Multiple sequence alignment - TraesCS7D01G293200

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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 TraesCS7D01G293200 chr7D 100.000 3458 0 0 1 3458 363038270 363041727 0.000000e+00 6386.0
1 TraesCS7D01G293200 chr7B 94.218 3459 106 24 1 3387 322474376 322477812 0.000000e+00 5193.0
2 TraesCS7D01G293200 chr7A 96.782 3108 54 16 304 3392 394836987 394833907 0.000000e+00 5144.0
3 TraesCS7D01G293200 chr7A 92.000 275 16 5 1 269 394856823 394856549 7.000000e-102 381.0
4 TraesCS7D01G293200 chr7A 100.000 31 0 0 274 304 394837030 394837000 1.340000e-04 58.4
5 TraesCS7D01G293200 chr4D 94.366 71 4 0 3386 3456 493754685 493754755 3.650000e-20 110.0
6 TraesCS7D01G293200 chr3D 93.151 73 5 0 3386 3458 126392333 126392405 1.310000e-19 108.0
7 TraesCS7D01G293200 chr3D 89.610 77 8 0 3382 3458 58405530 58405606 7.900000e-17 99.0
8 TraesCS7D01G293200 chr3D 88.750 80 8 1 3379 3458 498400470 498400392 2.840000e-16 97.1
9 TraesCS7D01G293200 chr5A 93.056 72 5 0 3387 3458 582587926 582587855 4.720000e-19 106.0
10 TraesCS7D01G293200 chr2D 90.667 75 7 0 3384 3458 548745480 548745554 2.200000e-17 100.0
11 TraesCS7D01G293200 chr2D 90.667 75 6 1 3382 3456 5726940 5727013 7.900000e-17 99.0
12 TraesCS7D01G293200 chrUn 90.541 74 6 1 3386 3458 99831392 99831465 2.840000e-16 97.1
13 TraesCS7D01G293200 chr5D 92.537 67 5 0 3392 3458 344691791 344691725 2.840000e-16 97.1


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 TraesCS7D01G293200 chr7D 363038270 363041727 3457 False 6386.0 6386 100.000 1 3458 1 chr7D.!!$F1 3457
1 TraesCS7D01G293200 chr7B 322474376 322477812 3436 False 5193.0 5193 94.218 1 3387 1 chr7B.!!$F1 3386
2 TraesCS7D01G293200 chr7A 394833907 394837030 3123 True 2601.2 5144 98.391 274 3392 2 chr7A.!!$R2 3118

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
330 347 0.387929 AGCCACACATATACCGACGG 59.612 55.0 13.61 13.61 0.0 4.79 F
1529 1555 0.475906 AGTCAATCTATGGGGGCTGC 59.524 55.0 0.00 0.00 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2069 0.469705 TTGGGTCTGGCATTTGCAGT 60.470 50.0 4.74 0.0 44.36 4.40 R
3385 3477 0.250989 CCCGTTGGAGTTGCCCTAAA 60.251 55.0 0.00 0.0 34.97 1.85 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
194 197 8.589338 AGAGCTTCTATGAAATACGGTATTCAT 58.411 33.333 13.41 17.47 45.54 2.57
330 347 0.387929 AGCCACACATATACCGACGG 59.612 55.000 13.61 13.61 0.00 4.79
355 372 8.758829 GGTCTAAAATGTTTTGAGGGGATTATT 58.241 33.333 1.16 0.00 0.00 1.40
357 374 9.540538 TCTAAAATGTTTTGAGGGGATTATTGA 57.459 29.630 1.16 0.00 0.00 2.57
557 582 3.857638 GGCGAGAAAAGCCGAAAAA 57.142 47.368 0.00 0.00 45.58 1.94
558 583 2.347697 GGCGAGAAAAGCCGAAAAAT 57.652 45.000 0.00 0.00 45.58 1.82
562 587 4.682401 GGCGAGAAAAGCCGAAAAATAAAA 59.318 37.500 0.00 0.00 45.58 1.52
564 589 5.388061 GCGAGAAAAGCCGAAAAATAAAACC 60.388 40.000 0.00 0.00 0.00 3.27
565 590 5.918576 CGAGAAAAGCCGAAAAATAAAACCT 59.081 36.000 0.00 0.00 0.00 3.50
566 591 6.087687 CGAGAAAAGCCGAAAAATAAAACCTC 59.912 38.462 0.00 0.00 0.00 3.85
569 594 2.829720 AGCCGAAAAATAAAACCTCCCC 59.170 45.455 0.00 0.00 0.00 4.81
673 698 1.602237 GACTCCCTGCCGAAATCCA 59.398 57.895 0.00 0.00 0.00 3.41
779 804 4.452733 CGCCCGACTCTCCCAACC 62.453 72.222 0.00 0.00 0.00 3.77
855 881 2.078392 AGTTCTTCCTCGTCTCGTCTC 58.922 52.381 0.00 0.00 0.00 3.36
974 1000 2.706190 ACCTTCACAGCTTCTAACACCT 59.294 45.455 0.00 0.00 0.00 4.00
1167 1193 2.290071 GGTTCCGGAATCTCCAAGAACA 60.290 50.000 22.04 0.00 44.74 3.18
1434 1460 1.377333 GGAAGGGGTTCGCCTTGAG 60.377 63.158 22.47 0.00 37.45 3.02
1512 1538 0.900182 TGAGCACGAGGGTGATGAGT 60.900 55.000 0.00 0.00 44.11 3.41
1529 1555 0.475906 AGTCAATCTATGGGGGCTGC 59.524 55.000 0.00 0.00 0.00 5.25
1593 1619 3.476552 GTTGATCCAGGTGAGTGAACAA 58.523 45.455 0.00 0.00 0.00 2.83
1698 1724 1.668751 CGGTCTCACAGCTCTCTAGAC 59.331 57.143 6.51 6.51 36.64 2.59
1745 1771 2.421424 GTGATGGCAAGATGACAGGAAC 59.579 50.000 0.00 0.00 39.76 3.62
1746 1772 2.040145 TGATGGCAAGATGACAGGAACA 59.960 45.455 0.00 0.00 39.76 3.18
1975 2001 0.909610 TGGAAGAGGAGGCGGTGAAT 60.910 55.000 0.00 0.00 0.00 2.57
2043 2069 0.604780 GTGAGAGCTTGAGGCAGCAA 60.605 55.000 0.00 0.00 42.84 3.91
2295 2321 3.132289 TCCGATTGCCGTCTTCTAATTCT 59.868 43.478 0.00 0.00 36.31 2.40
2400 2426 0.547712 AGGCAGCCCAAAGTAGGAGA 60.548 55.000 8.22 0.00 0.00 3.71
2522 2548 7.187824 AGATCATACTTTGTCTGTACCATGT 57.812 36.000 0.00 0.00 0.00 3.21
2523 2549 7.268586 AGATCATACTTTGTCTGTACCATGTC 58.731 38.462 0.00 0.00 0.00 3.06
2524 2550 6.353404 TCATACTTTGTCTGTACCATGTCA 57.647 37.500 0.00 0.00 0.00 3.58
2525 2551 6.946340 TCATACTTTGTCTGTACCATGTCAT 58.054 36.000 0.00 0.00 0.00 3.06
2526 2552 6.818142 TCATACTTTGTCTGTACCATGTCATG 59.182 38.462 5.79 5.79 0.00 3.07
2527 2553 5.227569 ACTTTGTCTGTACCATGTCATGA 57.772 39.130 14.67 0.00 0.00 3.07
2779 2833 5.292834 CGTCAAGACTGATGAATGTAGCAAT 59.707 40.000 0.00 0.00 40.52 3.56
2866 2920 4.515028 AAGATTGGCATCCAGATCTTGA 57.485 40.909 9.87 0.00 38.55 3.02
3113 3178 2.435372 TCTGTCCCAAACAAGCAACT 57.565 45.000 0.00 0.00 37.45 3.16
3228 3318 6.697019 AGAAGATGACCAAATTTGTTTGAACG 59.303 34.615 16.73 2.48 33.95 3.95
3265 3355 8.623903 TGCTATTTACATTTCAGGATTGTCATC 58.376 33.333 0.00 0.00 0.00 2.92
3382 3474 0.804989 GGATGGGTCAGCGTCAAAAG 59.195 55.000 0.00 0.00 0.00 2.27
3383 3475 1.610624 GGATGGGTCAGCGTCAAAAGA 60.611 52.381 0.00 0.00 0.00 2.52
3384 3476 1.734465 GATGGGTCAGCGTCAAAAGAG 59.266 52.381 0.00 0.00 0.00 2.85
3385 3477 0.468226 TGGGTCAGCGTCAAAAGAGT 59.532 50.000 0.00 0.00 0.00 3.24
3388 3480 3.135994 GGGTCAGCGTCAAAAGAGTTTA 58.864 45.455 0.00 0.00 0.00 2.01
3389 3481 3.186613 GGGTCAGCGTCAAAAGAGTTTAG 59.813 47.826 0.00 0.00 0.00 1.85
3390 3482 3.186613 GGTCAGCGTCAAAAGAGTTTAGG 59.813 47.826 0.00 0.00 0.00 2.69
3392 3484 2.095718 CAGCGTCAAAAGAGTTTAGGGC 60.096 50.000 0.00 0.00 0.00 5.19
3393 3485 1.877443 GCGTCAAAAGAGTTTAGGGCA 59.123 47.619 0.00 0.00 0.00 5.36
3394 3486 2.292292 GCGTCAAAAGAGTTTAGGGCAA 59.708 45.455 0.00 0.00 0.00 4.52
3395 3487 3.852205 GCGTCAAAAGAGTTTAGGGCAAC 60.852 47.826 0.00 0.00 0.00 4.17
3396 3488 3.564225 CGTCAAAAGAGTTTAGGGCAACT 59.436 43.478 0.00 0.00 39.84 3.16
3402 3494 1.804748 GAGTTTAGGGCAACTCCAACG 59.195 52.381 5.18 0.00 44.84 4.10
3403 3495 0.879090 GTTTAGGGCAACTCCAACGG 59.121 55.000 0.00 0.00 36.21 4.44
3404 3496 0.250989 TTTAGGGCAACTCCAACGGG 60.251 55.000 0.00 0.00 36.21 5.28
3405 3497 2.132089 TTAGGGCAACTCCAACGGGG 62.132 60.000 0.00 0.00 36.21 5.73
3409 3501 3.047877 CAACTCCAACGGGGCGAC 61.048 66.667 0.00 0.00 36.21 5.19
3421 3513 3.192922 GGCGACCCATTTCGTCCG 61.193 66.667 0.00 0.00 41.26 4.79
3422 3514 2.433664 GCGACCCATTTCGTCCGT 60.434 61.111 0.00 0.00 41.26 4.69
3423 3515 2.030958 GCGACCCATTTCGTCCGTT 61.031 57.895 0.00 0.00 41.26 4.44
3424 3516 1.785321 CGACCCATTTCGTCCGTTG 59.215 57.895 0.00 0.00 34.16 4.10
3425 3517 1.632046 CGACCCATTTCGTCCGTTGG 61.632 60.000 0.00 0.00 34.16 3.77
3426 3518 0.604511 GACCCATTTCGTCCGTTGGT 60.605 55.000 0.00 0.00 0.00 3.67
3427 3519 0.887387 ACCCATTTCGTCCGTTGGTG 60.887 55.000 0.00 0.00 0.00 4.17
3428 3520 0.887387 CCCATTTCGTCCGTTGGTGT 60.887 55.000 0.00 0.00 0.00 4.16
3429 3521 0.515564 CCATTTCGTCCGTTGGTGTC 59.484 55.000 0.00 0.00 0.00 3.67
3430 3522 0.515564 CATTTCGTCCGTTGGTGTCC 59.484 55.000 0.00 0.00 0.00 4.02
3431 3523 0.947180 ATTTCGTCCGTTGGTGTCCG 60.947 55.000 0.00 0.00 0.00 4.79
3432 3524 2.295472 TTTCGTCCGTTGGTGTCCGT 62.295 55.000 0.00 0.00 0.00 4.69
3433 3525 2.279650 CGTCCGTTGGTGTCCGTT 60.280 61.111 0.00 0.00 0.00 4.44
3434 3526 1.884004 CGTCCGTTGGTGTCCGTTT 60.884 57.895 0.00 0.00 0.00 3.60
3435 3527 1.644913 GTCCGTTGGTGTCCGTTTG 59.355 57.895 0.00 0.00 0.00 2.93
3436 3528 1.524165 TCCGTTGGTGTCCGTTTGG 60.524 57.895 0.00 0.00 0.00 3.28
3437 3529 2.548295 CCGTTGGTGTCCGTTTGGG 61.548 63.158 0.00 0.00 35.24 4.12
3438 3530 1.820481 CGTTGGTGTCCGTTTGGGT 60.820 57.895 0.00 0.00 37.00 4.51
3439 3531 1.778027 CGTTGGTGTCCGTTTGGGTC 61.778 60.000 0.00 0.00 37.00 4.46
3440 3532 1.524165 TTGGTGTCCGTTTGGGTCG 60.524 57.895 0.00 0.00 37.00 4.79
3442 3534 3.351416 GTGTCCGTTTGGGTCGGC 61.351 66.667 0.00 0.00 46.49 5.54
3443 3535 4.973055 TGTCCGTTTGGGTCGGCG 62.973 66.667 0.00 0.00 46.49 6.46
3455 3547 3.788817 TCGGCGCCGACATAAAAG 58.211 55.556 45.37 16.92 44.01 2.27
3456 3548 1.079681 TCGGCGCCGACATAAAAGT 60.080 52.632 45.37 0.00 44.01 2.66
3457 3549 1.079875 TCGGCGCCGACATAAAAGTC 61.080 55.000 45.37 4.15 44.01 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 347 9.586435 CAATAATCCCCTCAAAACATTTTAGAC 57.414 33.333 0.00 0.00 0.00 2.59
557 582 1.631181 GGAGGGGAGGGGAGGTTTTAT 60.631 57.143 0.00 0.00 0.00 1.40
558 583 0.253488 GGAGGGGAGGGGAGGTTTTA 60.253 60.000 0.00 0.00 0.00 1.52
569 594 3.083997 CGAACAGGGGGAGGGGAG 61.084 72.222 0.00 0.00 0.00 4.30
673 698 3.083997 GGCGATCAGTGGGAGGGT 61.084 66.667 0.00 0.00 0.00 4.34
705 730 1.210155 GCGAAATTGCTTGCTCCGT 59.790 52.632 0.00 0.00 0.00 4.69
779 804 3.060602 GGTCAGGACGAACAGAAAAGAG 58.939 50.000 0.00 0.00 0.00 2.85
855 881 2.607668 TAGCAGGAACGCGGATGTCG 62.608 60.000 12.47 0.00 42.76 4.35
936 962 1.819632 GTGAGCGGCGGGAATTGAT 60.820 57.895 9.78 0.00 0.00 2.57
1167 1193 2.036475 CGGTAATACTGCAGGCTCATCT 59.964 50.000 19.93 0.00 0.00 2.90
1354 1380 2.124570 GGCATCATGTGAGGGCGT 60.125 61.111 5.49 0.00 41.28 5.68
1434 1460 1.248486 GAGAAAGCCTTTCCACCCAC 58.752 55.000 13.45 0.00 40.54 4.61
1512 1538 1.053835 TCGCAGCCCCCATAGATTGA 61.054 55.000 0.00 0.00 0.00 2.57
1529 1555 3.782369 CGTCATGTCTTCAATTGCATTCG 59.218 43.478 0.00 2.93 0.00 3.34
1611 1637 1.227853 GTTGCGGTTCACTGACCCT 60.228 57.895 0.00 0.00 36.28 4.34
1745 1771 0.951040 GTCCTTCTTGACGGCACCTG 60.951 60.000 0.00 0.00 0.00 4.00
1746 1772 1.371558 GTCCTTCTTGACGGCACCT 59.628 57.895 0.00 0.00 0.00 4.00
1975 2001 3.329889 ATTGCTGGAGGCGTCCCA 61.330 61.111 22.25 11.32 43.15 4.37
2043 2069 0.469705 TTGGGTCTGGCATTTGCAGT 60.470 50.000 4.74 0.00 44.36 4.40
2295 2321 3.273048 GCGGGTGCAGCATTAACA 58.727 55.556 19.06 0.00 42.15 2.41
2520 2546 3.421919 TTGGAGCTTGACATCATGACA 57.578 42.857 0.00 0.00 0.00 3.58
2521 2547 4.771590 TTTTGGAGCTTGACATCATGAC 57.228 40.909 0.00 0.00 0.00 3.06
2522 2548 4.583907 TGTTTTTGGAGCTTGACATCATGA 59.416 37.500 0.00 0.00 0.00 3.07
2523 2549 4.873817 TGTTTTTGGAGCTTGACATCATG 58.126 39.130 0.00 0.00 0.00 3.07
2524 2550 5.733620 ATGTTTTTGGAGCTTGACATCAT 57.266 34.783 0.00 0.00 0.00 2.45
2525 2551 5.769662 ACTATGTTTTTGGAGCTTGACATCA 59.230 36.000 0.00 0.00 0.00 3.07
2526 2552 6.072508 TGACTATGTTTTTGGAGCTTGACATC 60.073 38.462 0.00 0.00 0.00 3.06
2527 2553 5.769662 TGACTATGTTTTTGGAGCTTGACAT 59.230 36.000 0.00 0.00 0.00 3.06
2742 2796 6.518493 TCAGTCTTGACGGTACAAAAACTAT 58.482 36.000 0.00 0.00 30.30 2.12
2885 2939 9.232473 CATTGGACTATCATTTCAGATCATGAT 57.768 33.333 8.25 8.25 41.89 2.45
3069 3131 3.077359 AGAGTACTGCTGCATTTCCAAC 58.923 45.455 1.31 0.00 0.00 3.77
3113 3178 4.038282 TGTTCGACTAAAACTGGACAGCTA 59.962 41.667 0.00 0.00 0.00 3.32
3202 3271 7.096477 CGTTCAAACAAATTTGGTCATCTTCTC 60.096 37.037 21.74 2.16 44.61 2.87
3228 3318 9.585099 TGAAATGTAAATAGCAAATGTTCATCC 57.415 29.630 0.00 0.00 0.00 3.51
3265 3355 3.659786 TCCTGTTGTTCGGTGTAATCAG 58.340 45.455 0.00 0.00 0.00 2.90
3383 3475 1.544759 CCGTTGGAGTTGCCCTAAACT 60.545 52.381 0.00 0.00 43.08 2.66
3384 3476 0.879090 CCGTTGGAGTTGCCCTAAAC 59.121 55.000 0.00 0.00 34.97 2.01
3385 3477 0.250989 CCCGTTGGAGTTGCCCTAAA 60.251 55.000 0.00 0.00 34.97 1.85
3388 3480 3.966543 CCCCGTTGGAGTTGCCCT 61.967 66.667 0.00 0.00 35.39 5.19
3392 3484 3.047877 GTCGCCCCGTTGGAGTTG 61.048 66.667 0.00 0.00 35.07 3.16
3393 3485 4.324991 GGTCGCCCCGTTGGAGTT 62.325 66.667 0.00 0.00 35.07 3.01
3403 3495 2.822701 GGACGAAATGGGTCGCCC 60.823 66.667 7.87 7.87 45.00 6.13
3404 3496 3.192922 CGGACGAAATGGGTCGCC 61.193 66.667 0.00 0.00 45.00 5.54
3405 3497 2.030958 AACGGACGAAATGGGTCGC 61.031 57.895 0.00 0.00 45.00 5.19
3406 3498 1.632046 CCAACGGACGAAATGGGTCG 61.632 60.000 0.00 0.00 46.54 4.79
3407 3499 0.604511 ACCAACGGACGAAATGGGTC 60.605 55.000 15.82 0.00 37.26 4.46
3408 3500 0.887387 CACCAACGGACGAAATGGGT 60.887 55.000 15.82 6.39 37.26 4.51
3409 3501 0.887387 ACACCAACGGACGAAATGGG 60.887 55.000 15.82 9.82 37.26 4.00
3410 3502 0.515564 GACACCAACGGACGAAATGG 59.484 55.000 0.00 6.57 38.91 3.16
3411 3503 0.515564 GGACACCAACGGACGAAATG 59.484 55.000 0.00 0.00 0.00 2.32
3412 3504 0.947180 CGGACACCAACGGACGAAAT 60.947 55.000 0.00 0.00 0.00 2.17
3413 3505 1.592131 CGGACACCAACGGACGAAA 60.592 57.895 0.00 0.00 0.00 3.46
3414 3506 2.027897 CGGACACCAACGGACGAA 59.972 61.111 0.00 0.00 0.00 3.85
3415 3507 2.295472 AAACGGACACCAACGGACGA 62.295 55.000 0.00 0.00 0.00 4.20
3416 3508 1.884004 AAACGGACACCAACGGACG 60.884 57.895 0.00 0.00 0.00 4.79
3417 3509 1.644913 CAAACGGACACCAACGGAC 59.355 57.895 0.00 0.00 0.00 4.79
3418 3510 1.524165 CCAAACGGACACCAACGGA 60.524 57.895 0.00 0.00 0.00 4.69
3419 3511 2.548295 CCCAAACGGACACCAACGG 61.548 63.158 0.00 0.00 0.00 4.44
3420 3512 1.778027 GACCCAAACGGACACCAACG 61.778 60.000 0.00 0.00 34.64 4.10
3421 3513 1.778027 CGACCCAAACGGACACCAAC 61.778 60.000 0.00 0.00 34.64 3.77
3422 3514 1.524165 CGACCCAAACGGACACCAA 60.524 57.895 0.00 0.00 34.64 3.67
3423 3515 2.109387 CGACCCAAACGGACACCA 59.891 61.111 0.00 0.00 34.64 4.17
3438 3530 1.079681 ACTTTTATGTCGGCGCCGA 60.080 52.632 45.37 45.37 46.87 5.54
3439 3531 1.347221 GACTTTTATGTCGGCGCCG 59.653 57.895 42.13 42.13 41.35 6.46


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

AutoCloner maintained by Alex Coulton.