Multiple sequence alignment - TraesCS2D01G228100

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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 TraesCS2D01G228100 chr2D 100.000 2303 0 0 1 2303 196791969 196789667 0.000000e+00 4253
1 TraesCS2D01G228100 chr2A 92.678 1598 75 17 739 2303 213097936 213096348 0.000000e+00 2265
2 TraesCS2D01G228100 chr2B 92.389 1603 68 17 739 2303 254238505 254236919 0.000000e+00 2235
3 TraesCS2D01G228100 chr7D 90.595 723 46 13 1 720 232930374 232929671 0.000000e+00 939
4 TraesCS2D01G228100 chr7D 93.781 402 20 5 1 398 594983640 594983240 1.180000e-167 599
5 TraesCS2D01G228100 chr7D 93.458 321 19 1 402 720 603805666 603805346 2.070000e-130 475
6 TraesCS2D01G228100 chr7D 92.835 321 19 2 402 720 448967007 448967325 1.610000e-126 462
7 TraesCS2D01G228100 chr7D 90.390 333 29 2 394 724 382527672 382527341 3.510000e-118 435
8 TraesCS2D01G228100 chr5D 94.030 402 18 4 1 398 44411927 44411528 2.530000e-169 604
9 TraesCS2D01G228100 chr5D 92.421 409 19 5 1 398 532649518 532649111 7.140000e-160 573
10 TraesCS2D01G228100 chr5D 92.308 377 26 3 23 398 41121533 41121907 1.210000e-147 532
11 TraesCS2D01G228100 chr5D 89.750 400 31 7 1 394 559110247 559110642 9.500000e-139 503
12 TraesCS2D01G228100 chr5D 91.131 327 28 1 396 722 41123641 41123966 2.100000e-120 442
13 TraesCS2D01G228100 chr5D 90.826 327 27 3 396 720 260844977 260845302 3.510000e-118 435
14 TraesCS2D01G228100 chr7A 91.892 407 20 8 1 398 65057887 65058289 7.190000e-155 556
15 TraesCS2D01G228100 chr6D 91.811 403 24 6 1 398 322579723 322579325 9.300000e-154 553
16 TraesCS2D01G228100 chr6D 90.909 330 25 3 396 720 115577617 115577946 2.720000e-119 438
17 TraesCS2D01G228100 chr5A 91.646 407 22 5 1 396 332573577 332573982 9.300000e-154 553
18 TraesCS2D01G228100 chr1D 92.447 331 22 2 396 723 308447128 308447458 9.630000e-129 470
19 TraesCS2D01G228100 chr1D 91.331 323 23 3 402 722 427036523 427036204 9.770000e-119 436
20 TraesCS2D01G228100 chr3D 90.881 329 27 2 396 722 552725727 552726054 2.720000e-119 438


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 TraesCS2D01G228100 chr2D 196789667 196791969 2302 True 4253 4253 100.0000 1 2303 1 chr2D.!!$R1 2302
1 TraesCS2D01G228100 chr2A 213096348 213097936 1588 True 2265 2265 92.6780 739 2303 1 chr2A.!!$R1 1564
2 TraesCS2D01G228100 chr2B 254236919 254238505 1586 True 2235 2235 92.3890 739 2303 1 chr2B.!!$R1 1564
3 TraesCS2D01G228100 chr7D 232929671 232930374 703 True 939 939 90.5950 1 720 1 chr7D.!!$R1 719
4 TraesCS2D01G228100 chr5D 41121533 41123966 2433 False 487 532 91.7195 23 722 2 chr5D.!!$F3 699

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
338 342 0.107214 GGAAGACATTCCGCCCATGA 60.107 55.0 0.0 0.0 45.5 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 3998 0.167251 AAATCAAGCGCCCGTTTACG 59.833 50.0 2.29 0.0 39.44 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
83 84 5.850557 TGACCACAAGTTCAAATTCATGT 57.149 34.783 0.00 0.00 0.00 3.21
149 150 3.311322 TGACACAAACGAAAGACACATCC 59.689 43.478 0.00 0.00 0.00 3.51
212 213 1.132643 CGACTCCTCCGAAGACGATTT 59.867 52.381 0.00 0.00 42.66 2.17
214 215 3.180613 GACTCCTCCGAAGACGATTTTC 58.819 50.000 0.00 0.00 42.66 2.29
230 234 2.182516 TTTCCCTCCTCCTCCTCATC 57.817 55.000 0.00 0.00 0.00 2.92
231 235 1.018840 TTCCCTCCTCCTCCTCATCA 58.981 55.000 0.00 0.00 0.00 3.07
232 236 1.249195 TCCCTCCTCCTCCTCATCAT 58.751 55.000 0.00 0.00 0.00 2.45
291 295 1.739466 GCAAGATCTTCAACGGCATCA 59.261 47.619 4.57 0.00 0.00 3.07
303 307 0.892358 CGGCATCATCATGGGAAGGG 60.892 60.000 0.00 0.00 0.00 3.95
304 308 0.541296 GGCATCATCATGGGAAGGGG 60.541 60.000 0.00 0.00 0.00 4.79
338 342 0.107214 GGAAGACATTCCGCCCATGA 60.107 55.000 0.00 0.00 45.50 3.07
385 390 3.111853 TGAGAGACGCAAAACTCATGT 57.888 42.857 0.00 0.00 35.01 3.21
400 405 2.300967 ATGTCTCCCATGCCGGTGT 61.301 57.895 1.90 0.00 30.69 4.16
410 2151 4.280019 GCCGGTGTTGGAGGGGTT 62.280 66.667 1.90 0.00 0.00 4.11
426 2167 1.819632 GTTGCGGCTGTAGGATGGG 60.820 63.158 0.00 0.00 0.00 4.00
515 2256 3.444805 GCGCGGAGGAGAGAGTGT 61.445 66.667 8.83 0.00 0.00 3.55
517 2258 2.041115 CGCGGAGGAGAGAGTGTGA 61.041 63.158 0.00 0.00 0.00 3.58
571 2312 2.038269 CGCCCCAAATACACAGCGT 61.038 57.895 0.00 0.00 38.81 5.07
584 2325 1.282570 CAGCGTGTGTTGGCGATTT 59.717 52.632 0.00 0.00 0.00 2.17
613 2356 1.564622 CCCAACTCAATATCGCGCG 59.435 57.895 26.76 26.76 0.00 6.86
615 2358 1.635810 CAACTCAATATCGCGCGCA 59.364 52.632 32.61 18.69 0.00 6.09
671 2414 4.217111 CGCGCGCGCTAAAATGGA 62.217 61.111 45.97 0.00 39.32 3.41
709 2452 0.793861 CTTGTTTAGCGCGGCTGTTA 59.206 50.000 8.83 0.00 40.10 2.41
722 2465 3.553922 GCGGCTGTTAGAGATGCTCTTAT 60.554 47.826 1.88 0.00 41.50 1.73
723 2466 4.321304 GCGGCTGTTAGAGATGCTCTTATA 60.321 45.833 1.88 0.00 41.50 0.98
724 2467 5.157781 CGGCTGTTAGAGATGCTCTTATAC 58.842 45.833 1.88 0.83 41.50 1.47
725 2468 5.278512 CGGCTGTTAGAGATGCTCTTATACA 60.279 44.000 1.88 4.88 41.50 2.29
726 2469 5.923684 GGCTGTTAGAGATGCTCTTATACAC 59.076 44.000 1.88 2.13 41.50 2.90
727 2470 5.923684 GCTGTTAGAGATGCTCTTATACACC 59.076 44.000 1.88 0.00 41.50 4.16
728 2471 6.239176 GCTGTTAGAGATGCTCTTATACACCT 60.239 42.308 1.88 0.00 41.50 4.00
729 2472 7.040340 GCTGTTAGAGATGCTCTTATACACCTA 60.040 40.741 1.88 0.00 41.50 3.08
730 2473 8.397575 TGTTAGAGATGCTCTTATACACCTAG 57.602 38.462 1.88 0.00 41.50 3.02
731 2474 8.218488 TGTTAGAGATGCTCTTATACACCTAGA 58.782 37.037 1.88 0.00 41.50 2.43
732 2475 9.238368 GTTAGAGATGCTCTTATACACCTAGAT 57.762 37.037 1.88 0.00 41.50 1.98
733 2476 7.701539 AGAGATGCTCTTATACACCTAGATG 57.298 40.000 0.00 0.00 37.60 2.90
734 2477 6.663093 AGAGATGCTCTTATACACCTAGATGG 59.337 42.308 0.00 0.00 37.60 3.51
735 2478 6.556639 AGATGCTCTTATACACCTAGATGGA 58.443 40.000 0.00 0.00 39.71 3.41
736 2479 6.663093 AGATGCTCTTATACACCTAGATGGAG 59.337 42.308 0.00 0.00 39.71 3.86
737 2480 5.080337 TGCTCTTATACACCTAGATGGAGG 58.920 45.833 0.00 0.00 42.89 4.30
743 2486 8.508601 TCTTATACACCTAGATGGAGGAAGTAA 58.491 37.037 0.00 0.00 39.15 2.24
781 2524 2.346284 TTACACGGCCTGCCCAACTT 62.346 55.000 0.00 0.00 0.00 2.66
784 2527 0.965363 CACGGCCTGCCCAACTTATT 60.965 55.000 0.00 0.00 0.00 1.40
785 2528 0.621609 ACGGCCTGCCCAACTTATTA 59.378 50.000 0.00 0.00 0.00 0.98
880 2634 2.325761 CGTCGCCTGCCTATATAACAC 58.674 52.381 0.00 0.00 0.00 3.32
882 2636 3.724374 GTCGCCTGCCTATATAACACAA 58.276 45.455 0.00 0.00 0.00 3.33
959 2713 7.911651 TCATACACAAAATCCTCTCTTCTTCT 58.088 34.615 0.00 0.00 0.00 2.85
1276 3030 3.269178 CTCAAGCACCTCAAGAATCTCC 58.731 50.000 0.00 0.00 0.00 3.71
1366 3122 2.969262 GGGAGACTAAGCTGCCTTCTAT 59.031 50.000 0.00 0.00 42.52 1.98
1369 3125 5.070580 GGGAGACTAAGCTGCCTTCTATTTA 59.929 44.000 0.00 0.00 42.52 1.40
1496 3253 1.319541 ATGGAGCAGATCAGCAATGC 58.680 50.000 13.03 4.28 40.29 3.56
1550 3307 4.837972 GGATCCTATCCTATCTTGTTGGC 58.162 47.826 3.84 0.00 46.19 4.52
1640 3397 8.267183 TGAGTCATTGAGATGCTAAATCCTTTA 58.733 33.333 0.00 0.00 33.14 1.85
1645 3402 5.994250 TGAGATGCTAAATCCTTTACTGCT 58.006 37.500 0.00 0.00 0.00 4.24
1684 3441 7.166142 GGATCTTATGTTTCGAGAAGTAAGTCG 59.834 40.741 0.00 0.00 37.54 4.18
1695 3452 5.163581 CGAGAAGTAAGTCGGGAATCCTTTA 60.164 44.000 0.00 0.00 32.40 1.85
1698 3455 7.104290 AGAAGTAAGTCGGGAATCCTTTAAAG 58.896 38.462 8.32 8.32 0.00 1.85
1699 3456 6.616237 AGTAAGTCGGGAATCCTTTAAAGA 57.384 37.500 16.98 3.50 0.00 2.52
1701 3458 7.455891 AGTAAGTCGGGAATCCTTTAAAGAAA 58.544 34.615 16.98 4.85 0.00 2.52
1702 3459 7.940688 AGTAAGTCGGGAATCCTTTAAAGAAAA 59.059 33.333 16.98 2.34 0.00 2.29
1703 3460 7.591421 AAGTCGGGAATCCTTTAAAGAAAAA 57.409 32.000 16.98 0.00 0.00 1.94
1705 3462 7.602753 AGTCGGGAATCCTTTAAAGAAAAATG 58.397 34.615 16.98 0.00 0.00 2.32
1772 3532 5.739358 GCAATCCACGATTAGCTTACCTACT 60.739 44.000 0.00 0.00 30.44 2.57
1860 3620 6.751514 ACGAAAGGTCATGCATTGTTAATA 57.248 33.333 0.00 0.00 0.00 0.98
1863 3623 6.907212 CGAAAGGTCATGCATTGTTAATAGTC 59.093 38.462 0.00 0.00 0.00 2.59
1892 3652 9.218525 TGAGAAAGTAGATTTGGGATCTAATCT 57.781 33.333 16.69 16.69 43.88 2.40
1915 3675 0.895100 TCATGCTGCCAGTTTGTCCC 60.895 55.000 0.00 0.00 0.00 4.46
1935 3696 4.639310 TCCCTAGTCGAGTATGAAGTTGAC 59.361 45.833 0.00 0.00 39.07 3.18
2017 3778 9.554724 CGATACACTGCTTTACAAACATTAAAT 57.445 29.630 0.00 0.00 0.00 1.40
2033 3794 7.707774 ACATTAAATTCTGGTTTGGAAAACG 57.292 32.000 0.00 0.00 0.00 3.60
2165 3928 4.996758 GGCAAGCAAAATGGACTAACAAAT 59.003 37.500 0.00 0.00 0.00 2.32
2216 3998 4.437390 CGGAAAATGAGCTGAACATACCAC 60.437 45.833 0.00 0.00 0.00 4.16
2283 4065 4.987408 TTGTTGACATATGGCATCAAGG 57.013 40.909 24.87 0.00 37.71 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.353938 AGTTTATGCCATGTTCATTGCATC 58.646 37.500 21.65 11.84 43.01 3.91
15 16 5.528043 TTGTGTGAAAGTTTATGCCATGT 57.472 34.783 0.00 0.00 0.00 3.21
25 26 6.686630 TCATCAACTTGTTTGTGTGAAAGTT 58.313 32.000 0.00 0.00 42.13 2.66
27 28 7.760131 ATTCATCAACTTGTTTGTGTGAAAG 57.240 32.000 9.74 0.00 40.68 2.62
63 64 4.648762 TGGACATGAATTTGAACTTGTGGT 59.351 37.500 0.00 0.00 0.00 4.16
83 84 3.221771 CTTGGTTGGATGAACTTGTGGA 58.778 45.455 0.00 0.00 34.66 4.02
149 150 1.137825 GAAGACGAGGACGAGGCTG 59.862 63.158 0.00 0.00 42.66 4.85
212 213 1.018840 TGATGAGGAGGAGGAGGGAA 58.981 55.000 0.00 0.00 0.00 3.97
214 215 1.698532 CAATGATGAGGAGGAGGAGGG 59.301 57.143 0.00 0.00 0.00 4.30
291 295 0.552367 TCACACCCCCTTCCCATGAT 60.552 55.000 0.00 0.00 0.00 2.45
385 390 2.350895 CAACACCGGCATGGGAGA 59.649 61.111 0.00 0.00 44.64 3.71
400 405 4.659172 CAGCCGCAACCCCTCCAA 62.659 66.667 0.00 0.00 0.00 3.53
410 2151 3.479203 CCCCATCCTACAGCCGCA 61.479 66.667 0.00 0.00 0.00 5.69
571 2312 1.511318 CGGTCCAAATCGCCAACACA 61.511 55.000 0.00 0.00 0.00 3.72
573 2314 2.622011 GCGGTCCAAATCGCCAACA 61.622 57.895 0.00 0.00 45.42 3.33
603 2344 0.942410 ATAACCGTGCGCGCGATATT 60.942 50.000 41.67 31.20 36.67 1.28
615 2358 3.122323 CGGGCACGCAATAACCGT 61.122 61.111 0.00 0.00 39.70 4.83
709 2452 7.476955 TCCATCTAGGTGTATAAGAGCATCTCT 60.477 40.741 1.52 0.00 41.88 3.10
722 2465 9.496710 TTTATTTACTTCCTCCATCTAGGTGTA 57.503 33.333 1.52 0.00 37.91 2.90
723 2466 7.989947 TTATTTACTTCCTCCATCTAGGTGT 57.010 36.000 1.52 0.00 37.91 4.16
763 2506 1.481901 TAAGTTGGGCAGGCCGTGTA 61.482 55.000 8.81 0.00 36.85 2.90
784 2527 8.158789 TCAATGGCATTATTGATGAGATCACTA 58.841 33.333 13.23 0.00 40.95 2.74
785 2528 7.002276 TCAATGGCATTATTGATGAGATCACT 58.998 34.615 13.23 0.00 40.95 3.41
880 2634 2.943345 GACGTGTGCGCCTGTCTTG 61.943 63.158 4.18 0.00 42.83 3.02
882 2636 4.664677 GGACGTGTGCGCCTGTCT 62.665 66.667 4.18 0.00 42.83 3.41
901 2655 0.991146 TGGTATCTGGAAGCTGGCAA 59.009 50.000 0.00 0.00 0.00 4.52
959 2713 2.257371 CGACGAGCCAACGAGGAA 59.743 61.111 2.86 0.00 41.22 3.36
1142 2896 3.443045 CGCCAGCCCTCGCAAATT 61.443 61.111 0.00 0.00 37.52 1.82
1170 2924 2.284625 ATCCTCACCGCCCTGACA 60.285 61.111 0.00 0.00 0.00 3.58
1349 3105 9.883142 ATGATATAAATAGAAGGCAGCTTAGTC 57.117 33.333 0.00 0.00 0.00 2.59
1366 3122 9.267084 TGTTGTTAGCTATTGCGATGATATAAA 57.733 29.630 0.00 0.00 45.42 1.40
1369 3125 7.442364 AGTTGTTGTTAGCTATTGCGATGATAT 59.558 33.333 0.00 0.00 45.42 1.63
1434 3191 1.819928 ACTATGCATCCACAAACGCA 58.180 45.000 0.19 0.00 39.01 5.24
1436 3193 6.921307 TGTACTATACTATGCATCCACAAACG 59.079 38.462 0.19 0.00 0.00 3.60
1439 3196 7.597288 ACTGTACTATACTATGCATCCACAA 57.403 36.000 0.19 0.00 0.00 3.33
1550 3307 2.740981 GAGTTTCATCAGCTGTCAGTGG 59.259 50.000 14.67 0.00 0.00 4.00
1645 3402 4.101585 ACATAAGATCCAAAGCTCATCGGA 59.898 41.667 0.00 0.00 0.00 4.55
1654 3411 7.602517 ACTTCTCGAAACATAAGATCCAAAG 57.397 36.000 0.00 0.00 0.00 2.77
1695 3452 9.396938 CAGAACAAAAGCAAAACATTTTTCTTT 57.603 25.926 8.36 8.36 42.49 2.52
1698 3455 6.800892 TGCAGAACAAAAGCAAAACATTTTTC 59.199 30.769 0.00 0.00 34.97 2.29
1699 3456 6.675987 TGCAGAACAAAAGCAAAACATTTTT 58.324 28.000 0.00 0.00 34.97 1.94
1701 3458 5.876612 TGCAGAACAAAAGCAAAACATTT 57.123 30.435 0.00 0.00 34.97 2.32
1702 3459 5.642919 TCTTGCAGAACAAAAGCAAAACATT 59.357 32.000 0.00 0.00 46.30 2.71
1703 3460 5.177326 TCTTGCAGAACAAAAGCAAAACAT 58.823 33.333 0.00 0.00 46.30 2.71
1705 3462 5.521372 AGATCTTGCAGAACAAAAGCAAAAC 59.479 36.000 0.00 0.00 46.30 2.43
1860 3620 5.422331 TCCCAAATCTACTTTCTCATCGACT 59.578 40.000 0.00 0.00 0.00 4.18
1863 3623 6.520272 AGATCCCAAATCTACTTTCTCATCG 58.480 40.000 0.00 0.00 0.00 3.84
1890 3650 3.076621 CAAACTGGCAGCATGAGTTAGA 58.923 45.455 15.89 0.00 39.69 2.10
1891 3651 2.816087 ACAAACTGGCAGCATGAGTTAG 59.184 45.455 22.37 3.86 39.69 2.34
1892 3652 2.813754 GACAAACTGGCAGCATGAGTTA 59.186 45.455 22.37 0.00 39.69 2.24
1893 3653 1.610522 GACAAACTGGCAGCATGAGTT 59.389 47.619 22.37 4.61 39.69 3.01
1894 3654 1.242076 GACAAACTGGCAGCATGAGT 58.758 50.000 22.37 11.62 39.69 3.41
1915 3675 5.574082 CAGGTCAACTTCATACTCGACTAG 58.426 45.833 0.00 0.00 0.00 2.57
1949 3710 1.542108 GCGAATAGGGATGCAAGCTCT 60.542 52.381 0.00 0.00 0.00 4.09
1958 3719 4.086706 AGGAATTTTCGCGAATAGGGAT 57.913 40.909 24.05 9.08 41.64 3.85
2017 3778 3.759618 AGTTGTCGTTTTCCAAACCAGAA 59.240 39.130 0.00 0.00 0.00 3.02
2033 3794 1.531578 GGAAACGAAGCTCCAGTTGTC 59.468 52.381 0.00 0.00 33.47 3.18
2125 3888 2.033372 TGCCCCGTCGATTTACAGATA 58.967 47.619 0.00 0.00 0.00 1.98
2165 3928 4.994217 TCGATGACAGTTTTTCATGCAGTA 59.006 37.500 0.00 0.00 33.70 2.74
2216 3998 0.167251 AAATCAAGCGCCCGTTTACG 59.833 50.000 2.29 0.00 39.44 3.18


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

AutoCloner maintained by Alex Coulton.