Multiple sequence alignment - TraesCS6D01G184900

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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 TraesCS6D01G184900 chr6D 100.000 3198 0 0 1 3198 237071854 237068657 0.000000e+00 5906
1 TraesCS6D01G184900 chr6D 86.061 660 54 13 2538 3195 235134891 235135514 0.000000e+00 675
2 TraesCS6D01G184900 chr1D 96.004 1977 40 11 857 2799 47848306 47850277 0.000000e+00 3177
3 TraesCS6D01G184900 chr1D 86.066 854 107 8 1 846 431249081 431248232 0.000000e+00 907
4 TraesCS6D01G184900 chr1D 98.034 407 8 0 2792 3198 47850977 47851383 0.000000e+00 708
5 TraesCS6D01G184900 chr1D 85.672 670 53 19 2529 3198 204022216 204021590 0.000000e+00 665
6 TraesCS6D01G184900 chr3D 97.776 1439 26 5 1263 2699 523247005 523248439 0.000000e+00 2475
7 TraesCS6D01G184900 chr3D 97.900 381 8 0 2818 3198 523248436 523248816 0.000000e+00 660
8 TraesCS6D01G184900 chr6A 91.402 849 64 5 2 847 308890268 308891110 0.000000e+00 1155
9 TraesCS6D01G184900 chr6A 85.881 857 105 11 1 847 144352914 144352064 0.000000e+00 898
10 TraesCS6D01G184900 chr2D 87.500 856 95 8 1 847 288141914 288141062 0.000000e+00 977
11 TraesCS6D01G184900 chr2D 93.878 49 3 0 1645 1693 385390338 385390290 1.230000e-09 75
12 TraesCS6D01G184900 chr4D 87.251 855 97 8 1 847 182330438 182331288 0.000000e+00 965
13 TraesCS6D01G184900 chr4D 86.651 854 99 11 1 847 121938771 121937926 0.000000e+00 931
14 TraesCS6D01G184900 chr3B 86.534 854 103 7 1 847 323702202 323701354 0.000000e+00 929
15 TraesCS6D01G184900 chr3B 88.772 668 49 8 2529 3195 598066901 598067543 0.000000e+00 795
16 TraesCS6D01G184900 chr3B 82.061 262 42 5 2672 2930 809083865 809083606 5.370000e-53 219
17 TraesCS6D01G184900 chr5B 86.433 855 102 11 1 847 180830206 180829358 0.000000e+00 924
18 TraesCS6D01G184900 chr5B 81.679 262 44 4 2672 2930 215893419 215893679 6.950000e-52 215
19 TraesCS6D01G184900 chr2A 86.332 856 101 11 2 847 594417432 594418281 0.000000e+00 918
20 TraesCS6D01G184900 chr2A 85.507 483 53 14 844 1313 349225307 349224829 3.710000e-134 488
21 TraesCS6D01G184900 chr2A 85.051 495 55 16 833 1313 590787124 590786635 1.330000e-133 486
22 TraesCS6D01G184900 chr2A 93.878 49 3 0 1645 1693 520993570 520993522 1.230000e-09 75
23 TraesCS6D01G184900 chrUn 89.655 667 51 7 2529 3194 8464805 8465454 0.000000e+00 833
24 TraesCS6D01G184900 chr7B 89.270 671 55 6 2529 3198 729406490 729405836 0.000000e+00 824
25 TraesCS6D01G184900 chr7B 88.674 671 59 6 2529 3198 459800260 459799606 0.000000e+00 802
26 TraesCS6D01G184900 chr7B 86.100 482 50 14 844 1313 721298084 721298560 1.320000e-138 503
27 TraesCS6D01G184900 chr4A 88.235 527 45 10 2662 3186 733554426 733554937 5.860000e-172 614
28 TraesCS6D01G184900 chr4A 86.071 481 49 15 847 1313 627000921 627001397 4.760000e-138 501
29 TraesCS6D01G184900 chr4A 90.647 278 19 5 2596 2873 374697723 374697993 2.340000e-96 363
30 TraesCS6D01G184900 chr2B 86.071 481 48 16 847 1313 127166749 127166274 1.710000e-137 499
31 TraesCS6D01G184900 chr2B 86.084 309 30 6 2117 2425 456343221 456342926 1.430000e-83 320
32 TraesCS6D01G184900 chr2B 85.174 317 31 13 1813 2118 456344287 456343976 8.610000e-81 311
33 TraesCS6D01G184900 chr3A 85.537 484 52 15 844 1313 698862553 698862074 1.030000e-134 490
34 TraesCS6D01G184900 chr6B 85.270 482 53 15 846 1313 474539979 474540456 6.200000e-132 481
35 TraesCS6D01G184900 chr1B 85.270 482 53 15 846 1313 235381986 235382463 6.200000e-132 481


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 TraesCS6D01G184900 chr6D 237068657 237071854 3197 True 5906.0 5906 100.000 1 3198 1 chr6D.!!$R1 3197
1 TraesCS6D01G184900 chr6D 235134891 235135514 623 False 675.0 675 86.061 2538 3195 1 chr6D.!!$F1 657
2 TraesCS6D01G184900 chr1D 47848306 47851383 3077 False 1942.5 3177 97.019 857 3198 2 chr1D.!!$F1 2341
3 TraesCS6D01G184900 chr1D 431248232 431249081 849 True 907.0 907 86.066 1 846 1 chr1D.!!$R2 845
4 TraesCS6D01G184900 chr1D 204021590 204022216 626 True 665.0 665 85.672 2529 3198 1 chr1D.!!$R1 669
5 TraesCS6D01G184900 chr3D 523247005 523248816 1811 False 1567.5 2475 97.838 1263 3198 2 chr3D.!!$F1 1935
6 TraesCS6D01G184900 chr6A 308890268 308891110 842 False 1155.0 1155 91.402 2 847 1 chr6A.!!$F1 845
7 TraesCS6D01G184900 chr6A 144352064 144352914 850 True 898.0 898 85.881 1 847 1 chr6A.!!$R1 846
8 TraesCS6D01G184900 chr2D 288141062 288141914 852 True 977.0 977 87.500 1 847 1 chr2D.!!$R1 846
9 TraesCS6D01G184900 chr4D 182330438 182331288 850 False 965.0 965 87.251 1 847 1 chr4D.!!$F1 846
10 TraesCS6D01G184900 chr4D 121937926 121938771 845 True 931.0 931 86.651 1 847 1 chr4D.!!$R1 846
11 TraesCS6D01G184900 chr3B 323701354 323702202 848 True 929.0 929 86.534 1 847 1 chr3B.!!$R1 846
12 TraesCS6D01G184900 chr3B 598066901 598067543 642 False 795.0 795 88.772 2529 3195 1 chr3B.!!$F1 666
13 TraesCS6D01G184900 chr5B 180829358 180830206 848 True 924.0 924 86.433 1 847 1 chr5B.!!$R1 846
14 TraesCS6D01G184900 chr2A 594417432 594418281 849 False 918.0 918 86.332 2 847 1 chr2A.!!$F1 845
15 TraesCS6D01G184900 chrUn 8464805 8465454 649 False 833.0 833 89.655 2529 3194 1 chrUn.!!$F1 665
16 TraesCS6D01G184900 chr7B 729405836 729406490 654 True 824.0 824 89.270 2529 3198 1 chr7B.!!$R2 669
17 TraesCS6D01G184900 chr7B 459799606 459800260 654 True 802.0 802 88.674 2529 3198 1 chr7B.!!$R1 669
18 TraesCS6D01G184900 chr4A 733554426 733554937 511 False 614.0 614 88.235 2662 3186 1 chr4A.!!$F3 524
19 TraesCS6D01G184900 chr2B 456342926 456344287 1361 True 315.5 320 85.629 1813 2425 2 chr2B.!!$R2 612

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
944 966 0.248866 CACAAAACAACCCGCAGTCC 60.249 55.0 0.0 0.0 0.0 3.85 F
1362 1410 1.543944 TTGGCTGCTGATCGAGGTCA 61.544 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1810 0.949397 TACACGCTAGCCATAGACCG 59.051 55.000 9.66 0.0 0.00 4.79 R
2787 3609 1.080093 CGTCGGTGTACAGCCACAT 60.080 57.895 20.24 0.0 37.06 3.21 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
109 110 5.945784 CCTGATCATTGTGTCCCTAAGAAAA 59.054 40.000 0.00 0.00 0.00 2.29
120 121 3.200825 TCCCTAAGAAAAGGAGGCATCAG 59.799 47.826 0.00 0.00 39.15 2.90
125 126 2.027192 AGAAAAGGAGGCATCAGCGTTA 60.027 45.455 0.00 0.00 43.41 3.18
255 256 7.038659 CCCTTGCCGTTTTATTAATCAAATCA 58.961 34.615 0.00 0.00 0.00 2.57
314 315 8.648698 TTCTTGATGGATATTCTGGTTTTTCA 57.351 30.769 0.00 0.00 0.00 2.69
323 326 7.979537 GGATATTCTGGTTTTTCACAAATACCC 59.020 37.037 6.26 0.00 0.00 3.69
400 403 3.305199 GCTTATAGACGTATGCCTTCCGT 60.305 47.826 0.00 0.00 37.56 4.69
426 429 1.273327 GCAATGCACCTGCTACCTTTT 59.727 47.619 13.99 0.00 42.66 2.27
458 463 9.920133 TGTATGATTGCTATATTCTCTGACTTC 57.080 33.333 0.00 0.00 0.00 3.01
517 528 8.522830 TGTTTATGGGACTTCTTTTGATGATTC 58.477 33.333 0.00 0.00 0.00 2.52
543 554 2.143122 GCAACCTTGATCGAGTTGTGA 58.857 47.619 18.11 0.00 42.25 3.58
548 559 3.322254 ACCTTGATCGAGTTGTGAAGAGT 59.678 43.478 9.19 0.00 0.00 3.24
595 610 3.806949 TGGGAGAAGTGCCACTTTATT 57.193 42.857 12.09 0.74 39.76 1.40
601 616 6.379386 GGAGAAGTGCCACTTTATTGTAAAC 58.621 40.000 12.09 0.00 38.80 2.01
750 766 7.769044 TCATGCTGGTTTCTATAGAAGGTTTAC 59.231 37.037 14.63 9.88 35.21 2.01
837 856 8.783093 TGTTTTGATGATGATTTCGTAGAAGTT 58.217 29.630 0.00 0.00 45.90 2.66
871 890 8.128322 TCTCTCCCTAATAATAAAGCAGCTAG 57.872 38.462 0.00 0.00 0.00 3.42
944 966 0.248866 CACAAAACAACCCGCAGTCC 60.249 55.000 0.00 0.00 0.00 3.85
963 985 6.877322 GCAGTCCCTGTTTAAGTGAATACTAA 59.123 38.462 0.00 0.00 32.86 2.24
1362 1410 1.543944 TTGGCTGCTGATCGAGGTCA 61.544 55.000 0.00 0.00 0.00 4.02
1400 1448 7.050970 ACTCTCTGTATGTGTCTTGTGTTAA 57.949 36.000 0.00 0.00 0.00 2.01
1633 1681 2.847366 TTTGCCTTCCATACCCCGGC 62.847 60.000 0.00 0.00 41.06 6.13
1762 1810 3.507233 TGTGTTGGAAGCATCTTGGATTC 59.493 43.478 0.00 0.00 32.60 2.52
2119 2699 4.030913 CTGATGGTAGGAAAGTAGACCCA 58.969 47.826 0.00 0.00 0.00 4.51
2508 3327 3.304726 CGAGAGATAGGCGTTGATTGCTA 60.305 47.826 0.00 0.00 0.00 3.49
2663 3485 3.138304 GAGAGATAGAGAGCGCAGAGAA 58.862 50.000 11.47 0.00 0.00 2.87
2669 3491 0.179113 GAGAGCGCAGAGAAAGAGGG 60.179 60.000 11.47 0.00 0.00 4.30
2787 3609 3.141398 GTGCCTCAAGTTTCTGACATCA 58.859 45.455 0.00 0.00 0.00 3.07
2788 3610 3.755378 GTGCCTCAAGTTTCTGACATCAT 59.245 43.478 0.00 0.00 0.00 2.45
2828 4357 0.031585 TTCGCCGATAATCCGTCTGG 59.968 55.000 0.00 0.00 0.00 3.86
2884 4413 3.698040 CCTGAGGTACATACTACGGTGTT 59.302 47.826 0.00 0.00 0.00 3.32
3056 4586 6.584563 CGATCAAAGGAGATAAAGCTAGCTAC 59.415 42.308 19.70 10.07 0.00 3.58
3092 4623 2.005451 GAACAGCTGCTGTATGACAGG 58.995 52.381 33.11 6.01 44.62 4.00
3103 4635 7.761249 GCTGCTGTATGACAGGAAAAATTTAAT 59.239 33.333 8.61 0.00 45.86 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 1.202698 GGAATAACGCTGATGCCTCCT 60.203 52.381 0.00 0.00 35.36 3.69
210 211 6.681729 AGGGGTAATGATATTTTCTAGCGA 57.318 37.500 0.00 0.00 0.00 4.93
314 315 5.127491 TCTTCTTTTGACACGGGTATTTGT 58.873 37.500 0.00 0.00 0.00 2.83
323 326 6.530913 TTCTCTTGATCTTCTTTTGACACG 57.469 37.500 0.00 0.00 0.00 4.49
400 403 3.119173 GGTAGCAGGTGCATTGCATAAAA 60.119 43.478 22.89 0.00 43.92 1.52
458 463 7.015226 TCCATGCTCAACAATAATTTCGTAG 57.985 36.000 0.00 0.00 0.00 3.51
461 466 6.497437 TCATCCATGCTCAACAATAATTTCG 58.503 36.000 0.00 0.00 0.00 3.46
517 528 5.049405 ACAACTCGATCAAGGTTGCTTAAAG 60.049 40.000 12.79 0.00 42.55 1.85
543 554 8.738645 ACAAGATTAGTTTCTTCACAACTCTT 57.261 30.769 0.00 0.00 35.95 2.85
548 559 8.731275 TTCAGACAAGATTAGTTTCTTCACAA 57.269 30.769 0.00 0.00 33.69 3.33
595 610 4.998672 CCAAGGACAATACCTTCGTTTACA 59.001 41.667 0.00 0.00 46.94 2.41
601 616 1.339631 TGCCCAAGGACAATACCTTCG 60.340 52.381 0.00 0.00 46.94 3.79
632 648 7.069085 AGCTTTATCTACCACAATACCTCGTTA 59.931 37.037 0.00 0.00 0.00 3.18
671 687 8.099364 TCTTTAGGACATGTCATTTTCTCAAC 57.901 34.615 26.47 5.80 0.00 3.18
717 733 5.649782 ATAGAAACCAGCATGACCAAAAG 57.350 39.130 0.00 0.00 39.69 2.27
806 823 9.558648 CTACGAAATCATCATCAAAACAAATGA 57.441 29.630 0.00 0.00 36.40 2.57
841 860 9.784531 CTGCTTTATTATTAGGGAGAGATTTCA 57.215 33.333 0.00 0.00 0.00 2.69
842 861 8.726068 GCTGCTTTATTATTAGGGAGAGATTTC 58.274 37.037 0.00 0.00 0.00 2.17
845 864 7.566658 AGCTGCTTTATTATTAGGGAGAGAT 57.433 36.000 0.00 0.00 0.00 2.75
846 865 7.730784 ACTAGCTGCTTTATTATTAGGGAGAGA 59.269 37.037 7.79 0.00 0.00 3.10
847 866 7.816995 CACTAGCTGCTTTATTATTAGGGAGAG 59.183 40.741 7.79 0.00 0.00 3.20
848 867 7.671302 CACTAGCTGCTTTATTATTAGGGAGA 58.329 38.462 7.79 0.00 0.00 3.71
849 868 6.370166 GCACTAGCTGCTTTATTATTAGGGAG 59.630 42.308 7.79 0.00 43.33 4.30
850 869 6.231211 GCACTAGCTGCTTTATTATTAGGGA 58.769 40.000 7.79 0.00 43.33 4.20
851 870 6.487689 GCACTAGCTGCTTTATTATTAGGG 57.512 41.667 7.79 0.00 43.33 3.53
871 890 2.048503 ACGTACGGCCAGAAGCAC 60.049 61.111 21.06 0.00 46.50 4.40
911 933 7.039293 GGGTTGTTTTGTGAAATATAGAAGGGT 60.039 37.037 0.00 0.00 0.00 4.34
921 943 2.167487 ACTGCGGGTTGTTTTGTGAAAT 59.833 40.909 0.00 0.00 0.00 2.17
922 944 1.546476 ACTGCGGGTTGTTTTGTGAAA 59.454 42.857 0.00 0.00 0.00 2.69
927 949 1.106944 AGGGACTGCGGGTTGTTTTG 61.107 55.000 0.00 0.00 37.18 2.44
1362 1410 2.282040 GAGTTGCAGGCCAGCAGT 60.282 61.111 22.89 14.48 46.54 4.40
1486 1534 8.908786 ACATGAAACTGTTTCTTCATCTTCTA 57.091 30.769 27.75 9.29 39.66 2.10
1633 1681 0.600255 ACGCAGAAAGACGGAACTGG 60.600 55.000 0.00 0.00 0.00 4.00
1762 1810 0.949397 TACACGCTAGCCATAGACCG 59.051 55.000 9.66 0.00 0.00 4.79
1786 1834 6.203915 AGACACACTGCATTATTAAAACGTCA 59.796 34.615 0.00 0.00 0.00 4.35
2119 2699 2.105993 GGGGGTTATATCGGTCTTGCTT 59.894 50.000 0.00 0.00 0.00 3.91
2508 3327 4.159135 CAGCTCAATCAAGCCCTAAATTGT 59.841 41.667 0.00 0.00 43.56 2.71
2540 3359 4.324563 CCCTCTCTGTTCTCTCTCTCTCTT 60.325 50.000 0.00 0.00 0.00 2.85
2663 3485 2.039084 GGTTCAGTGATGTGTCCCTCTT 59.961 50.000 0.00 0.00 0.00 2.85
2669 3491 2.554032 CCAAAGGGTTCAGTGATGTGTC 59.446 50.000 0.00 0.00 0.00 3.67
2787 3609 1.080093 CGTCGGTGTACAGCCACAT 60.080 57.895 20.24 0.00 37.06 3.21
2788 3610 2.194889 TCGTCGGTGTACAGCCACA 61.195 57.895 20.24 7.11 37.06 4.17
2884 4413 7.555195 AGTCTTTGATGACAGATGCAATTGATA 59.445 33.333 10.34 0.00 39.27 2.15
3056 4586 7.066766 AGCAGCTGTTCTTCCTAGATAAAAATG 59.933 37.037 16.64 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.