Multiple sequence alignment - TraesCS1D01G084400

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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 TraesCS1D01G084400 chr1D 100.000 4010 0 0 1 4010 68444970 68448979 0.000000e+00 7406
1 TraesCS1D01G084400 chr1A 97.599 3999 69 16 1 3987 66891401 66895384 0.000000e+00 6828
2 TraesCS1D01G084400 chr1B 96.402 4002 101 19 1 3984 109727337 109731313 0.000000e+00 6553
3 TraesCS1D01G084400 chr1B 83.712 264 26 6 3116 3371 217805927 217805673 2.410000e-57 233
4 TraesCS1D01G084400 chr3D 84.173 139 22 0 1407 1545 352367945 352367807 6.990000e-28 135
5 TraesCS1D01G084400 chr2B 84.000 125 20 0 1419 1543 152844326 152844202 1.960000e-23 121
6 TraesCS1D01G084400 chr2A 89.247 93 10 0 1419 1511 100826054 100825962 2.530000e-22 117
7 TraesCS1D01G084400 chr2D 88.889 90 10 0 1422 1511 101872850 101872761 1.180000e-20 111
8 TraesCS1D01G084400 chr7B 82.927 123 17 4 1419 1539 452961950 452962070 1.520000e-19 108
9 TraesCS1D01G084400 chr7A 82.540 126 18 4 1419 1542 486237271 486237148 1.520000e-19 108
10 TraesCS1D01G084400 chr7D 86.316 95 9 4 1419 1511 436114205 436114297 2.550000e-17 100


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 TraesCS1D01G084400 chr1D 68444970 68448979 4009 False 7406 7406 100.000 1 4010 1 chr1D.!!$F1 4009
1 TraesCS1D01G084400 chr1A 66891401 66895384 3983 False 6828 6828 97.599 1 3987 1 chr1A.!!$F1 3986
2 TraesCS1D01G084400 chr1B 109727337 109731313 3976 False 6553 6553 96.402 1 3984 1 chr1B.!!$F1 3983

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
50 51 0.605319 CTTGCTGCTCCGGGTAAACA 60.605 55.000 0.00 0.00 0.00 2.83 F
54 55 1.068541 GCTGCTCCGGGTAAACAAAAG 60.069 52.381 0.00 0.00 0.00 2.27 F
1064 1080 1.005630 GGAGACTTCTGCTGTGCGT 60.006 57.895 0.00 0.00 0.00 5.24 F
1842 1866 1.203364 AGGACCTCTGGTTCCAGTGAT 60.203 52.381 18.68 5.14 35.25 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1080 0.886043 ACTCACGCAGCTTGCAATCA 60.886 50.000 0.00 0.0 45.36 2.57 R
1923 1947 1.676014 GGGCGCTTCTTGTCATACACT 60.676 52.381 7.64 0.0 0.00 3.55 R
2067 2091 2.910199 CTGTAGCCTAATTGCTGCTGA 58.090 47.619 0.00 0.0 43.42 4.26 R
3539 3573 0.035725 TGCTGAATGGTGAGCTCCTG 60.036 55.000 12.15 0.0 36.11 3.86 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
50 51 0.605319 CTTGCTGCTCCGGGTAAACA 60.605 55.000 0.00 0.00 0.00 2.83
54 55 1.068541 GCTGCTCCGGGTAAACAAAAG 60.069 52.381 0.00 0.00 0.00 2.27
227 228 4.415596 TCTTGGGCCTGACACATAAAATT 58.584 39.130 4.53 0.00 0.00 1.82
278 281 2.168621 CACGAACGAACAGCAGCG 59.831 61.111 0.14 0.00 0.00 5.18
282 285 3.300667 GAACGAACAGCAGCGGCAG 62.301 63.158 12.44 5.49 44.61 4.85
560 569 2.673200 GCAGAGGCAGATGGACCCA 61.673 63.158 0.00 0.00 40.72 4.51
761 774 4.578105 AGCAACCAAGTGAAGAAGAAGAAG 59.422 41.667 0.00 0.00 0.00 2.85
762 775 4.576463 GCAACCAAGTGAAGAAGAAGAAGA 59.424 41.667 0.00 0.00 0.00 2.87
763 776 5.066505 GCAACCAAGTGAAGAAGAAGAAGAA 59.933 40.000 0.00 0.00 0.00 2.52
1000 1013 4.716784 AGTCACTATACCCTCTGCATTTCA 59.283 41.667 0.00 0.00 0.00 2.69
1064 1080 1.005630 GGAGACTTCTGCTGTGCGT 60.006 57.895 0.00 0.00 0.00 5.24
1358 1378 3.637769 TCTTCTCCTCCTAAGAAGGCTC 58.362 50.000 11.73 0.00 46.37 4.70
1842 1866 1.203364 AGGACCTCTGGTTCCAGTGAT 60.203 52.381 18.68 5.14 35.25 3.06
1923 1947 1.203758 CAATCTTCAATGCTGCTGCCA 59.796 47.619 13.47 1.72 38.71 4.92
2067 2091 4.261867 GGTCCAACGCTGTATTTTCCTTTT 60.262 41.667 0.00 0.00 0.00 2.27
3376 3406 0.804156 GAGAGAGTAAGCACGGCTGC 60.804 60.000 0.00 0.00 44.63 5.25
3399 3429 5.297029 GCGAGAAAAGGAGGCAAGTATTTAT 59.703 40.000 0.00 0.00 0.00 1.40
3482 3514 4.428294 ACATATGCTCAACTATGGCTGT 57.572 40.909 1.58 0.00 31.07 4.40
3497 3529 2.632028 TGGCTGTGCATTATGGTTTGTT 59.368 40.909 0.00 0.00 0.00 2.83
3523 3555 6.947644 TGATTACATCATAGTGCTGCAAAT 57.052 33.333 2.77 0.00 33.59 2.32
3524 3556 6.731164 TGATTACATCATAGTGCTGCAAATG 58.269 36.000 16.20 16.20 33.59 2.32
3525 3557 6.319405 TGATTACATCATAGTGCTGCAAATGT 59.681 34.615 19.65 17.37 33.59 2.71
3528 3562 4.336433 ACATCATAGTGCTGCAAATGTACC 59.664 41.667 19.65 1.92 0.00 3.34
3539 3573 3.257127 TGCAAATGTACCTAAACTTGGCC 59.743 43.478 0.00 0.00 0.00 5.36
3549 3583 0.538287 AAACTTGGCCAGGAGCTCAC 60.538 55.000 23.57 5.01 43.05 3.51
3564 3598 2.025981 AGCTCACCATTCAGCAACCATA 60.026 45.455 0.00 0.00 38.18 2.74
3570 3604 4.012374 ACCATTCAGCAACCATAGAACTG 58.988 43.478 0.00 0.00 0.00 3.16
3582 3616 5.079643 ACCATAGAACTGAAGCCATTTTGT 58.920 37.500 0.00 0.00 0.00 2.83
3590 3624 3.976169 TGAAGCCATTTTGTGTGCTTAC 58.024 40.909 0.00 0.00 41.39 2.34
3603 3637 5.126779 TGTGTGCTTACTTGGTTTATCACA 58.873 37.500 0.00 0.00 0.00 3.58
3609 3643 8.015658 GTGCTTACTTGGTTTATCACAAACTAG 58.984 37.037 0.00 0.00 0.00 2.57
3700 3734 7.726738 ACTTAAAAAGGCCAAATAGAGTACCAA 59.273 33.333 5.01 0.00 0.00 3.67
3740 3774 3.385749 ATCGCTGTACCAAGGGCGG 62.386 63.158 6.36 0.00 46.31 6.13
3954 3988 8.188799 GGTTCCCAAACAATAGATTAGCTTTAC 58.811 37.037 0.00 0.00 37.10 2.01
3997 4031 7.977789 ACATCACACAACTATTTACATCACA 57.022 32.000 0.00 0.00 0.00 3.58
3998 4032 7.806690 ACATCACACAACTATTTACATCACAC 58.193 34.615 0.00 0.00 0.00 3.82
3999 4033 7.443879 ACATCACACAACTATTTACATCACACA 59.556 33.333 0.00 0.00 0.00 3.72
4000 4034 7.793927 TCACACAACTATTTACATCACACAA 57.206 32.000 0.00 0.00 0.00 3.33
4001 4035 7.635423 TCACACAACTATTTACATCACACAAC 58.365 34.615 0.00 0.00 0.00 3.32
4002 4036 7.497579 TCACACAACTATTTACATCACACAACT 59.502 33.333 0.00 0.00 0.00 3.16
4003 4037 8.769891 CACACAACTATTTACATCACACAACTA 58.230 33.333 0.00 0.00 0.00 2.24
4004 4038 9.332502 ACACAACTATTTACATCACACAACTAA 57.667 29.630 0.00 0.00 0.00 2.24
4005 4039 9.594038 CACAACTATTTACATCACACAACTAAC 57.406 33.333 0.00 0.00 0.00 2.34
4006 4040 9.332502 ACAACTATTTACATCACACAACTAACA 57.667 29.630 0.00 0.00 0.00 2.41
4007 4041 9.811655 CAACTATTTACATCACACAACTAACAG 57.188 33.333 0.00 0.00 0.00 3.16
4008 4042 8.547967 ACTATTTACATCACACAACTAACAGG 57.452 34.615 0.00 0.00 0.00 4.00
4009 4043 6.817765 ATTTACATCACACAACTAACAGGG 57.182 37.500 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 0.263172 TTTCCCCCACCTGCAAGAAA 59.737 50.000 0.00 0.00 34.07 2.52
282 285 2.746362 ACTCATCTTTGTTAGCTGCTGC 59.254 45.455 13.43 7.62 40.05 5.25
283 286 5.368256 AAACTCATCTTTGTTAGCTGCTG 57.632 39.130 13.43 0.00 0.00 4.41
284 287 7.510549 TTAAAACTCATCTTTGTTAGCTGCT 57.489 32.000 7.57 7.57 0.00 4.24
560 569 4.342092 AGCACAAGCCAGTGAAAGTAAAAT 59.658 37.500 10.06 0.00 42.05 1.82
1000 1013 1.217057 ATCCATGGCTGAAGGGGTGT 61.217 55.000 6.96 0.00 0.00 4.16
1064 1080 0.886043 ACTCACGCAGCTTGCAATCA 60.886 50.000 0.00 0.00 45.36 2.57
1358 1378 5.379706 AATTGGATTGACTAAGAGAGGGG 57.620 43.478 0.00 0.00 0.00 4.79
1403 1423 2.156098 ACCTTTGGAGCCCTGCAGA 61.156 57.895 17.39 0.00 31.08 4.26
1842 1866 2.970324 GCGCTTGACGGGTTGACA 60.970 61.111 0.00 0.00 43.93 3.58
1923 1947 1.676014 GGGCGCTTCTTGTCATACACT 60.676 52.381 7.64 0.00 0.00 3.55
2067 2091 2.910199 CTGTAGCCTAATTGCTGCTGA 58.090 47.619 0.00 0.00 43.42 4.26
3376 3406 6.538742 TCATAAATACTTGCCTCCTTTTCTCG 59.461 38.462 0.00 0.00 0.00 4.04
3399 3429 6.070596 CCATCTGCATGGTAGGTAGATATTCA 60.071 42.308 0.00 0.00 44.46 2.57
3482 3514 7.834803 TGTAATCATGAACAAACCATAATGCA 58.165 30.769 0.00 0.00 0.00 3.96
3514 3546 4.022416 CCAAGTTTAGGTACATTTGCAGCA 60.022 41.667 0.00 0.00 0.00 4.41
3516 3548 4.485163 GCCAAGTTTAGGTACATTTGCAG 58.515 43.478 0.00 0.00 0.00 4.41
3523 3555 2.304761 CTCCTGGCCAAGTTTAGGTACA 59.695 50.000 7.01 0.00 0.00 2.90
3524 3556 2.940083 GCTCCTGGCCAAGTTTAGGTAC 60.940 54.545 7.01 0.00 34.27 3.34
3525 3557 1.280998 GCTCCTGGCCAAGTTTAGGTA 59.719 52.381 7.01 0.00 34.27 3.08
3528 3562 1.003580 TGAGCTCCTGGCCAAGTTTAG 59.996 52.381 12.15 0.76 43.05 1.85
3539 3573 0.035725 TGCTGAATGGTGAGCTCCTG 60.036 55.000 12.15 0.00 36.11 3.86
3549 3583 4.264253 TCAGTTCTATGGTTGCTGAATGG 58.736 43.478 0.00 0.00 33.84 3.16
3564 3598 3.491447 GCACACAAAATGGCTTCAGTTCT 60.491 43.478 0.00 0.00 0.00 3.01
3570 3604 4.243007 AGTAAGCACACAAAATGGCTTC 57.757 40.909 0.49 0.00 41.27 3.86
3582 3616 6.320164 AGTTTGTGATAAACCAAGTAAGCACA 59.680 34.615 1.02 0.00 33.70 4.57
3603 3637 4.082354 CCTAGCTCGTACCACAACTAGTTT 60.082 45.833 5.07 0.00 0.00 2.66
3609 3643 1.542915 TCACCTAGCTCGTACCACAAC 59.457 52.381 0.00 0.00 0.00 3.32
3650 3684 3.182152 AGGCTAGCTTTTCTGGAGGTTA 58.818 45.455 15.72 0.00 0.00 2.85
3700 3734 4.872664 TGTTGAACGTTGAAACCAAGTTT 58.127 34.783 5.00 0.00 38.54 2.66
3740 3774 3.619038 GCAGGAGCATTAGTATTATCGCC 59.381 47.826 0.00 0.00 41.58 5.54
3741 3775 4.499183 AGCAGGAGCATTAGTATTATCGC 58.501 43.478 0.00 0.00 45.49 4.58
3742 3776 9.803315 TTATTAGCAGGAGCATTAGTATTATCG 57.197 33.333 0.00 0.00 45.49 2.92
3908 3942 6.712547 GGAACCTGATTTCATAGGTCCATTAG 59.287 42.308 9.01 0.00 46.28 1.73


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

AutoCloner maintained by Alex Coulton.