Multiple sequence alignment - TraesCS6D01G371700

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 TraesCS6D01G371700 chr6D 100.000 2558 0 0 1 2558 456949088 456951645 0.000000e+00 4724.0
1 TraesCS6D01G371700 chr6D 85.920 902 70 13 715 1567 470543284 470544177 0.000000e+00 909.0
2 TraesCS6D01G371700 chr6D 92.723 481 32 3 2081 2558 388529260 388528780 0.000000e+00 691.0
3 TraesCS6D01G371700 chr6D 92.067 479 36 2 2081 2558 388440639 388440162 0.000000e+00 673.0
4 TraesCS6D01G371700 chr6D 84.169 379 39 16 1 366 83485527 83485897 5.240000e-92 348.0
5 TraesCS6D01G371700 chr5A 95.928 1719 47 9 3 1706 602795676 602793966 0.000000e+00 2765.0
6 TraesCS6D01G371700 chr5A 96.610 826 20 6 9 830 602820127 602819306 0.000000e+00 1363.0
7 TraesCS6D01G371700 chr5A 94.620 855 26 6 869 1706 602818795 602817944 0.000000e+00 1306.0
8 TraesCS6D01G371700 chr5A 91.714 881 47 3 1704 2558 602792500 602791620 0.000000e+00 1199.0
9 TraesCS6D01G371700 chr5A 93.139 481 30 3 2081 2558 602709787 602709307 0.000000e+00 702.0
10 TraesCS6D01G371700 chr5A 92.739 482 31 4 2081 2558 27797101 27796620 0.000000e+00 693.0
11 TraesCS6D01G371700 chr5A 95.330 364 17 0 1704 2067 602816159 602815796 1.710000e-161 579.0
12 TraesCS6D01G371700 chr6A 86.129 757 54 15 853 1567 615309099 615309846 0.000000e+00 769.0
13 TraesCS6D01G371700 chr6A 83.746 849 74 15 734 1534 615271757 615272589 0.000000e+00 745.0
14 TraesCS6D01G371700 chr6A 87.500 120 12 2 704 822 615308984 615309101 4.440000e-28 135.0
15 TraesCS6D01G371700 chr6B 84.813 777 77 20 820 1567 720612845 720612081 0.000000e+00 743.0
16 TraesCS6D01G371700 chr6B 90.244 41 3 1 639 678 118554434 118554394 5.000000e-03 52.8
17 TraesCS6D01G371700 chr1D 92.308 481 33 4 2081 2558 284715136 284714657 0.000000e+00 680.0
18 TraesCS6D01G371700 chr1D 82.008 239 27 6 343 579 250221580 250221804 3.360000e-44 189.0
19 TraesCS6D01G371700 chr3D 92.340 483 28 6 2081 2558 541664448 541664926 0.000000e+00 678.0
20 TraesCS6D01G371700 chr3D 84.404 109 12 5 474 579 431446572 431446466 4.500000e-18 102.0
21 TraesCS6D01G371700 chr3D 84.416 77 12 0 592 668 224514611 224514687 2.730000e-10 76.8
22 TraesCS6D01G371700 chr2B 91.875 480 35 4 2081 2556 389453616 389454095 0.000000e+00 667.0
23 TraesCS6D01G371700 chr5B 91.684 481 34 6 2082 2558 255303362 255303840 0.000000e+00 662.0
24 TraesCS6D01G371700 chr5B 78.676 136 17 9 328 458 509820579 509820451 2.110000e-11 80.5
25 TraesCS6D01G371700 chr2D 80.339 590 76 27 9 586 20321747 20322308 6.590000e-111 411.0
26 TraesCS6D01G371700 chr7D 87.320 347 31 8 24 360 602796795 602797138 3.990000e-103 385.0
27 TraesCS6D01G371700 chr7D 84.987 373 41 11 1 360 20000092 20000462 5.200000e-97 364.0
28 TraesCS6D01G371700 chr7D 85.479 365 35 15 5 360 609440518 609440873 5.200000e-97 364.0
29 TraesCS6D01G371700 chr7D 84.737 380 36 14 1 365 72769739 72769367 6.730000e-96 361.0
30 TraesCS6D01G371700 chr7D 79.694 458 65 14 135 579 180715852 180716294 3.200000e-79 305.0
31 TraesCS6D01G371700 chr7A 87.179 351 30 11 24 364 144571817 144571472 3.990000e-103 385.0
32 TraesCS6D01G371700 chr7A 82.353 85 15 0 594 678 728324926 728325010 9.820000e-10 75.0
33 TraesCS6D01G371700 chr5D 85.791 373 42 9 1 365 537172795 537172426 3.990000e-103 385.0
34 TraesCS6D01G371700 chr7B 78.982 452 45 26 135 571 687811010 687811426 1.950000e-66 263.0
35 TraesCS6D01G371700 chr7B 83.333 96 16 0 583 678 486443862 486443957 3.510000e-14 89.8
36 TraesCS6D01G371700 chr3B 77.681 457 74 24 141 578 121483126 121482679 1.170000e-63 254.0
37 TraesCS6D01G371700 chr1B 76.520 477 61 33 141 578 92586141 92586605 1.990000e-51 213.0
38 TraesCS6D01G371700 chr3A 89.189 111 11 1 579 689 667200597 667200488 1.230000e-28 137.0
39 TraesCS6D01G371700 chr4D 87.234 94 10 2 1807 1898 16113815 16113908 3.480000e-19 106.0
40 TraesCS6D01G371700 chr4A 80.952 126 16 7 337 460 665461570 665461689 2.710000e-15 93.5
41 TraesCS6D01G371700 chr1A 96.078 51 2 0 1656 1706 530753203 530753153 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 TraesCS6D01G371700 chr6D 456949088 456951645 2557 False 4724.000000 4724 100.0000 1 2558 1 chr6D.!!$F2 2557
1 TraesCS6D01G371700 chr6D 470543284 470544177 893 False 909.000000 909 85.9200 715 1567 1 chr6D.!!$F3 852
2 TraesCS6D01G371700 chr5A 602791620 602795676 4056 True 1982.000000 2765 93.8210 3 2558 2 chr5A.!!$R3 2555
3 TraesCS6D01G371700 chr5A 602815796 602820127 4331 True 1082.666667 1363 95.5200 9 2067 3 chr5A.!!$R4 2058
4 TraesCS6D01G371700 chr6A 615271757 615272589 832 False 745.000000 745 83.7460 734 1534 1 chr6A.!!$F1 800
5 TraesCS6D01G371700 chr6A 615308984 615309846 862 False 452.000000 769 86.8145 704 1567 2 chr6A.!!$F2 863
6 TraesCS6D01G371700 chr6B 720612081 720612845 764 True 743.000000 743 84.8130 820 1567 1 chr6B.!!$R2 747
7 TraesCS6D01G371700 chr2D 20321747 20322308 561 False 411.000000 411 80.3390 9 586 1 chr2D.!!$F1 577

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
844 906 1.472662 AAGTCTAGCCTGGTGTGCGT 61.473 55.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 4565 0.029989 ATACCCCTCCACCCCTTCTC 60.03 60.0 0.0 0.0 0.0 2.87 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
123 127 8.779303 TGATCAACATTTTTGTATACACGTTCT 58.221 29.630 4.68 0.00 0.00 3.01
603 654 2.512515 GAGCGTGTGATGGGGAGC 60.513 66.667 0.00 0.00 0.00 4.70
661 712 9.476202 AAAGTTTTTGAGATAAGCCATGTAAAC 57.524 29.630 0.00 0.00 0.00 2.01
662 713 7.602753 AGTTTTTGAGATAAGCCATGTAAACC 58.397 34.615 0.00 0.00 0.00 3.27
844 906 1.472662 AAGTCTAGCCTGGTGTGCGT 61.473 55.000 0.00 0.00 0.00 5.24
845 907 1.738099 GTCTAGCCTGGTGTGCGTG 60.738 63.158 0.00 0.00 0.00 5.34
980 1540 2.147958 TCAAACATCACCTACGCAACC 58.852 47.619 0.00 0.00 0.00 3.77
1158 1719 3.425713 CGGCTGCAACACGAGCAT 61.426 61.111 0.50 0.00 41.82 3.79
1257 1818 5.860941 AGATGAAGAGTATCGTGGACATT 57.139 39.130 0.00 0.00 42.67 2.71
1365 1926 2.438975 TACCTGGGCGACGACGAT 60.439 61.111 12.29 0.00 42.66 3.73
1510 2101 3.284251 TGGGAGAGGAGGAGGGCA 61.284 66.667 0.00 0.00 0.00 5.36
1553 2144 0.815734 GTACTAGCCGCAGAACAGGA 59.184 55.000 0.00 0.00 0.00 3.86
1651 2242 9.562583 TGTTAAGTTGCATCCGTATTTAATTTC 57.437 29.630 0.00 0.00 0.00 2.17
1657 2248 5.524281 TGCATCCGTATTTAATTTCGTGCTA 59.476 36.000 13.55 4.44 0.00 3.49
1671 2262 4.136517 TCGTGCTATTTTCCAAACGTTC 57.863 40.909 0.00 0.00 33.07 3.95
1708 4086 5.593010 AGATCCAAACGATGCTACTCTTAC 58.407 41.667 0.00 0.00 0.00 2.34
1711 4089 5.790593 TCCAAACGATGCTACTCTTACTTT 58.209 37.500 0.00 0.00 0.00 2.66
1735 4113 3.202906 TCCCTTAATTACGTGCATGAGC 58.797 45.455 14.17 0.00 42.57 4.26
1776 4154 1.635487 AGAAAATAGAGGCCCAGTGCA 59.365 47.619 0.00 0.00 43.89 4.57
1782 4160 2.603075 AGAGGCCCAGTGCAAAATAA 57.397 45.000 0.00 0.00 43.89 1.40
1812 4190 1.645034 CCATCGATATGACCATCGGC 58.355 55.000 0.00 0.00 46.14 5.54
1863 4241 8.947115 AGTACTAGTATTTGCACTTCCATTTTC 58.053 33.333 5.75 0.00 0.00 2.29
2060 4438 6.167685 AGAAACAAAAAGGTACAAAACACCC 58.832 36.000 0.00 0.00 36.67 4.61
2094 4472 5.380900 TGTTGAACATTGTGGTAGGATTGA 58.619 37.500 0.00 0.00 0.00 2.57
2108 4486 9.213799 GTGGTAGGATTGAAATATCTTGATCTC 57.786 37.037 0.00 0.00 0.00 2.75
2142 4520 4.904241 AGGTGGTTCTCTCTCAGAAAATG 58.096 43.478 0.00 0.00 43.10 2.32
2150 4528 6.535963 TCTCTCTCAGAAAATGTATGCTGA 57.464 37.500 0.00 0.00 36.13 4.26
2159 4537 7.119699 TCAGAAAATGTATGCTGAAAGTGTAGG 59.880 37.037 0.00 0.00 34.71 3.18
2172 4550 4.437930 GAAAGTGTAGGCACATTCTGATGC 60.438 45.833 8.01 0.00 44.91 3.91
2185 4565 6.539103 CACATTCTGATGCCTCTCATATATGG 59.461 42.308 12.78 4.14 36.72 2.74
2194 4574 4.693420 CCTCTCATATATGGAGAAGGGGT 58.307 47.826 22.67 0.00 40.64 4.95
2195 4575 4.469227 CCTCTCATATATGGAGAAGGGGTG 59.531 50.000 22.67 9.48 40.64 4.61
2196 4576 4.429505 TCTCATATATGGAGAAGGGGTGG 58.570 47.826 12.78 0.00 38.40 4.61
2197 4577 4.109600 TCTCATATATGGAGAAGGGGTGGA 59.890 45.833 12.78 0.00 38.40 4.02
2198 4578 4.429505 TCATATATGGAGAAGGGGTGGAG 58.570 47.826 12.78 0.00 0.00 3.86
2199 4579 2.124560 ATATGGAGAAGGGGTGGAGG 57.875 55.000 0.00 0.00 0.00 4.30
2222 4603 6.368779 GGGTATATATAGCCTCCACACAAA 57.631 41.667 26.86 0.00 45.18 2.83
2225 4606 7.336931 GGGTATATATAGCCTCCACACAAAATG 59.663 40.741 26.86 0.00 45.18 2.32
2239 4620 3.241784 CACAAAATGCAACCGTTACACAC 59.758 43.478 0.00 0.00 0.00 3.82
2248 4629 3.202829 ACCGTTACACACATTTGACCT 57.797 42.857 0.00 0.00 0.00 3.85
2276 4657 5.074584 GGTCAGACCGAATAGAAGAACTT 57.925 43.478 3.05 0.00 0.00 2.66
2303 4684 5.049474 TGAGACCGATTCAGTTCAAAATGTG 60.049 40.000 0.00 0.00 0.00 3.21
2336 4740 2.346365 GGTGGGACCGACTGGAAC 59.654 66.667 6.59 0.00 39.21 3.62
2384 4788 3.127030 GCTTAGGGAAAACATCAACTCGG 59.873 47.826 0.00 0.00 0.00 4.63
2405 4809 1.137404 GCGCCGATTGCATCAACTT 59.863 52.632 0.00 0.00 41.33 2.66
2409 4813 1.733389 GCCGATTGCATCAACTTGGTG 60.733 52.381 0.00 0.00 40.77 4.17
2479 4883 2.029244 GTGTGACCGATTGCATAACTCG 59.971 50.000 0.00 0.00 0.00 4.18
2480 4884 2.094442 TGTGACCGATTGCATAACTCGA 60.094 45.455 9.27 0.00 34.41 4.04
2493 4897 5.647658 TGCATAACTCGATGAGACCAAAATT 59.352 36.000 0.00 0.00 33.32 1.82
2512 4916 7.095940 CCAAAATTAATGCAACAAGTCACAGAG 60.096 37.037 0.00 0.00 0.00 3.35
2522 4926 4.383861 TCACAGAGCGCTGGCAGG 62.384 66.667 18.48 7.62 46.60 4.85
2540 4944 0.108898 GGGCCATCTCGATGAGATCG 60.109 60.000 4.39 2.00 45.03 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 53 9.832445 ACATATACGAAAATGTAGAGTGGAAAT 57.168 29.630 0.00 0.00 34.61 2.17
123 127 3.339141 TGTTGCATAAGCGGTCAATGTA 58.661 40.909 10.47 4.67 46.23 2.29
638 689 6.526674 CGGTTTACATGGCTTATCTCAAAAAC 59.473 38.462 0.00 0.00 0.00 2.43
661 712 5.128335 ACAACTAATACTACCTCCTTTCCGG 59.872 44.000 0.00 0.00 0.00 5.14
662 713 6.218108 ACAACTAATACTACCTCCTTTCCG 57.782 41.667 0.00 0.00 0.00 4.30
914 1452 4.569162 GGAAACACACTTTTAACAAAGGGC 59.431 41.667 0.00 0.00 46.19 5.19
980 1540 1.081892 CACCGATCAGCAAGTTGGAG 58.918 55.000 4.75 0.00 0.00 3.86
1257 1818 1.080093 GTCGTCGCCCTTGATGTCA 60.080 57.895 0.00 0.00 0.00 3.58
1510 2101 2.571653 TCCGTTGGTCATCTGGATTCTT 59.428 45.455 0.00 0.00 0.00 2.52
1553 2144 7.331193 GGTACTAGACGAACAAACTGAATCAAT 59.669 37.037 0.00 0.00 0.00 2.57
1642 2233 8.643752 CGTTTGGAAAATAGCACGAAATTAAAT 58.356 29.630 0.00 0.00 0.00 1.40
1651 2242 2.900046 CGAACGTTTGGAAAATAGCACG 59.100 45.455 7.72 0.00 0.00 5.34
1657 2248 7.140048 TGCTAAAATACGAACGTTTGGAAAAT 58.860 30.769 19.53 4.40 0.00 1.82
1671 2262 7.847487 TCGTTTGGATCTATTGCTAAAATACG 58.153 34.615 0.00 0.00 0.00 3.06
1708 4086 5.873179 TGCACGTAATTAAGGGAGAAAAG 57.127 39.130 4.71 0.00 0.00 2.27
1711 4089 5.092554 TCATGCACGTAATTAAGGGAGAA 57.907 39.130 4.71 0.00 0.00 2.87
1735 4113 0.603569 AGTTACGGCACTGAGACCAG 59.396 55.000 0.00 0.00 45.76 4.00
1757 4135 2.128771 TGCACTGGGCCTCTATTTTC 57.871 50.000 4.53 0.00 43.89 2.29
1763 4141 2.603075 TTATTTTGCACTGGGCCTCT 57.397 45.000 4.53 0.00 43.89 3.69
1863 4241 7.277174 AGGAAAAGAACCAACATTACTTCTG 57.723 36.000 0.00 0.00 0.00 3.02
1896 4274 5.792741 CCCAATCATAAAAGGTGCTTTTGA 58.207 37.500 0.00 0.00 42.61 2.69
2060 4438 4.201910 ACAATGTTCAACAGAAACTCACCG 60.202 41.667 0.00 0.00 0.00 4.94
2108 4486 3.997021 GAGAACCACCTACTCATGTGTTG 59.003 47.826 5.63 4.08 0.00 3.33
2159 4537 2.034104 TGAGAGGCATCAGAATGTGC 57.966 50.000 0.00 0.00 40.66 4.57
2172 4550 4.469227 CACCCCTTCTCCATATATGAGAGG 59.531 50.000 21.37 17.17 0.00 3.69
2185 4565 0.029989 ATACCCCTCCACCCCTTCTC 60.030 60.000 0.00 0.00 0.00 2.87
2196 4576 4.650131 GTGTGGAGGCTATATATACCCCTC 59.350 50.000 18.41 18.41 41.01 4.30
2197 4577 4.046747 TGTGTGGAGGCTATATATACCCCT 59.953 45.833 6.84 6.84 0.00 4.79
2198 4578 4.359105 TGTGTGGAGGCTATATATACCCC 58.641 47.826 1.06 6.34 0.00 4.95
2199 4579 6.368779 TTTGTGTGGAGGCTATATATACCC 57.631 41.667 0.00 0.00 0.00 3.69
2222 4603 4.047822 CAAATGTGTGTAACGGTTGCATT 58.952 39.130 14.59 2.66 42.39 3.56
2225 4606 3.040099 GTCAAATGTGTGTAACGGTTGC 58.960 45.455 3.07 2.36 42.39 4.17
2276 4657 1.967779 TGAACTGAATCGGTCTCACCA 59.032 47.619 0.00 0.00 38.47 4.17
2303 4684 2.537401 CCACCGAGATTCCTAACGTTC 58.463 52.381 2.82 0.00 0.00 3.95
2351 4755 1.424638 TCCCTAAGCCCTAGCACATC 58.575 55.000 0.00 0.00 43.56 3.06
2405 4809 0.033504 GCTTCACTTCGGTCTCACCA 59.966 55.000 0.00 0.00 38.47 4.17
2409 4813 3.062774 GCTTATTGCTTCACTTCGGTCTC 59.937 47.826 0.00 0.00 38.95 3.36
2439 4843 0.443869 CCGAGTTGGCTTGACATTCG 59.556 55.000 4.58 4.58 0.00 3.34
2479 4883 7.599998 ACTTGTTGCATTAATTTTGGTCTCATC 59.400 33.333 0.00 0.00 0.00 2.92
2480 4884 7.444299 ACTTGTTGCATTAATTTTGGTCTCAT 58.556 30.769 0.00 0.00 0.00 2.90
2493 4897 2.480037 CGCTCTGTGACTTGTTGCATTA 59.520 45.455 0.00 0.00 0.00 1.90
2531 4935 4.634004 ACCGATACAGATCTCGATCTCATC 59.366 45.833 6.46 10.72 45.78 2.92
2532 4936 4.394610 CACCGATACAGATCTCGATCTCAT 59.605 45.833 6.46 3.88 45.78 2.90


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

AutoCloner maintained by Alex Coulton.