A01G089700 chr2D 95.833 360 14 1 583 942 16065481 16065839 4.730000e-162 580
11 TraesCS6A01G089700 chrUn 93.738 543 24 3 54 587 19085509 19084968 0.000000e+00 806
12 TraesCS6A01G089700 chr6B 89.247 558 36 7 54 587 93836678 93837235 0.000000e+00 676
13 TraesCS6A01G089700 chr1B 93.838 357 22 0 586 942 645321435 645321791 2.890000e-149 538
14 TraesCS6A01G089700 chr5A 92.935 368 23 3 577 944 689409588 689409224 1.340000e-147 532


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 TraesCS6A01G089700 chr6A 57900572 57903120 2548 False 4708 4708 100.000 1 2549 1 chr6A.!!$F1 2548
1 TraesCS6A01G089700 chr6A 203518948 203520916 1968 True 3256 3256 96.548 584 2549 1 chr6A.!!$R1 1965
2 TraesCS6A01G089700 chr6A 617220903 617222869 1966 True 3253 3253 96.646 588 2539 1 chr6A.!!$R2 1951
3 TraesCS6A01G089700 chr2A 233255260 233257220 1960 False 3280 3280 96.843 587 2549 1 chr2A.!!$F1 1962
4 TraesCS6A01G089700 chr2A 611723175 611725146 1971 True 3258 3258 96.506 580 2549 1 chr2A.!!$R1 1969
5 TraesCS6A01G089700 chr2A 674413105 674415066 1961 True 3068 3068 94.870 583 2548 1 chr2A.!!$R2 1965
6 TraesCS6A01G089700 chr3A 735555339 735557315 1976 False 3267 3267 96.614 586 2549 1 chr3A.!!$F1 1963
7 TraesCS6A01G089700 chr7B 552930165 552932152 1987 True 3251 3251 96.328 580 2549 1 chr7B.!!$R1 1969
8 TraesCS6A01G089700 chr2D 498469687 498471644 1957 True 3116 3116 95.369 588 2549 1 chr2D.!!$R1 1961
9 TraesCS6A01G089700 chr2D 547240811 547242743 1932 True 3003 3003 94.555 588 2549 1 chr2D.!!$R2 1961
10 TraesCS6A01G089700 chrUn 19084968 19085509 541 True 806 806 93.738 54 587 1 chrUn.!!$R1 533
11 TraesCS6A01G089700 chr6B 93836678 93837235 557 False 676 676 89.247 54 587 1 chr6B.!!$F1 533

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
619 646 0.257328 TTTTGCCCTCAGTGGTGTCA 59.743 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2270 0.036671 AGTTACCAACGCAGCCCTAC 60.037 55.0 0.0 0.0 36.23 3.18 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
23 24 6.544928 ACATGATATGAACACCTAGACACA 57.455 37.500 0.00 0.00 0.00 3.72
24 25 6.946340 ACATGATATGAACACCTAGACACAA 58.054 36.000 0.00 0.00 0.00 3.33
25 26 6.818644 ACATGATATGAACACCTAGACACAAC 59.181 38.462 0.00 0.00 0.00 3.32
26 27 5.730550 TGATATGAACACCTAGACACAACC 58.269 41.667 0.00 0.00 0.00 3.77
27 28 5.247337 TGATATGAACACCTAGACACAACCA 59.753 40.000 0.00 0.00 0.00 3.67
28 29 3.188159 TGAACACCTAGACACAACCAC 57.812 47.619 0.00 0.00 0.00 4.16
29 30 2.502130 TGAACACCTAGACACAACCACA 59.498 45.455 0.00 0.00 0.00 4.17
30 31 3.055021 TGAACACCTAGACACAACCACAA 60.055 43.478 0.00 0.00 0.00 3.33
31 32 2.914059 ACACCTAGACACAACCACAAC 58.086 47.619 0.00 0.00 0.00 3.32
32 33 2.237643 ACACCTAGACACAACCACAACA 59.762 45.455 0.00 0.00 0.00 3.33
33 34 3.275143 CACCTAGACACAACCACAACAA 58.725 45.455 0.00 0.00 0.00 2.83
34 35 3.692101 CACCTAGACACAACCACAACAAA 59.308 43.478 0.00 0.00 0.00 2.83
35 36 3.692593 ACCTAGACACAACCACAACAAAC 59.307 43.478 0.00 0.00 0.00 2.93
36 37 3.945285 CCTAGACACAACCACAACAAACT 59.055 43.478 0.00 0.00 0.00 2.66
37 38 5.120399 CCTAGACACAACCACAACAAACTA 58.880 41.667 0.00 0.00 0.00 2.24
38 39 5.763204 CCTAGACACAACCACAACAAACTAT 59.237 40.000 0.00 0.00 0.00 2.12
39 40 5.751243 AGACACAACCACAACAAACTATC 57.249 39.130 0.00 0.00 0.00 2.08
40 41 5.189928 AGACACAACCACAACAAACTATCA 58.810 37.500 0.00 0.00 0.00 2.15
41 42 5.650266 AGACACAACCACAACAAACTATCAA 59.350 36.000 0.00 0.00 0.00 2.57
42 43 6.321181 AGACACAACCACAACAAACTATCAAT 59.679 34.615 0.00 0.00 0.00 2.57
43 44 7.500892 AGACACAACCACAACAAACTATCAATA 59.499 33.333 0.00 0.00 0.00 1.90
44 45 7.422399 ACACAACCACAACAAACTATCAATAC 58.578 34.615 0.00 0.00 0.00 1.89
45 46 6.861055 CACAACCACAACAAACTATCAATACC 59.139 38.462 0.00 0.00 0.00 2.73
46 47 6.775629 ACAACCACAACAAACTATCAATACCT 59.224 34.615 0.00 0.00 0.00 3.08
47 48 7.040686 ACAACCACAACAAACTATCAATACCTC 60.041 37.037 0.00 0.00 0.00 3.85
48 49 6.779860 ACCACAACAAACTATCAATACCTCT 58.220 36.000 0.00 0.00 0.00 3.69
49 50 7.913789 ACCACAACAAACTATCAATACCTCTA 58.086 34.615 0.00 0.00 0.00 2.43
50 51 7.822822 ACCACAACAAACTATCAATACCTCTAC 59.177 37.037 0.00 0.00 0.00 2.59
51 52 7.280205 CCACAACAAACTATCAATACCTCTACC 59.720 40.741 0.00 0.00 0.00 3.18
52 53 7.280205 CACAACAAACTATCAATACCTCTACCC 59.720 40.741 0.00 0.00 0.00 3.69
75 76 2.348666 CCGGTGACTCTCATTTTTAGCG 59.651 50.000 0.00 0.00 0.00 4.26
94 95 2.159653 GCGTGTGCTCATGGAGTAAAAG 60.160 50.000 9.85 0.00 38.39 2.27
105 106 7.148171 GCTCATGGAGTAAAAGACTTGCTATTT 60.148 37.037 0.00 0.00 39.06 1.40
293 310 1.751351 TGGCGGATGTTTTGTGTTCAA 59.249 42.857 0.00 0.00 0.00 2.69
294 311 2.124122 GGCGGATGTTTTGTGTTCAAC 58.876 47.619 0.00 0.00 32.93 3.18
320 340 4.201851 CGTTGTTAGAAGATTGAGCCATGG 60.202 45.833 7.63 7.63 0.00 3.66
459 485 1.154197 GGGTTTGTACTCGGTGAAGC 58.846 55.000 0.00 0.00 0.00 3.86
480 506 7.229306 TGAAGCTCACAAATGTTTCAGTCTATT 59.771 33.333 0.00 0.00 0.00 1.73
619 646 0.257328 TTTTGCCCTCAGTGGTGTCA 59.743 50.000 0.00 0.00 0.00 3.58
629 656 4.503123 CCTCAGTGGTGTCAATGTACTCAA 60.503 45.833 0.00 0.00 39.67 3.02
658 685 1.733912 TCAGATGCGAATTGTGCTCAC 59.266 47.619 0.00 0.00 0.00 3.51
702 729 1.462283 CGACTCGTTCCGTGAACTCTA 59.538 52.381 12.80 1.43 40.05 2.43
713 740 1.538950 GTGAACTCTACCGTCTCCGTT 59.461 52.381 0.00 0.00 0.00 4.44
755 782 1.151899 TTACAGGTGGGACCAGGCT 60.152 57.895 0.00 0.00 41.95 4.58
1280 1343 0.179062 GTCGATGCTCTGGCCAAGAT 60.179 55.000 7.01 0.00 37.74 2.40
1411 1474 3.441922 CACTGACAGAGAGCTAGCTGTTA 59.558 47.826 24.99 10.46 44.77 2.41
2114 2181 8.310122 AGGGCATTACATTGAGAAAAACATAT 57.690 30.769 0.00 0.00 0.00 1.78
2202 2270 2.411290 GCGTGGGTTTGTGGTGTG 59.589 61.111 0.00 0.00 0.00 3.82
2221 2289 0.036671 GTAGGGCTGCGTTGGTAACT 60.037 55.000 0.00 0.00 37.61 2.24
2516 2589 8.195617 TCATGACTTTTTGTTTGAATGAAACC 57.804 30.769 0.00 0.00 43.04 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.258727 GGTTGTGTCTAGGTGTTCATATCATG 59.741 42.308 0.00 0.00 0.00 3.07
4 5 5.581085 GTGGTTGTGTCTAGGTGTTCATATC 59.419 44.000 0.00 0.00 0.00 1.63
6 7 4.345547 TGTGGTTGTGTCTAGGTGTTCATA 59.654 41.667 0.00 0.00 0.00 2.15
9 10 3.188159 TGTGGTTGTGTCTAGGTGTTC 57.812 47.619 0.00 0.00 0.00 3.18
10 11 3.275999 GTTGTGGTTGTGTCTAGGTGTT 58.724 45.455 0.00 0.00 0.00 3.32
11 12 2.237643 TGTTGTGGTTGTGTCTAGGTGT 59.762 45.455 0.00 0.00 0.00 4.16
12 13 2.912771 TGTTGTGGTTGTGTCTAGGTG 58.087 47.619 0.00 0.00 0.00 4.00
13 14 3.637911 TTGTTGTGGTTGTGTCTAGGT 57.362 42.857 0.00 0.00 0.00 3.08
14 15 3.945285 AGTTTGTTGTGGTTGTGTCTAGG 59.055 43.478 0.00 0.00 0.00 3.02
15 16 6.481976 TGATAGTTTGTTGTGGTTGTGTCTAG 59.518 38.462 0.00 0.00 0.00 2.43
16 17 6.350103 TGATAGTTTGTTGTGGTTGTGTCTA 58.650 36.000 0.00 0.00 0.00 2.59
17 18 5.189928 TGATAGTTTGTTGTGGTTGTGTCT 58.810 37.500 0.00 0.00 0.00 3.41
18 19 5.493133 TGATAGTTTGTTGTGGTTGTGTC 57.507 39.130 0.00 0.00 0.00 3.67
19 20 5.906113 TTGATAGTTTGTTGTGGTTGTGT 57.094 34.783 0.00 0.00 0.00 3.72
20 21 6.861055 GGTATTGATAGTTTGTTGTGGTTGTG 59.139 38.462 0.00 0.00 0.00 3.33
21 22 6.775629 AGGTATTGATAGTTTGTTGTGGTTGT 59.224 34.615 0.00 0.00 0.00 3.32
22 23 7.174946 AGAGGTATTGATAGTTTGTTGTGGTTG 59.825 37.037 0.00 0.00 0.00 3.77
23 24 7.231467 AGAGGTATTGATAGTTTGTTGTGGTT 58.769 34.615 0.00 0.00 0.00 3.67
24 25 6.779860 AGAGGTATTGATAGTTTGTTGTGGT 58.220 36.000 0.00 0.00 0.00 4.16
25 26 7.280205 GGTAGAGGTATTGATAGTTTGTTGTGG 59.720 40.741 0.00 0.00 0.00 4.17
26 27 7.280205 GGGTAGAGGTATTGATAGTTTGTTGTG 59.720 40.741 0.00 0.00 0.00 3.33
27 28 7.336396 GGGTAGAGGTATTGATAGTTTGTTGT 58.664 38.462 0.00 0.00 0.00 3.32
28 29 6.766467 GGGGTAGAGGTATTGATAGTTTGTTG 59.234 42.308 0.00 0.00 0.00 3.33
29 30 6.126565 GGGGGTAGAGGTATTGATAGTTTGTT 60.127 42.308 0.00 0.00 0.00 2.83
30 31 5.368816 GGGGGTAGAGGTATTGATAGTTTGT 59.631 44.000 0.00 0.00 0.00 2.83
31 32 5.866207 GGGGGTAGAGGTATTGATAGTTTG 58.134 45.833 0.00 0.00 0.00 2.93
51 52 0.328258 AAAATGAGAGTCACCGGGGG 59.672 55.000 2.42 0.00 0.00 5.40
52 53 2.200373 AAAAATGAGAGTCACCGGGG 57.800 50.000 6.32 0.00 0.00 5.73
75 76 4.319177 AGTCTTTTACTCCATGAGCACAC 58.681 43.478 0.00 0.00 30.33 3.82
94 95 1.474077 CTGCACCCCAAATAGCAAGTC 59.526 52.381 0.00 0.00 36.44 3.01
105 106 0.260230 TTGTTTCCTTCTGCACCCCA 59.740 50.000 0.00 0.00 0.00 4.96
229 230 4.669206 TGTGGATTTTGCTGTTCAATGT 57.331 36.364 0.00 0.00 34.12 2.71
277 293 4.668289 ACGAAGTTGAACACAAAACATCC 58.332 39.130 0.00 0.00 37.78 3.51
294 311 4.690748 TGGCTCAATCTTCTAACAACGAAG 59.309 41.667 0.00 0.00 39.32 3.79
413 439 2.703416 TGATGTTCCTAGCACAAGCAG 58.297 47.619 0.00 0.00 45.49 4.24
442 468 2.475487 GTGAGCTTCACCGAGTACAAAC 59.525 50.000 0.00 0.00 41.37 2.93
598 625 0.550914 ACACCACTGAGGGCAAAAGA 59.449 50.000 0.00 0.00 43.89 2.52
619 646 5.324409 TCTGAGGGCAAAATTGAGTACATT 58.676 37.500 0.00 0.00 0.00 2.71
629 656 1.838112 TTCGCATCTGAGGGCAAAAT 58.162 45.000 5.18 0.00 0.00 1.82
658 685 1.305930 GCACGGACTAGGGGCAAAAG 61.306 60.000 0.00 0.00 0.00 2.27
755 782 2.192664 TAAAATTGGCCGTCTCTGCA 57.807 45.000 0.00 0.00 0.00 4.41
914 977 1.267574 CCCTCCACAGCTAGCTTCCA 61.268 60.000 16.46 0.00 0.00 3.53
1280 1343 5.999600 TCTTCTTGCAGTTCATTCATCAGAA 59.000 36.000 0.00 0.00 38.31 3.02
1363 1426 1.573108 TCGCCCTCCATCTCTTCTTT 58.427 50.000 0.00 0.00 0.00 2.52
1388 1451 1.818060 CAGCTAGCTCTCTGTCAGTGT 59.182 52.381 16.15 0.00 0.00 3.55
1411 1474 5.942826 CCTTCTTCTTCAACATCCTAAGCTT 59.057 40.000 3.48 3.48 0.00 3.74
2202 2270 0.036671 AGTTACCAACGCAGCCCTAC 60.037 55.000 0.00 0.00 36.23 3.18
2221 2289 2.040278 AGTCTTGCCATTTGTCCTAGCA 59.960 45.455 0.00 0.00 0.00 3.49
2516 2589 3.787001 GGGGGTGAGAAGCCCTCG 61.787 72.222 12.46 0.00 44.92 4.63


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

AutoCloner maintained by Alex Coulton.