Multiple sequence alignment - TraesCS6A01G075400

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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 TraesCS6A01G075400 chr6A 100.000 1646 0 0 1 1646 45406575 45408220 0.000000e+00 3040.0
1 TraesCS6A01G075400 chr6A 100.000 582 0 0 1970 2551 45408544 45409125 0.000000e+00 1075.0
2 TraesCS6A01G075400 chr6A 84.818 685 100 4 4 687 13083631 13082950 0.000000e+00 686.0
3 TraesCS6A01G075400 chr6A 79.484 697 89 34 850 1533 16720326 16719671 1.800000e-121 446.0
4 TraesCS6A01G075400 chr3D 94.530 841 41 3 758 1594 603321283 603322122 0.000000e+00 1293.0
5 TraesCS6A01G075400 chr3D 87.459 606 28 9 1970 2551 603322184 603322765 0.000000e+00 654.0
6 TraesCS6A01G075400 chrUn 92.086 935 38 9 713 1646 112539923 112539024 0.000000e+00 1284.0
7 TraesCS6A01G075400 chrUn 95.017 582 29 0 1970 2551 112538989 112538408 0.000000e+00 915.0
8 TraesCS6A01G075400 chrUn 90.196 153 15 0 2399 2551 95996417 95996569 1.550000e-47 200.0
9 TraesCS6A01G075400 chr6B 90.299 835 63 8 713 1533 77989399 77990229 0.000000e+00 1077.0
10 TraesCS6A01G075400 chr6B 90.433 669 47 7 994 1646 78267520 78268187 0.000000e+00 865.0
11 TraesCS6A01G075400 chr6B 90.235 553 40 6 994 1533 78312049 78312600 0.000000e+00 710.0
12 TraesCS6A01G075400 chr6B 87.285 582 41 6 1975 2529 77990414 77990989 3.580000e-178 634.0
13 TraesCS6A01G075400 chr6B 81.818 781 102 18 782 1544 59100352 59101110 1.000000e-173 619.0
14 TraesCS6A01G075400 chr6B 89.783 323 26 3 2207 2528 78271167 78271483 8.500000e-110 407.0
15 TraesCS6A01G075400 chr6B 89.783 323 26 3 2207 2528 78315735 78316051 8.500000e-110 407.0
16 TraesCS6A01G075400 chr6B 88.415 328 32 2 2202 2528 78273773 78274095 8.560000e-105 390.0
17 TraesCS6A01G075400 chr6B 88.415 328 32 2 2202 2528 78318382 78318704 8.560000e-105 390.0
18 TraesCS6A01G075400 chr6B 93.506 154 7 1 1496 1646 78312623 78312776 2.550000e-55 226.0
19 TraesCS6A01G075400 chr6B 90.196 153 12 2 1496 1645 77990222 77990374 2.000000e-46 196.0
20 TraesCS6A01G075400 chr6B 97.368 38 1 0 1496 1533 78312593 78312630 5.890000e-07 65.8
21 TraesCS6A01G075400 chr5A 94.614 687 35 1 1 687 403283051 403283735 0.000000e+00 1062.0
22 TraesCS6A01G075400 chr5A 84.942 684 101 2 4 687 514202649 514201968 0.000000e+00 691.0
23 TraesCS6A01G075400 chr1A 94.178 687 37 2 1 687 540141089 540141772 0.000000e+00 1044.0
24 TraesCS6A01G075400 chr5B 93.459 688 42 2 1 688 629905837 629906521 0.000000e+00 1018.0
25 TraesCS6A01G075400 chr5B 84.431 167 26 0 1303 1469 629926058 629925892 5.650000e-37 165.0
26 TraesCS6A01G075400 chr3B 92.868 687 47 2 1 687 547149561 547150245 0.000000e+00 996.0
27 TraesCS6A01G075400 chr3B 93.587 421 24 3 758 1175 810520715 810520295 2.150000e-175 625.0
28 TraesCS6A01G075400 chr3B 96.567 233 8 0 1970 2202 810520095 810519863 1.110000e-103 387.0
29 TraesCS6A01G075400 chr3B 93.567 171 8 1 1479 1646 810520302 810520132 4.210000e-63 252.0
30 TraesCS6A01G075400 chr3B 90.728 151 12 2 2402 2551 420877284 420877135 1.550000e-47 200.0
31 TraesCS6A01G075400 chr3A 92.878 688 26 3 1 688 728411105 728411769 0.000000e+00 977.0
32 TraesCS6A01G075400 chr1B 90.196 663 62 3 25 687 451559465 451560124 0.000000e+00 861.0
33 TraesCS6A01G075400 chr1B 80.909 660 74 33 849 1500 587472755 587473370 8.260000e-130 473.0
34 TraesCS6A01G075400 chr7D 87.500 688 82 4 2 689 70057925 70057242 0.000000e+00 791.0
35 TraesCS6A01G075400 chr7D 87.302 63 8 0 2202 2264 71314485 71314547 3.520000e-09 73.1
36 TraesCS6A01G075400 chr5D 87.209 172 22 0 1298 1469 509024206 509024035 2.000000e-46 196.0
37 TraesCS6A01G075400 chr5D 83.832 167 27 0 1303 1469 501449774 501449608 2.630000e-35 159.0
38 TraesCS6A01G075400 chr7B 90.476 63 6 0 2202 2264 13801878 13801940 1.630000e-12 84.2


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 TraesCS6A01G075400 chr6A 45406575 45409125 2550 False 2057.500000 3040 100.000000 1 2551 2 chr6A.!!$F1 2550
1 TraesCS6A01G075400 chr6A 13082950 13083631 681 True 686.000000 686 84.818000 4 687 1 chr6A.!!$R1 683
2 TraesCS6A01G075400 chr6A 16719671 16720326 655 True 446.000000 446 79.484000 850 1533 1 chr6A.!!$R2 683
3 TraesCS6A01G075400 chr3D 603321283 603322765 1482 False 973.500000 1293 90.994500 758 2551 2 chr3D.!!$F1 1793
4 TraesCS6A01G075400 chrUn 112538408 112539923 1515 True 1099.500000 1284 93.551500 713 2551 2 chrUn.!!$R1 1838
5 TraesCS6A01G075400 chr6B 77989399 77990989 1590 False 635.666667 1077 89.260000 713 2529 3 chr6B.!!$F2 1816
6 TraesCS6A01G075400 chr6B 59100352 59101110 758 False 619.000000 619 81.818000 782 1544 1 chr6B.!!$F1 762
7 TraesCS6A01G075400 chr6B 78267520 78274095 6575 False 554.000000 865 89.543667 994 2528 3 chr6B.!!$F3 1534
8 TraesCS6A01G075400 chr6B 78312049 78318704 6655 False 359.760000 710 91.861400 994 2528 5 chr6B.!!$F4 1534
9 TraesCS6A01G075400 chr5A 403283051 403283735 684 False 1062.000000 1062 94.614000 1 687 1 chr5A.!!$F1 686
10 TraesCS6A01G075400 chr5A 514201968 514202649 681 True 691.000000 691 84.942000 4 687 1 chr5A.!!$R1 683
11 TraesCS6A01G075400 chr1A 540141089 540141772 683 False 1044.000000 1044 94.178000 1 687 1 chr1A.!!$F1 686
12 TraesCS6A01G075400 chr5B 629905837 629906521 684 False 1018.000000 1018 93.459000 1 688 1 chr5B.!!$F1 687
13 TraesCS6A01G075400 chr3B 547149561 547150245 684 False 996.000000 996 92.868000 1 687 1 chr3B.!!$F1 686
14 TraesCS6A01G075400 chr3B 810519863 810520715 852 True 421.333333 625 94.573667 758 2202 3 chr3B.!!$R2 1444
15 TraesCS6A01G075400 chr3A 728411105 728411769 664 False 977.000000 977 92.878000 1 688 1 chr3A.!!$F1 687
16 TraesCS6A01G075400 chr1B 451559465 451560124 659 False 861.000000 861 90.196000 25 687 1 chr1B.!!$F1 662
17 TraesCS6A01G075400 chr1B 587472755 587473370 615 False 473.000000 473 80.909000 849 1500 1 chr1B.!!$F2 651
18 TraesCS6A01G075400 chr7D 70057242 70057925 683 True 791.000000 791 87.500000 2 689 1 chr7D.!!$R1 687

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
248 252 2.010497 GGCTTTTGGAAGATCGGAGAC 58.990 52.381 0.00 0.0 34.07 3.36 F
378 383 2.123897 GCGAGGCCCTCTCTCTCT 60.124 66.667 9.52 0.0 40.30 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1094 1.300233 CTTGAGGTAGCGCCCGATC 60.300 63.158 2.29 0.0 38.26 3.69 R
2279 5115 1.070758 TGTCTGCAGGACTTCTGTTCC 59.929 52.381 15.13 0.0 45.08 3.62 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
235 239 3.655486 TGAATGTTGATGCAGGCTTTTG 58.345 40.909 0.00 0.00 0.00 2.44
248 252 2.010497 GGCTTTTGGAAGATCGGAGAC 58.990 52.381 0.00 0.00 34.07 3.36
378 383 2.123897 GCGAGGCCCTCTCTCTCT 60.124 66.667 9.52 0.00 40.30 3.10
379 384 2.193536 GCGAGGCCCTCTCTCTCTC 61.194 68.421 9.52 0.00 40.30 3.20
552 557 4.991056 TCATGAGAATAGGAAGCATAACGC 59.009 41.667 0.00 0.00 42.91 4.84
777 783 5.146010 AGAAACAAGCAAAGTTGACCAAA 57.854 34.783 0.00 0.00 0.00 3.28
810 816 4.179579 GCCAAATCGGTGCGCTCC 62.180 66.667 18.51 18.51 36.97 4.70
845 851 2.442272 CTCCCACGGATCGACCCT 60.442 66.667 0.00 0.00 34.64 4.34
974 984 2.277373 CGCACCTCGAGTAGCGTC 60.277 66.667 29.36 8.81 39.54 5.19
1210 1229 3.317603 TTGTTCGACATCTGATCTGCA 57.682 42.857 0.00 0.00 0.00 4.41
1370 1399 3.333189 CGCCACCTGATGATCGCG 61.333 66.667 0.00 0.00 0.00 5.87
1469 1498 3.435186 GCGCTGCTCCCCAAGAAC 61.435 66.667 0.00 0.00 0.00 3.01
1554 1649 1.135402 CCGCAGCCACAAATTAAGGAC 60.135 52.381 0.00 0.00 0.00 3.85
1573 1668 4.406972 AGGACTAGCTGTCTGCAATTGATA 59.593 41.667 10.34 0.00 44.74 2.15
1618 1713 6.642131 GCTTTTGCTTCTGAACATTTGTCATA 59.358 34.615 0.00 0.00 43.35 2.15
1994 2089 2.239907 AGTACTCAATTTCAGCCCCTCC 59.760 50.000 0.00 0.00 0.00 4.30
2047 2142 2.019984 CCTATCAAGCTGCAGGAAACC 58.980 52.381 17.12 0.00 0.00 3.27
2124 2221 1.954927 CGGGGGAAGCTTATGAGTTC 58.045 55.000 0.00 0.00 0.00 3.01
2291 5127 2.003301 GATGCTTCGGAACAGAAGTCC 58.997 52.381 13.94 2.41 46.82 3.85
2326 5162 4.599041 TGCCAAGTTATAGCTTGACCATT 58.401 39.130 25.73 0.00 46.34 3.16
2327 5163 4.398988 TGCCAAGTTATAGCTTGACCATTG 59.601 41.667 25.73 12.07 46.34 2.82
2364 5200 4.215613 GCAGACAATTTAACCTTCCGAACT 59.784 41.667 0.00 0.00 0.00 3.01
2409 5245 4.143986 GCTAGATGCAAACTACTCCCTT 57.856 45.455 0.00 0.00 42.31 3.95
2410 5246 4.518249 GCTAGATGCAAACTACTCCCTTT 58.482 43.478 0.00 0.00 42.31 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
378 383 0.539438 AACCTGCAAATCCAAGGCGA 60.539 50.000 0.00 0.00 0.00 5.54
379 384 0.109132 GAACCTGCAAATCCAAGGCG 60.109 55.000 0.00 0.00 0.00 5.52
489 494 0.534412 ATGACTCCTCTCGTGCTTGG 59.466 55.000 0.00 0.00 0.00 3.61
615 620 9.561069 GGATACAGATAATATCGGGCAAAATAT 57.439 33.333 5.47 0.00 30.94 1.28
739 744 9.174166 TGCTTGTTTCTAAGTCTTCTTTAAAGT 57.826 29.630 14.74 0.00 35.36 2.66
761 766 2.159114 ACGCATTTGGTCAACTTTGCTT 60.159 40.909 9.31 0.93 0.00 3.91
810 816 2.180204 GCACCGGATGGACCAATCG 61.180 63.158 9.46 5.53 39.21 3.34
985 995 1.382692 GCCATCTTGCTGCTTCTCCC 61.383 60.000 0.00 0.00 0.00 4.30
1059 1073 2.995574 CCGACGGGGAACTGGAGT 60.996 66.667 5.81 0.00 42.76 3.85
1080 1094 1.300233 CTTGAGGTAGCGCCCGATC 60.300 63.158 2.29 0.00 38.26 3.69
1210 1229 1.470996 GGCAGATGCTCGAGGAGGAT 61.471 60.000 15.58 0.00 43.17 3.24
1494 1586 2.351276 GGCGGCCTTCTTCTTGGA 59.649 61.111 12.87 0.00 0.00 3.53
1554 1649 6.259387 TCACAATATCAATTGCAGACAGCTAG 59.741 38.462 0.00 0.00 45.41 3.42
1573 1668 2.019249 CAGGTGGCGATCATTCACAAT 58.981 47.619 10.77 0.00 33.45 2.71
2021 2116 3.969976 TCCTGCAGCTTGATAGGTCTATT 59.030 43.478 8.66 0.00 0.00 1.73
2047 2142 5.685954 CAGGCATGATTCATTCAAAGATTCG 59.314 40.000 0.00 0.00 38.03 3.34
2124 2221 5.692204 AGAACGTAGAAGATGGAAATATGCG 59.308 40.000 0.00 0.00 0.00 4.73
2279 5115 1.070758 TGTCTGCAGGACTTCTGTTCC 59.929 52.381 15.13 0.00 45.08 3.62
2291 5127 4.445452 AACTTGGCATATTTGTCTGCAG 57.555 40.909 7.63 7.63 40.18 4.41
2306 5142 6.124088 GACAATGGTCAAGCTATAACTTGG 57.876 41.667 14.37 2.12 45.77 3.61
2364 5200 3.994392 GTCGAATGCTTCTCAGGTTTGTA 59.006 43.478 0.00 0.00 0.00 2.41
2409 5245 7.504574 GCTAAAAGGCCTTATATTAGGGAACAA 59.495 37.037 26.13 1.83 35.74 2.83
2410 5246 7.002276 GCTAAAAGGCCTTATATTAGGGAACA 58.998 38.462 26.13 2.41 35.74 3.18


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

AutoCloner maintained by Alex Coulton.