Multiple sequence alignment - TraesCS6B01G140000

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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 TraesCS6B01G140000 chr6B 100.000 4550 0 0 1 4550 137379625 137384174 0.000000e+00 8403
1 TraesCS6B01G140000 chr6B 87.425 501 42 8 4057 4550 144964198 144964684 1.430000e-154 556
2 TraesCS6B01G140000 chr6B 84.314 408 49 8 4148 4549 122296177 122295779 7.140000e-103 385
3 TraesCS6B01G140000 chr6D 95.406 3875 103 38 721 4550 63725825 63729669 0.000000e+00 6100
4 TraesCS6B01G140000 chr6D 88.757 507 42 6 4057 4550 69946011 69946515 1.400000e-169 606
5 TraesCS6B01G140000 chr6D 84.029 407 49 11 4149 4549 48857175 48857571 1.190000e-100 377
6 TraesCS6B01G140000 chr6D 93.125 160 11 0 3 162 389872496 389872655 7.610000e-58 235
7 TraesCS6B01G140000 chr6A 94.889 3483 126 26 628 4087 80875434 80878887 0.000000e+00 5398
8 TraesCS6B01G140000 chr6A 88.294 504 45 6 4059 4550 87759469 87759970 3.920000e-165 592
9 TraesCS6B01G140000 chr6A 82.108 408 51 13 4148 4549 65803530 65803139 3.390000e-86 329
10 TraesCS6B01G140000 chr6A 84.314 255 22 8 4075 4316 80879067 80879316 2.740000e-57 233
11 TraesCS6B01G140000 chr5B 93.548 2635 140 13 996 3605 407215316 407217945 0.000000e+00 3897
12 TraesCS6B01G140000 chr5D 93.440 2637 144 10 996 3608 344546417 344543786 0.000000e+00 3884
13 TraesCS6B01G140000 chr5D 96.032 126 5 0 1 126 413567350 413567475 5.970000e-49 206
14 TraesCS6B01G140000 chr5D 90.909 77 6 1 4057 4132 23824852 23824928 8.050000e-18 102
15 TraesCS6B01G140000 chr5A 92.873 2638 155 14 996 3605 447535166 447537798 0.000000e+00 3799
16 TraesCS6B01G140000 chr1D 96.378 635 22 1 1 634 5046371 5047005 0.000000e+00 1044
17 TraesCS6B01G140000 chr4A 96.220 635 23 1 1 634 403390393 403389759 0.000000e+00 1038
18 TraesCS6B01G140000 chr4A 91.793 329 24 3 2 328 620711033 620711360 5.370000e-124 455
19 TraesCS6B01G140000 chr2D 95.190 395 18 1 2 395 55232952 55232558 1.390000e-174 623
20 TraesCS6B01G140000 chr2D 82.937 504 84 2 137 639 425242916 425242414 1.930000e-123 453
21 TraesCS6B01G140000 chr1A 89.308 477 23 5 3512 3988 278128856 278129304 1.420000e-159 573
22 TraesCS6B01G140000 chr4D 83.399 506 78 6 137 639 383853533 383853031 8.920000e-127 464
23 TraesCS6B01G140000 chr2A 92.414 145 11 0 3844 3988 5609568 5609712 1.660000e-49 207
24 TraesCS6B01G140000 chr2A 96.296 81 3 0 3512 3592 5609372 5609452 2.860000e-27 134
25 TraesCS6B01G140000 chr2B 84.659 176 20 7 950 1123 324624091 324623921 7.830000e-38 169
26 TraesCS6B01G140000 chr3A 90.909 77 6 1 4057 4132 723439304 723439228 8.050000e-18 102
27 TraesCS6B01G140000 chr7B 89.744 78 8 0 333 410 628014940 628014863 2.900000e-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 TraesCS6B01G140000 chr6B 137379625 137384174 4549 False 8403.0 8403 100.0000 1 4550 1 chr6B.!!$F1 4549
1 TraesCS6B01G140000 chr6D 63725825 63729669 3844 False 6100.0 6100 95.4060 721 4550 1 chr6D.!!$F2 3829
2 TraesCS6B01G140000 chr6D 69946011 69946515 504 False 606.0 606 88.7570 4057 4550 1 chr6D.!!$F3 493
3 TraesCS6B01G140000 chr6A 80875434 80879316 3882 False 2815.5 5398 89.6015 628 4316 2 chr6A.!!$F2 3688
4 TraesCS6B01G140000 chr6A 87759469 87759970 501 False 592.0 592 88.2940 4059 4550 1 chr6A.!!$F1 491
5 TraesCS6B01G140000 chr5B 407215316 407217945 2629 False 3897.0 3897 93.5480 996 3605 1 chr5B.!!$F1 2609
6 TraesCS6B01G140000 chr5D 344543786 344546417 2631 True 3884.0 3884 93.4400 996 3608 1 chr5D.!!$R1 2612
7 TraesCS6B01G140000 chr5A 447535166 447537798 2632 False 3799.0 3799 92.8730 996 3605 1 chr5A.!!$F1 2609
8 TraesCS6B01G140000 chr1D 5046371 5047005 634 False 1044.0 1044 96.3780 1 634 1 chr1D.!!$F1 633
9 TraesCS6B01G140000 chr4A 403389759 403390393 634 True 1038.0 1038 96.2200 1 634 1 chr4A.!!$R1 633
10 TraesCS6B01G140000 chr2D 425242414 425242916 502 True 453.0 453 82.9370 137 639 1 chr2D.!!$R2 502
11 TraesCS6B01G140000 chr4D 383853031 383853533 502 True 464.0 464 83.3990 137 639 1 chr4D.!!$R1 502

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
717 719 0.811915 CACGGATGAAGGAGACGAGT 59.188 55.000 0.0 0.0 0.00 4.18 F
1839 1924 2.190578 CCTGGGTCTGATTCGGGC 59.809 66.667 0.0 0.0 0.00 6.13 F
2235 2320 1.257743 TCCTCAGAACAGGGAAGTCG 58.742 55.000 0.0 0.0 33.81 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1993 0.680921 CCACCAAGACGGCCATCAAT 60.681 55.000 0.00 0.0 39.03 2.57 R
2784 2869 2.029020 TCCAGTCAGAGAATGGTCAACG 60.029 50.000 12.53 0.0 46.34 4.10 R
3873 3965 2.568509 TCTGTGTGAAGCATGATCTGGA 59.431 45.455 0.00 0.0 0.00 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
54 55 2.359900 GATCTTTGTGATGCCTTCGGT 58.640 47.619 0.00 0.00 35.14 4.69
221 222 3.939740 TTGCTTCATGGATAGCCTTCT 57.060 42.857 0.00 0.00 36.56 2.85
383 385 3.284449 GGCCCAAACGCAACGAGT 61.284 61.111 0.00 0.00 0.00 4.18
395 397 3.003275 ACGCAACGAGTCATTGAACAATT 59.997 39.130 2.50 0.00 0.00 2.32
609 611 4.080186 TCAGATGATCCTGCAATTCCTTCA 60.080 41.667 0.00 0.00 34.28 3.02
675 677 0.875059 GTTTTGAAGGGCGGACAGAG 59.125 55.000 0.00 0.00 0.00 3.35
710 712 3.781307 CGGCCCACGGATGAAGGA 61.781 66.667 0.00 0.00 39.42 3.36
711 713 2.190578 GGCCCACGGATGAAGGAG 59.809 66.667 0.00 0.00 0.00 3.69
712 714 2.367202 GGCCCACGGATGAAGGAGA 61.367 63.158 0.00 0.00 0.00 3.71
713 715 1.153349 GCCCACGGATGAAGGAGAC 60.153 63.158 0.00 0.00 0.00 3.36
714 716 1.141881 CCCACGGATGAAGGAGACG 59.858 63.158 0.00 0.00 0.00 4.18
717 719 0.811915 CACGGATGAAGGAGACGAGT 59.188 55.000 0.00 0.00 0.00 4.18
732 734 2.821688 GAGTAGACGACGGGCCTCG 61.822 68.421 19.32 19.32 45.88 4.63
733 735 4.549516 GTAGACGACGGGCCTCGC 62.550 72.222 20.39 14.61 43.89 5.03
813 829 3.445987 TCCCTCTCTTCTCCTTTCTTCC 58.554 50.000 0.00 0.00 0.00 3.46
990 1033 3.718210 GAGAACCCTAGCGCCCACG 62.718 68.421 2.29 0.00 44.07 4.94
1413 1498 3.112709 GTGGCGCTCGTCTCCAAC 61.113 66.667 7.64 0.00 0.00 3.77
1583 1668 4.143333 CACCTACGACCTGCCCGG 62.143 72.222 0.00 0.00 39.35 5.73
1839 1924 2.190578 CCTGGGTCTGATTCGGGC 59.809 66.667 0.00 0.00 0.00 6.13
1908 1993 2.976840 GCCTGCGGTGAAAATGCGA 61.977 57.895 0.00 0.00 0.00 5.10
1917 2002 2.195922 GTGAAAATGCGATTGATGGCC 58.804 47.619 0.00 0.00 0.00 5.36
2018 2103 3.131046 CCCATGGTTCAAGACTTTATGGC 59.869 47.826 11.73 0.00 35.15 4.40
2046 2131 4.803426 CGGCGAGTCTGCTCACCC 62.803 72.222 0.00 0.00 40.04 4.61
2094 2179 2.489722 GCTTGAAGGTGAATTGGAGGAC 59.510 50.000 0.00 0.00 0.00 3.85
2235 2320 1.257743 TCCTCAGAACAGGGAAGTCG 58.742 55.000 0.00 0.00 33.81 4.18
2373 2458 1.341080 CTTTGGAGGCATTGGTGGTT 58.659 50.000 0.00 0.00 0.00 3.67
2844 2929 5.077134 AGCCTAATTGCATTGTTTCTTCC 57.923 39.130 0.00 0.00 0.00 3.46
3537 3624 4.242475 CTGAATACTACAGCCGTGTTTCA 58.758 43.478 0.00 0.00 38.19 2.69
3761 3849 7.807977 ACACTGAAATATCTTTGACTTGTGT 57.192 32.000 0.00 0.00 0.00 3.72
3762 3850 7.642669 ACACTGAAATATCTTTGACTTGTGTG 58.357 34.615 0.00 0.00 33.39 3.82
3763 3851 7.498900 ACACTGAAATATCTTTGACTTGTGTGA 59.501 33.333 0.00 0.00 33.39 3.58
3764 3852 7.800380 CACTGAAATATCTTTGACTTGTGTGAC 59.200 37.037 0.00 0.00 0.00 3.67
3768 3856 2.917933 TCTTTGACTTGTGTGACTGGG 58.082 47.619 0.00 0.00 0.00 4.45
3805 3893 2.241160 TGTGAATTGAGTGCCAGCATT 58.759 42.857 0.00 0.00 0.00 3.56
3873 3965 5.410355 AAAGCAATGCATCTGTTTGGTAT 57.590 34.783 8.35 0.00 31.40 2.73
3895 3987 2.937149 CCAGATCATGCTTCACACAGAG 59.063 50.000 0.00 0.00 0.00 3.35
4049 4146 3.610242 CGACTGATTTCAGACTACTGTGC 59.390 47.826 14.29 0.00 46.59 4.57
4098 4389 0.530870 TGAACATGACCGCGACAACA 60.531 50.000 8.23 1.92 0.00 3.33
4258 4556 4.018415 ACTTTGTATCAGGGTGGCACTTAT 60.018 41.667 18.45 8.43 0.00 1.73
4325 4625 4.142227 GCGTCCTAAACTGTCTCCATCTTA 60.142 45.833 0.00 0.00 0.00 2.10
4393 4694 6.169557 TGTACATGAACAGGTAAGAACAGT 57.830 37.500 0.00 0.00 28.80 3.55
4476 4782 2.575532 TCTGTTGCTGCTAGCTTGTTT 58.424 42.857 17.23 0.00 42.97 2.83
4539 4846 9.401058 AGCTAAGCTTAATGATGAAAGTGTATT 57.599 29.630 7.74 0.00 33.89 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.257750 CCATGTGGACGGAGGACTCA 61.258 60.000 1.32 0.00 37.39 3.41
54 55 0.036388 GAGAGGATGGAACGTGCCAA 60.036 55.000 21.97 2.80 42.16 4.52
59 60 1.617947 GGCAGGAGAGGATGGAACGT 61.618 60.000 0.00 0.00 0.00 3.99
383 385 4.656100 TCCCTCCTGAATTGTTCAATGA 57.344 40.909 0.00 0.00 39.58 2.57
609 611 2.183679 AGACGAAGAGAGGATTGGCTT 58.816 47.619 0.00 0.00 0.00 4.35
675 677 0.938637 CGTCGATCTGGATGCTCTGC 60.939 60.000 0.00 0.00 0.00 4.26
703 705 2.937799 GTCGTCTACTCGTCTCCTTCAT 59.062 50.000 0.00 0.00 0.00 2.57
704 706 2.344950 GTCGTCTACTCGTCTCCTTCA 58.655 52.381 0.00 0.00 0.00 3.02
705 707 1.324134 CGTCGTCTACTCGTCTCCTTC 59.676 57.143 0.00 0.00 0.00 3.46
706 708 1.357907 CGTCGTCTACTCGTCTCCTT 58.642 55.000 0.00 0.00 0.00 3.36
708 710 1.427592 CCCGTCGTCTACTCGTCTCC 61.428 65.000 0.00 0.00 0.00 3.71
709 711 2.005220 CCCGTCGTCTACTCGTCTC 58.995 63.158 0.00 0.00 0.00 3.36
710 712 2.105466 GCCCGTCGTCTACTCGTCT 61.105 63.158 0.00 0.00 0.00 4.18
711 713 2.402787 GCCCGTCGTCTACTCGTC 59.597 66.667 0.00 0.00 0.00 4.20
712 714 3.130160 GGCCCGTCGTCTACTCGT 61.130 66.667 0.00 0.00 0.00 4.18
713 715 2.821688 GAGGCCCGTCGTCTACTCG 61.822 68.421 0.00 0.00 0.00 4.18
714 716 2.821688 CGAGGCCCGTCGTCTACTC 61.822 68.421 0.00 0.00 35.14 2.59
732 734 3.070576 GGGCTGGGGAACACATGC 61.071 66.667 0.00 0.00 0.00 4.06
733 735 1.000739 ATGGGCTGGGGAACACATG 59.999 57.895 0.00 0.00 0.00 3.21
734 736 1.000739 CATGGGCTGGGGAACACAT 59.999 57.895 0.00 0.00 0.00 3.21
735 737 1.508667 ATCATGGGCTGGGGAACACA 61.509 55.000 0.00 0.00 0.00 3.72
736 738 0.550914 TATCATGGGCTGGGGAACAC 59.449 55.000 0.00 0.00 0.00 3.32
971 1014 3.081409 TGGGCGCTAGGGTTCTCC 61.081 66.667 7.64 0.00 0.00 3.71
1839 1924 2.271800 GAGAGGTAATTGCCTGACACG 58.728 52.381 20.84 0.00 39.34 4.49
1908 1993 0.680921 CCACCAAGACGGCCATCAAT 60.681 55.000 0.00 0.00 39.03 2.57
1917 2002 1.097547 GGCATCCATCCACCAAGACG 61.098 60.000 0.00 0.00 0.00 4.18
2046 2131 2.351738 GCTTCGGACCATTTCAAACAGG 60.352 50.000 0.00 0.00 0.00 4.00
2094 2179 4.142902 ACAATGAAGAACTCGCCAAATACG 60.143 41.667 0.00 0.00 0.00 3.06
2235 2320 5.238214 ACAGCAAACTCTGAGAAAGTTGATC 59.762 40.000 12.44 0.00 37.06 2.92
2316 2401 0.951040 CAAGCCCACCTCGACTTGTC 60.951 60.000 3.68 0.00 35.81 3.18
2373 2458 1.352017 TCAATCCTCTTGGCTGCTTCA 59.648 47.619 0.00 0.00 0.00 3.02
2784 2869 2.029020 TCCAGTCAGAGAATGGTCAACG 60.029 50.000 12.53 0.00 46.34 4.10
2844 2929 3.773560 TGTCCCTTCCTTGTAAAATGGG 58.226 45.455 0.00 0.00 34.76 4.00
3384 3471 4.783764 ATCTTCACCCATTTTCCGAAAC 57.216 40.909 0.00 0.00 0.00 2.78
3537 3624 6.218019 CACACACTCATTTCATTTGTTGGAT 58.782 36.000 0.00 0.00 0.00 3.41
3690 3778 8.836413 GCAAATACCAGCACTTCAAATATACTA 58.164 33.333 0.00 0.00 0.00 1.82
3761 3849 9.693739 ACAATACATAAATAATCAACCCAGTCA 57.306 29.630 0.00 0.00 0.00 3.41
3762 3850 9.950680 CACAATACATAAATAATCAACCCAGTC 57.049 33.333 0.00 0.00 0.00 3.51
3763 3851 9.693739 TCACAATACATAAATAATCAACCCAGT 57.306 29.630 0.00 0.00 0.00 4.00
3805 3893 9.485206 GAAGTACCAAGTGTAGTATTTGAGAAA 57.515 33.333 0.00 0.00 32.64 2.52
3873 3965 2.568509 TCTGTGTGAAGCATGATCTGGA 59.431 45.455 0.00 0.00 0.00 3.86
3895 3987 7.276438 TGACGCAATACATATGATAGAATGAGC 59.724 37.037 10.38 0.39 0.00 4.26
4049 4146 9.294030 GCAAAACACCTTCTAGAATTATCAATG 57.706 33.333 5.44 3.05 0.00 2.82
4098 4389 7.546250 TTCCAAGAAAGTAAGTCTGAGATCT 57.454 36.000 0.00 0.00 0.00 2.75
4258 4556 5.646360 GGTTAAGCATAACTAGGAACAGCAA 59.354 40.000 11.30 0.00 41.01 3.91
4325 4625 4.401022 TCATCAGTTTTTCATGAGCCTGT 58.599 39.130 0.00 0.00 0.00 4.00
4393 4694 4.811969 AGAATTCAATCATGCCTTGCAA 57.188 36.364 8.44 0.00 43.62 4.08


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

AutoCloner maintained by Alex Coulton.