Multiple sequence alignment - TraesCS7A01G507900

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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 TraesCS7A01G507900 chr7A 100.000 5071 0 0 1 5071 694543623 694548693 0.000000e+00 9365
1 TraesCS7A01G507900 chr7D 97.537 5076 113 6 1 5071 602899386 602904454 0.000000e+00 8671
2 TraesCS7A01G507900 chr7B 96.320 5081 142 13 1 5071 683510808 683515853 0.000000e+00 8305
3 TraesCS7A01G507900 chr6D 85.504 476 56 10 4600 5069 232768564 232768096 7.630000e-133 484


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 TraesCS7A01G507900 chr7A 694543623 694548693 5070 False 9365 9365 100.000 1 5071 1 chr7A.!!$F1 5070
1 TraesCS7A01G507900 chr7D 602899386 602904454 5068 False 8671 8671 97.537 1 5071 1 chr7D.!!$F1 5070
2 TraesCS7A01G507900 chr7B 683510808 683515853 5045 False 8305 8305 96.320 1 5071 1 chr7B.!!$F1 5070

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
510 514 1.568504 AATAGCCGGGAAGTCTGTGA 58.431 50.000 2.18 0.0 0.0 3.58 F
2239 2250 1.067821 GGCGGTGAATTTTGGTTGACA 59.932 47.619 0.00 0.0 0.0 3.58 F
2977 2988 1.443802 CCTTCTGGCTTCGTTCTTCC 58.556 55.000 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2370 1.14831 CCTCAATTGCAACGAGACGT 58.852 50.0 23.09 0.0 43.97 4.34 R
3375 3386 0.17691 TGACTGCGTTGACCTCACAA 59.823 50.0 0.00 0.0 0.00 3.33 R
4572 4585 1.03703 GGGGGCAATTTCGCTCATCA 61.037 55.0 0.00 0.0 32.33 3.07 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
88 92 7.821359 GGTAGTACATACGGACTGATATGAGTA 59.179 40.741 2.06 0.00 34.99 2.59
165 169 2.309755 TGAACGGAGGGAGTAGTTCCTA 59.690 50.000 0.00 0.00 45.98 2.94
210 214 4.141298 TGAATTTCCCCAAAAATTGCAGGT 60.141 37.500 0.00 0.00 38.59 4.00
220 224 2.584835 AATTGCAGGTAGGTGCTTCA 57.415 45.000 0.00 0.00 44.32 3.02
223 227 1.896220 TGCAGGTAGGTGCTTCAAAG 58.104 50.000 0.00 0.00 44.32 2.77
462 466 6.760298 CACTCTGATATTGTGCATACAGAACT 59.240 38.462 0.00 0.00 38.23 3.01
510 514 1.568504 AATAGCCGGGAAGTCTGTGA 58.431 50.000 2.18 0.00 0.00 3.58
629 633 6.713762 TTCTTTAATTACATCCATGGCAGG 57.286 37.500 6.96 0.81 0.00 4.85
679 683 8.246430 TCTGTAAATCAATACGGAGGATTAGT 57.754 34.615 0.00 0.00 36.49 2.24
684 688 5.117355 TCAATACGGAGGATTAGTTAGCG 57.883 43.478 0.00 0.00 0.00 4.26
799 803 7.624360 TGTAAACCATTGATTAGGTGATCAC 57.376 36.000 17.91 17.91 38.37 3.06
1093 1104 8.830915 AGGATTTCTTTACTCTGACTGAGATA 57.169 34.615 15.53 2.79 45.39 1.98
1353 1364 6.716628 AGTTCAGCAGAAGGTTTGATAAATGA 59.283 34.615 0.00 0.00 33.63 2.57
1509 1520 2.284754 TGGAGCAGTGCACCAAATTA 57.715 45.000 29.14 8.08 45.44 1.40
1546 1557 4.493350 CGACAAATAGATGCAAAAGAAGCG 59.507 41.667 0.00 0.00 33.85 4.68
1608 1619 8.406172 CAGGAAATGGAAAATAATAAACACGG 57.594 34.615 0.00 0.00 0.00 4.94
1645 1656 3.837213 GCAACTGCAGAAGCTAAATCA 57.163 42.857 23.35 0.00 42.74 2.57
1657 1668 7.415541 GCAGAAGCTAAATCAAACCATGATACA 60.416 37.037 0.00 0.00 42.11 2.29
1765 1776 2.292267 CCAAATTCCTCGGATGGACAG 58.708 52.381 0.00 0.00 35.58 3.51
1883 1894 4.562082 TGACGTAGGTTTAGTCACCAATG 58.438 43.478 0.00 0.00 39.63 2.82
1965 1976 2.602257 TCGACCATAGATGCCAAGTG 57.398 50.000 0.00 0.00 0.00 3.16
2222 2233 3.525537 ACAGATGATAAAGACACTGGCG 58.474 45.455 0.00 0.00 0.00 5.69
2239 2250 1.067821 GGCGGTGAATTTTGGTTGACA 59.932 47.619 0.00 0.00 0.00 3.58
2308 2319 3.450457 AGTTGAATGCAGTAGAGGGAGAG 59.550 47.826 0.00 0.00 0.00 3.20
2438 2449 4.563580 GCAGTTCTCCTGACATTAGTTCCA 60.564 45.833 0.00 0.00 44.49 3.53
2602 2613 4.252971 TGACAGCGGTCCTATTAATAGC 57.747 45.455 15.86 6.30 43.65 2.97
2977 2988 1.443802 CCTTCTGGCTTCGTTCTTCC 58.556 55.000 0.00 0.00 0.00 3.46
3301 3312 5.104193 AGTCATGATTATGGGCAAGAGAGTT 60.104 40.000 0.00 0.00 34.97 3.01
3302 3313 5.008415 GTCATGATTATGGGCAAGAGAGTTG 59.992 44.000 0.00 0.00 34.97 3.16
3455 3466 1.246056 TTCTCAACCTGCTGCCATGC 61.246 55.000 0.00 0.00 0.00 4.06
3672 3683 3.178540 AAGGCGCACGAAGGGAAGT 62.179 57.895 10.83 0.00 0.00 3.01
3819 3830 2.356780 GGGATATCTACCCCCGGCG 61.357 68.421 0.00 0.00 41.38 6.46
3896 3907 1.000233 CCTGGGGCCTTGCACAATA 60.000 57.895 0.84 0.00 30.93 1.90
3942 3953 2.143122 TGGAAGATGCGTGAAACTGAC 58.857 47.619 0.00 0.00 31.75 3.51
4023 4034 7.913789 TGGTACAACATGTAGATTTAGTTCCT 58.086 34.615 0.00 0.00 32.84 3.36
4044 4055 4.107622 CTGTGAGCACAACTTCTTTTTGG 58.892 43.478 4.72 0.00 41.33 3.28
4136 4147 9.677567 TGAAATAAACTCTTTTATGCTGTGTTC 57.322 29.630 0.00 0.00 37.85 3.18
4354 4366 3.365832 CACATTTTAGCTGCCTATTGCG 58.634 45.455 0.00 0.00 45.60 4.85
4403 4415 2.549926 CCAAACTGGTGGCAAAACTTC 58.450 47.619 0.00 0.00 31.35 3.01
4435 4447 0.401738 AAGGAGCCAGCTGCAACTTA 59.598 50.000 13.86 0.00 44.83 2.24
4436 4448 0.622665 AGGAGCCAGCTGCAACTTAT 59.377 50.000 13.86 0.00 44.83 1.73
4437 4449 1.020437 GGAGCCAGCTGCAACTTATC 58.980 55.000 8.66 0.00 44.83 1.75
4438 4450 1.679944 GGAGCCAGCTGCAACTTATCA 60.680 52.381 8.66 0.00 44.83 2.15
4454 4467 7.533426 CAACTTATCAGGGAAAGAATCAACTG 58.467 38.462 0.00 0.00 36.47 3.16
4488 4501 8.034313 AGATCAGGTCAGCAATAATAACCTTA 57.966 34.615 0.00 0.00 38.27 2.69
4489 4502 8.494433 AGATCAGGTCAGCAATAATAACCTTAA 58.506 33.333 0.00 0.00 38.27 1.85
4598 4612 1.839424 CGAAATTGCCCCCTTCTCTT 58.161 50.000 0.00 0.00 0.00 2.85
4606 4620 1.216990 CCCCCTTCTCTTAGGTGCAT 58.783 55.000 0.00 0.00 33.17 3.96
4726 4740 6.704310 ACATCCTTGATTTTTGGAAAGATGG 58.296 36.000 0.00 0.00 31.69 3.51
4731 4745 5.726980 TGATTTTTGGAAAGATGGACCTG 57.273 39.130 0.00 0.00 0.00 4.00
4809 4823 2.438021 TCAGTAGTTCAACCAGCCAACT 59.562 45.455 0.00 0.00 34.68 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 124 8.358148 TCACTATCAGAAGACGTTCTAACTTTT 58.642 33.333 0.00 0.00 41.40 2.27
165 169 0.244994 CAGCACGCTGACTAGGAAGT 59.755 55.000 13.87 0.00 46.30 3.01
210 214 3.476552 CTTCCACACTTTGAAGCACCTA 58.523 45.455 0.00 0.00 32.37 3.08
298 302 8.696609 GAGAATCAGCTGCTGTTCAAAGGAAC 62.697 46.154 29.15 16.18 44.06 3.62
346 350 9.265901 CAAACAGCAGCAGTAGTATCTAATAAT 57.734 33.333 0.00 0.00 0.00 1.28
347 351 7.710907 CCAAACAGCAGCAGTAGTATCTAATAA 59.289 37.037 0.00 0.00 0.00 1.40
348 352 7.210174 CCAAACAGCAGCAGTAGTATCTAATA 58.790 38.462 0.00 0.00 0.00 0.98
349 353 6.051717 CCAAACAGCAGCAGTAGTATCTAAT 58.948 40.000 0.00 0.00 0.00 1.73
350 354 5.419542 CCAAACAGCAGCAGTAGTATCTAA 58.580 41.667 0.00 0.00 0.00 2.10
351 355 4.141937 CCCAAACAGCAGCAGTAGTATCTA 60.142 45.833 0.00 0.00 0.00 1.98
462 466 4.098654 GCTCCAGAAGAGTGTGAGCTTATA 59.901 45.833 0.00 0.00 45.21 0.98
559 563 0.923729 ATACCTGCACCATTGGGGGA 60.924 55.000 7.16 2.29 41.63 4.81
629 633 2.352651 TGCTGATGTTAATTCTGCTCGC 59.647 45.455 15.96 0.00 38.45 5.03
679 683 4.890088 ACTATTGTTTCACTCCACGCTAA 58.110 39.130 0.00 0.00 0.00 3.09
684 688 6.456501 AGACACTACTATTGTTTCACTCCAC 58.543 40.000 0.00 0.00 0.00 4.02
828 832 7.233553 AGCAGCCAAGACATCACTAGTATATTA 59.766 37.037 0.00 0.00 0.00 0.98
879 888 3.194116 CCATGACAATTAGCAACAGCCTT 59.806 43.478 0.00 0.00 0.00 4.35
938 947 1.071699 GGGTGGTCAACAGAAGTAGCA 59.928 52.381 0.00 0.00 0.00 3.49
1025 1036 2.238084 ATCTCCCTGCAGTAGTGTCA 57.762 50.000 13.81 0.00 0.00 3.58
1093 1104 3.443681 CCGTAGTTGAAATGCCATCCTTT 59.556 43.478 0.00 0.00 0.00 3.11
1353 1364 4.499696 GCCGCTCCAATGCAGTTAATATTT 60.500 41.667 0.00 0.00 0.00 1.40
1509 1520 2.595750 TTGTCGGTCATTTTCCCCAT 57.404 45.000 0.00 0.00 0.00 4.00
1546 1557 3.462021 CTTAAGATCAGCAGCCTGGTAC 58.538 50.000 0.00 0.00 39.61 3.34
1608 1619 1.515736 GCAGCTTCATTTGCTCCGC 60.516 57.895 0.00 0.00 38.92 5.54
1645 1656 6.542370 CCGAGGAAGTTAATGTATCATGGTTT 59.458 38.462 0.00 0.00 0.00 3.27
1657 1668 4.635699 AGGAACAACCGAGGAAGTTAAT 57.364 40.909 0.00 0.00 44.74 1.40
1765 1776 2.552743 GTTCACCTGCACTAAAACCTCC 59.447 50.000 0.00 0.00 0.00 4.30
1965 1976 5.777802 TCTCTGAGTTGACATTCTCAAGAC 58.222 41.667 4.32 0.00 39.69 3.01
2222 2233 5.922544 CAGATCTTGTCAACCAAAATTCACC 59.077 40.000 0.00 0.00 31.20 4.02
2239 2250 2.354259 CCAAAGCTCTTCGCAGATCTT 58.646 47.619 0.00 0.00 42.61 2.40
2308 2319 1.272490 TCTGTCGATGGTGGTGACTTC 59.728 52.381 0.00 0.00 33.81 3.01
2359 2370 1.148310 CCTCAATTGCAACGAGACGT 58.852 50.000 23.09 0.00 43.97 4.34
2438 2449 7.861629 TCCACATGAGGACTATCTACATTTTT 58.138 34.615 7.91 0.00 31.23 1.94
2977 2988 3.766591 AGATATCCTTGGGAGCTATGTCG 59.233 47.826 0.00 0.00 34.05 4.35
3301 3312 0.250467 GCTCCTTCTGTCCAAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
3302 3313 0.250467 TGCTCCTTCTGTCCAAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
3375 3386 0.176910 TGACTGCGTTGACCTCACAA 59.823 50.000 0.00 0.00 0.00 3.33
3376 3387 0.392706 ATGACTGCGTTGACCTCACA 59.607 50.000 0.00 0.00 0.00 3.58
3455 3466 2.166907 TAGAGAGGAGGAGGCAAAGG 57.833 55.000 0.00 0.00 0.00 3.11
3819 3830 1.726853 ACTAACATTGGACGCTCAGC 58.273 50.000 0.00 0.00 0.00 4.26
3896 3907 2.086869 CATGTGCGGAACTTCTTCCAT 58.913 47.619 0.61 0.00 45.99 3.41
3942 3953 6.992063 AAACCACTCATAGCTGAAACATAG 57.008 37.500 0.00 0.00 0.00 2.23
4023 4034 3.509575 ACCAAAAAGAAGTTGTGCTCACA 59.490 39.130 0.00 0.00 39.98 3.58
4435 4447 5.012893 GGTTCAGTTGATTCTTTCCCTGAT 58.987 41.667 0.00 0.00 33.70 2.90
4436 4448 4.398319 GGTTCAGTTGATTCTTTCCCTGA 58.602 43.478 0.00 0.00 32.50 3.86
4437 4449 3.507622 GGGTTCAGTTGATTCTTTCCCTG 59.492 47.826 0.00 0.00 0.00 4.45
4438 4450 3.399305 AGGGTTCAGTTGATTCTTTCCCT 59.601 43.478 0.00 0.00 38.00 4.20
4454 4467 2.679349 GCTGACCTGATCTCAAGGGTTC 60.679 54.545 2.86 0.00 31.60 3.62
4572 4585 1.037030 GGGGGCAATTTCGCTCATCA 61.037 55.000 0.00 0.00 32.33 3.07
4606 4620 4.524802 AAATCTGGAATGCATAGGTGGA 57.475 40.909 0.00 0.00 0.00 4.02
4616 4630 7.118535 TGTGCATTTGATCAAAAATCTGGAATG 59.881 33.333 23.91 14.87 33.56 2.67
4724 4738 6.369629 TCTGAAAGGTTTAAAATCAGGTCCA 58.630 36.000 15.69 1.82 38.39 4.02
4880 4895 1.137872 CAGAGGGCAGATACAGTGTCC 59.862 57.143 0.00 0.00 40.26 4.02


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

AutoCloner maintained by Alex Coulton.