Multiple sequence alignment - TraesCS7A01G061100

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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 TraesCS7A01G061100 chr7A 100.000 3317 0 0 1 3317 30095575 30092259 0.000000e+00 6126
1 TraesCS7A01G061100 chr7D 90.527 3399 212 41 1 3317 29836605 29833235 0.000000e+00 4392
2 TraesCS7A01G061100 chr7D 96.721 61 2 0 2816 2876 29833709 29833649 5.850000e-18 102
3 TraesCS7A01G061100 chr4A 89.583 3408 201 47 1 3317 699883081 699886425 0.000000e+00 4185


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 TraesCS7A01G061100 chr7A 30092259 30095575 3316 True 6126 6126 100.000 1 3317 1 chr7A.!!$R1 3316
1 TraesCS7A01G061100 chr7D 29833235 29836605 3370 True 2247 4392 93.624 1 3317 2 chr7D.!!$R1 3316
2 TraesCS7A01G061100 chr4A 699883081 699886425 3344 False 4185 4185 89.583 1 3317 1 chr4A.!!$F1 3316

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
579 616 0.182775 GTGAGGAACTGGGGTGTTGT 59.817 55.0 0.0 0.00 41.55 3.32 F
641 690 0.537188 ATGTCCGGTGTTAGCTCTGG 59.463 55.0 0.0 0.31 36.29 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2134 0.321653 ATGCCTCGTCTTTCGCCTTT 60.322 50.0 0.0 0.0 39.67 3.11 R
2519 2621 0.944386 GGCTTTTCGACACTGCTGAA 59.056 50.0 0.0 0.0 0.00 3.02 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
27 28 2.798148 GAAACGGACGGGCCAGATGT 62.798 60.000 10.86 0.00 35.94 3.06
88 89 3.809013 CCCCTTCCCATCCCACCG 61.809 72.222 0.00 0.00 0.00 4.94
255 288 2.805827 ATCCACCCATCCACCCACCT 62.806 60.000 0.00 0.00 0.00 4.00
270 307 3.822192 CCTCGTCCGCGGACATCA 61.822 66.667 46.26 32.09 44.77 3.07
275 312 2.443952 TCCGCGGACATCATCCCT 60.444 61.111 27.28 0.00 46.04 4.20
318 355 1.377725 CTCAAATCTGGGCGGTGCT 60.378 57.895 0.00 0.00 0.00 4.40
371 408 4.814294 GGTACAGCGCCCTCGTGG 62.814 72.222 2.29 0.00 38.14 4.94
475 512 2.019984 ACCGGTTGTAGATACTCCGAC 58.980 52.381 20.16 4.37 42.25 4.79
485 522 1.041447 ATACTCCGACGAACCCCCTG 61.041 60.000 0.00 0.00 0.00 4.45
490 527 1.298667 CGACGAACCCCCTGGATTT 59.701 57.895 0.00 0.00 34.81 2.17
492 529 0.393944 GACGAACCCCCTGGATTTCC 60.394 60.000 0.00 0.00 34.81 3.13
497 534 0.784154 ACCCCCTGGATTTCCCCTTT 60.784 55.000 0.00 0.00 34.81 3.11
501 538 1.478631 CCTGGATTTCCCCTTTGCTC 58.521 55.000 0.00 0.00 34.29 4.26
508 545 2.852495 TTCCCCTTTGCTCTAGCGCG 62.852 60.000 0.00 0.00 45.83 6.86
511 548 2.397252 CTTTGCTCTAGCGCGCAC 59.603 61.111 35.10 16.91 45.83 5.34
541 578 2.391879 GGATCTACAACATCCGCGTAC 58.608 52.381 4.92 0.00 30.62 3.67
549 586 3.500680 ACAACATCCGCGTACTGATTTTT 59.499 39.130 4.92 0.00 0.00 1.94
550 587 4.691685 ACAACATCCGCGTACTGATTTTTA 59.308 37.500 4.92 0.00 0.00 1.52
552 589 4.501071 ACATCCGCGTACTGATTTTTAGT 58.499 39.130 4.92 0.00 0.00 2.24
555 592 2.606272 CCGCGTACTGATTTTTAGTCCC 59.394 50.000 4.92 0.00 0.00 4.46
556 593 3.255725 CGCGTACTGATTTTTAGTCCCA 58.744 45.455 0.00 0.00 0.00 4.37
557 594 3.680937 CGCGTACTGATTTTTAGTCCCAA 59.319 43.478 0.00 0.00 0.00 4.12
558 595 4.435121 CGCGTACTGATTTTTAGTCCCAAC 60.435 45.833 0.00 0.00 0.00 3.77
568 605 3.764237 TTAGTCCCAACTGTGAGGAAC 57.236 47.619 0.97 0.00 36.92 3.62
579 616 0.182775 GTGAGGAACTGGGGTGTTGT 59.817 55.000 0.00 0.00 41.55 3.32
641 690 0.537188 ATGTCCGGTGTTAGCTCTGG 59.463 55.000 0.00 0.31 36.29 3.86
664 725 0.593128 ATTTGTGAGTGTTCTGGCGC 59.407 50.000 0.00 0.00 0.00 6.53
693 758 4.163458 TGCCATTAGTTAGTACCCCTGAAG 59.837 45.833 0.00 0.00 0.00 3.02
694 759 4.407945 GCCATTAGTTAGTACCCCTGAAGA 59.592 45.833 0.00 0.00 0.00 2.87
699 764 4.095211 AGTTAGTACCCCTGAAGAGGTTC 58.905 47.826 0.00 0.00 37.73 3.62
750 815 6.484308 GCAAGGTTTGAGTAGTTAGTTAACCA 59.516 38.462 0.88 0.00 36.88 3.67
801 866 4.814294 ATTCGGACGTCGGGCAGC 62.814 66.667 21.27 0.30 39.77 5.25
835 900 9.660180 TTATTTCCATTTATTTGCTTTGGGTAC 57.340 29.630 0.00 0.00 0.00 3.34
891 956 1.440938 TTTTGCACCCGTGGTCGAAG 61.441 55.000 0.00 0.00 39.71 3.79
960 1026 3.068024 TGTTGCAAATGAAGGTGGAAGAC 59.932 43.478 0.00 0.00 0.00 3.01
1085 1152 2.461945 GCTTTAGAAGGACCGGCGC 61.462 63.158 0.00 0.00 0.00 6.53
1159 1226 0.651031 GAGCAAGTATTTCGCGGACC 59.349 55.000 6.13 0.00 0.00 4.46
1329 1402 2.391389 GGCTCTTGGCGTTCTTCGG 61.391 63.158 0.00 0.00 42.94 4.30
1362 1435 0.787787 TCAAATCCGAGTTCGTTGCG 59.212 50.000 0.48 0.00 37.74 4.85
1494 1567 2.202395 TTTGCAAGCTCCCAGTGCC 61.202 57.895 0.00 0.00 37.48 5.01
1561 1634 1.370609 CATGGAGACTTCAGCTGCTG 58.629 55.000 23.31 23.31 0.00 4.41
1710 1783 2.105993 ACTGTTGTCAACCCTTAGGACC 59.894 50.000 13.13 0.00 36.73 4.46
1890 1963 0.679505 TTGTCTCGGTGGTTCAGGAG 59.320 55.000 0.00 0.00 0.00 3.69
1911 1984 4.725490 AGGAGAAGTATAGCTCAGGTCTC 58.275 47.826 0.00 0.00 32.83 3.36
1989 2062 1.890552 ATGGCTCTGTGATTCTCCCT 58.109 50.000 0.00 0.00 0.00 4.20
2061 2134 0.241749 CAAAGCGCTTCCTTGATGCA 59.758 50.000 25.24 0.00 33.20 3.96
2082 2155 1.716172 GGCGAAAGACGAGGCATTC 59.284 57.895 0.00 0.00 45.77 2.67
2181 2254 1.954382 CAGTCGGATATCCTGTCGGAA 59.046 52.381 19.61 0.00 44.02 4.30
2452 2553 9.081997 CATGTTCTATACAGTTCAGTTCTTCTC 57.918 37.037 0.00 0.00 40.83 2.87
2480 2581 0.313672 TCTTGTTGCAAATCACCGGC 59.686 50.000 0.00 0.00 0.00 6.13
2519 2621 0.595588 CGTGCGGAGATATCTGAGCT 59.404 55.000 22.16 0.00 0.00 4.09
2522 2624 2.035193 GTGCGGAGATATCTGAGCTTCA 59.965 50.000 22.16 6.89 0.00 3.02
2523 2625 2.295629 TGCGGAGATATCTGAGCTTCAG 59.704 50.000 22.16 6.79 45.59 3.02
2525 2627 2.295629 CGGAGATATCTGAGCTTCAGCA 59.704 50.000 10.74 0.97 43.95 4.41
2553 2655 9.781834 TGTCGAAAAGCCTATAATTATTGTTTG 57.218 29.630 2.68 0.00 0.00 2.93
2638 2741 0.900647 CCGAGTGACTCCCAGTTCCT 60.901 60.000 7.07 0.00 0.00 3.36
2755 2858 7.227711 GCCAAAAACTCTCTCTAAAGAAAGAGT 59.772 37.037 9.68 9.68 43.02 3.24
2821 2927 1.902508 CTGTTTACTCCCTCTGCCTCA 59.097 52.381 0.00 0.00 0.00 3.86
2829 2935 2.364970 CTCCCTCTGCCTCAAGATGTAG 59.635 54.545 0.00 0.00 0.00 2.74
2953 3084 2.613133 GCTTCTGTCCTGATCTTGCATC 59.387 50.000 0.00 0.00 0.00 3.91
2961 3092 5.046376 TGTCCTGATCTTGCATCAAGTCTTA 60.046 40.000 6.47 0.00 41.66 2.10
3162 3300 3.181506 GCCAGGAAAGTCATTCTTTAGCG 60.182 47.826 0.00 0.00 45.15 4.26
3183 3321 4.153475 GCGTTCTTGTACAGCTTAATGGAA 59.847 41.667 0.00 0.00 0.00 3.53
3190 3328 2.699954 ACAGCTTAATGGAAGTGGACG 58.300 47.619 0.00 0.00 37.49 4.79
3191 3329 2.009774 CAGCTTAATGGAAGTGGACGG 58.990 52.381 0.00 0.00 37.49 4.79
3219 3357 9.120538 GCATCAGATAGGTTTGGAAATTTAGTA 57.879 33.333 0.00 0.00 0.00 1.82
3261 3399 4.680110 CACTAAACCGCTCGAATCGAATAT 59.320 41.667 6.84 0.00 34.74 1.28
3295 3438 1.152881 GGCCATCCTAACCCAGCTG 60.153 63.158 6.78 6.78 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.291043 ATCTGGCCCGTCCGTTTCT 61.291 57.895 0.00 0.00 37.80 2.52
70 71 3.429580 GGTGGGATGGGAAGGGGG 61.430 72.222 0.00 0.00 0.00 5.40
71 72 3.809013 CGGTGGGATGGGAAGGGG 61.809 72.222 0.00 0.00 0.00 4.79
241 274 3.009115 ACGAGGTGGGTGGATGGG 61.009 66.667 0.00 0.00 0.00 4.00
263 300 1.592669 CGCGACAGGGATGATGTCC 60.593 63.158 0.00 0.00 43.36 4.02
265 302 1.402896 ATCCGCGACAGGGATGATGT 61.403 55.000 8.23 0.00 42.63 3.06
267 304 0.469917 AAATCCGCGACAGGGATGAT 59.530 50.000 8.23 0.00 43.43 2.45
270 307 1.227263 CGAAATCCGCGACAGGGAT 60.227 57.895 8.23 0.00 46.14 3.85
315 352 2.490217 GCTTCTAGCGACGGAGCA 59.510 61.111 7.12 0.00 40.15 4.26
335 372 4.525949 GCGCGTCCTCCCTAACCC 62.526 72.222 8.43 0.00 0.00 4.11
452 489 1.202498 GGAGTATCTACAACCGGTGGC 60.202 57.143 8.52 0.00 33.73 5.01
475 512 1.076995 GGGAAATCCAGGGGGTTCG 60.077 63.158 1.22 0.00 37.91 3.95
485 522 2.302260 GCTAGAGCAAAGGGGAAATCC 58.698 52.381 0.00 0.00 41.59 3.01
490 527 2.584608 GCGCTAGAGCAAAGGGGA 59.415 61.111 14.09 0.00 42.21 4.81
492 529 3.567797 GCGCGCTAGAGCAAAGGG 61.568 66.667 26.67 2.68 42.91 3.95
508 545 2.363711 TAGATCCGTGGGCATCGTGC 62.364 60.000 1.92 1.92 44.08 5.34
511 548 0.104120 TTGTAGATCCGTGGGCATCG 59.896 55.000 0.00 0.00 0.00 3.84
541 578 5.182001 CCTCACAGTTGGGACTAAAAATCAG 59.818 44.000 0.00 0.00 33.90 2.90
549 586 2.632996 CAGTTCCTCACAGTTGGGACTA 59.367 50.000 3.51 0.00 40.03 2.59
550 587 1.417890 CAGTTCCTCACAGTTGGGACT 59.582 52.381 0.00 0.00 42.61 3.85
552 589 0.764890 CCAGTTCCTCACAGTTGGGA 59.235 55.000 0.00 0.00 0.00 4.37
555 592 0.474184 ACCCCAGTTCCTCACAGTTG 59.526 55.000 0.00 0.00 0.00 3.16
556 593 0.474184 CACCCCAGTTCCTCACAGTT 59.526 55.000 0.00 0.00 0.00 3.16
557 594 0.694444 ACACCCCAGTTCCTCACAGT 60.694 55.000 0.00 0.00 0.00 3.55
558 595 0.474184 AACACCCCAGTTCCTCACAG 59.526 55.000 0.00 0.00 0.00 3.66
568 605 2.362077 CTCCAGAAAAACAACACCCCAG 59.638 50.000 0.00 0.00 0.00 4.45
627 673 2.386661 ATTGACCAGAGCTAACACCG 57.613 50.000 0.00 0.00 0.00 4.94
628 674 3.821033 ACAAATTGACCAGAGCTAACACC 59.179 43.478 0.00 0.00 0.00 4.16
641 690 3.632189 GCCAGAACACTCACAAATTGAC 58.368 45.455 0.00 0.00 0.00 3.18
664 725 4.443034 GGGTACTAACTAATGGCACTGGAG 60.443 50.000 0.00 0.00 0.00 3.86
674 735 5.851418 ACCTCTTCAGGGGTACTAACTAAT 58.149 41.667 0.00 0.00 45.53 1.73
750 815 0.247736 GAGTCGGCATTCAGACACCT 59.752 55.000 0.00 0.00 39.67 4.00
835 900 7.148306 GGTTATACATAAATCCTACGGCATTGG 60.148 40.741 0.00 0.00 0.00 3.16
841 906 6.367969 GTGCTGGTTATACATAAATCCTACGG 59.632 42.308 0.00 0.00 0.00 4.02
891 956 4.145876 TCATGAAAACACGATCAGTTGC 57.854 40.909 0.00 0.00 0.00 4.17
960 1026 0.462225 CTGGAGATCAGTGGCAGCAG 60.462 60.000 0.00 0.00 38.64 4.24
980 1046 7.664318 TCTCCATAGTGAGCGATAAAGTATACA 59.336 37.037 5.50 0.00 32.22 2.29
1159 1226 0.524862 GCATCACTTTGACCCAGCAG 59.475 55.000 0.00 0.00 0.00 4.24
1173 1243 1.195442 TACCACCAGAACGGGCATCA 61.195 55.000 0.00 0.00 40.22 3.07
1329 1402 0.107945 ATTTGAGAGAGGTCGCTGCC 60.108 55.000 0.00 0.00 0.00 4.85
1362 1435 1.141053 AGGTATCCGATGCAGGTTTCC 59.859 52.381 0.00 0.00 0.00 3.13
1494 1567 3.181511 TGAAAACAGTCTTGACAGCGTTG 60.182 43.478 0.00 0.00 0.00 4.10
1569 1642 1.338484 GCAGCAGTCTTGAGGTCATCA 60.338 52.381 0.00 0.00 35.62 3.07
1593 1666 2.641305 AGCATGAAGTCAATCTGCTCC 58.359 47.619 0.00 0.00 38.78 4.70
1620 1693 0.452987 CAATTGCAGGGTCATCACCG 59.547 55.000 0.00 0.00 44.91 4.94
1701 1774 1.041437 GATCCAGTCCGGTCCTAAGG 58.959 60.000 0.00 0.00 35.57 2.69
1710 1783 1.144936 GGCCAAGAGATCCAGTCCG 59.855 63.158 0.00 0.00 0.00 4.79
1890 1963 4.518970 CAGAGACCTGAGCTATACTTCTCC 59.481 50.000 7.77 0.00 43.02 3.71
1911 1984 0.595095 GCTTTGTCTTCACAGCCCAG 59.405 55.000 0.00 0.00 40.31 4.45
1989 2062 1.065926 AGATGCGCTCTGGATGTTGAA 60.066 47.619 9.73 0.00 31.12 2.69
2040 2113 1.336240 GCATCAAGGAAGCGCTTTGTT 60.336 47.619 25.84 17.38 35.30 2.83
2061 2134 0.321653 ATGCCTCGTCTTTCGCCTTT 60.322 50.000 0.00 0.00 39.67 3.11
2087 2160 4.778143 ACAAGCCCGCGTCCATCC 62.778 66.667 4.92 0.00 0.00 3.51
2115 2188 3.252944 TCAATGAAACAATTGCGCTCTCA 59.747 39.130 9.73 1.93 37.44 3.27
2452 2553 5.630680 GTGATTTGCAACAAGAACATACTGG 59.369 40.000 0.00 0.00 0.00 4.00
2519 2621 0.944386 GGCTTTTCGACACTGCTGAA 59.056 50.000 0.00 0.00 0.00 3.02
2522 2624 2.770164 ATAGGCTTTTCGACACTGCT 57.230 45.000 0.00 0.00 0.00 4.24
2523 2625 5.485662 AATTATAGGCTTTTCGACACTGC 57.514 39.130 0.00 0.00 0.00 4.40
2525 2627 8.732746 ACAATAATTATAGGCTTTTCGACACT 57.267 30.769 0.00 0.00 0.00 3.55
2584 2686 8.927675 TCTTAACCTGGTTTACACAATGTAAT 57.072 30.769 18.58 0.00 41.83 1.89
2587 2689 6.362248 ACTCTTAACCTGGTTTACACAATGT 58.638 36.000 18.58 5.00 0.00 2.71
2588 2690 6.877611 ACTCTTAACCTGGTTTACACAATG 57.122 37.500 18.58 1.09 0.00 2.82
2589 2691 6.489022 GGAACTCTTAACCTGGTTTACACAAT 59.511 38.462 18.58 0.00 0.00 2.71
2590 2692 5.824097 GGAACTCTTAACCTGGTTTACACAA 59.176 40.000 18.58 4.47 0.00 3.33
2591 2693 5.131475 AGGAACTCTTAACCTGGTTTACACA 59.869 40.000 18.58 0.00 32.39 3.72
2592 2694 5.469084 CAGGAACTCTTAACCTGGTTTACAC 59.531 44.000 18.58 3.74 44.96 2.90
2699 2802 0.449388 GGAAAGCATGCCAGAGAACG 59.551 55.000 15.66 0.00 0.00 3.95
2755 2858 2.892852 CCTGGAAGAAGCAACCATCAAA 59.107 45.455 0.00 0.00 34.07 2.69
2953 3084 7.454260 AAGGGAATTAACTTGCTAAGACTTG 57.546 36.000 0.00 0.00 0.00 3.16
2961 3092 7.468141 CCTTTCTTAAGGGAATTAACTTGCT 57.532 36.000 1.85 0.00 46.10 3.91
3038 3173 4.646945 TGAACACCACAAAAGCCTGATAAA 59.353 37.500 0.00 0.00 0.00 1.40
3100 3236 6.989169 TGCAAAGCACAAACTTAATAACCAAT 59.011 30.769 0.00 0.00 31.71 3.16
3109 3245 4.620609 CGCATATTGCAAAGCACAAACTTA 59.379 37.500 18.06 0.00 45.36 2.24
3134 3270 2.797177 ATGACTTTCCTGGCCTCTTC 57.203 50.000 3.32 0.00 0.00 2.87
3162 3300 6.348540 CCACTTCCATTAAGCTGTACAAGAAC 60.349 42.308 0.00 0.00 38.93 3.01
3183 3321 1.410517 CTATCTGATGCACCGTCCACT 59.589 52.381 0.00 0.00 0.00 4.00
3190 3328 3.281727 TCCAAACCTATCTGATGCACC 57.718 47.619 0.00 0.00 0.00 5.01
3191 3329 5.841957 ATTTCCAAACCTATCTGATGCAC 57.158 39.130 0.00 0.00 0.00 4.57
3219 3357 7.652524 TTAGTGAAGACAATGATCTCTAGCT 57.347 36.000 0.00 0.00 0.00 3.32
3261 3399 4.883006 GGATGGCCCGTAATTTAGTGTTTA 59.117 41.667 0.00 0.00 0.00 2.01
3295 3438 2.746362 GGGCTAATGATGCATGAGTAGC 59.254 50.000 29.62 29.62 31.04 3.58


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

AutoCloner maintained by Alex Coulton.