Multiple sequence alignment - TraesCS1D01G403600

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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 TraesCS1D01G403600 chr1D 100.000 3431 0 0 1 3431 468346676 468350106 0.000000e+00 6336.0
1 TraesCS1D01G403600 chr1D 86.677 668 78 7 1342 1999 468257114 468257780 0.000000e+00 730.0
2 TraesCS1D01G403600 chr1D 80.769 676 107 16 2667 3330 468359980 468360644 1.100000e-139 507.0
3 TraesCS1D01G403600 chr1D 88.846 260 25 3 2376 2633 468257771 468258028 1.990000e-82 316.0
4 TraesCS1D01G403600 chr1D 89.474 114 9 2 28 141 468340434 468340544 1.280000e-29 141.0
5 TraesCS1D01G403600 chr1D 100.000 33 0 0 160 192 468340486 468340518 1.030000e-05 62.1
6 TraesCS1D01G403600 chr1A 94.728 3433 110 31 1 3389 561279198 561282603 0.000000e+00 5271.0
7 TraesCS1D01G403600 chr1A 85.059 937 96 28 1056 1991 561202001 561202894 0.000000e+00 915.0
8 TraesCS1D01G403600 chr1A 79.764 677 103 23 2667 3330 561290445 561291100 8.680000e-126 460.0
9 TraesCS1D01G403600 chr1A 85.425 247 32 3 2389 2633 561204591 561204835 1.580000e-63 254.0
10 TraesCS1D01G403600 chr1A 89.474 114 9 2 28 141 561272898 561273008 1.280000e-29 141.0
11 TraesCS1D01G403600 chr1A 100.000 33 0 0 160 192 561272950 561272982 1.030000e-05 62.1
12 TraesCS1D01G403600 chr1A 97.059 34 0 1 160 192 561279278 561279311 4.780000e-04 56.5
13 TraesCS1D01G403600 chr1B 92.672 2470 124 22 758 3207 647142181 647144613 0.000000e+00 3506.0
14 TraesCS1D01G403600 chr1B 90.278 432 35 5 168 595 647141283 647141711 2.990000e-155 558.0
15 TraesCS1D01G403600 chr1B 91.852 135 8 2 28 162 647109725 647109856 5.850000e-43 185.0


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 TraesCS1D01G403600 chr1D 468346676 468350106 3430 False 6336.00 6336 100.0000 1 3431 1 chr1D.!!$F1 3430
1 TraesCS1D01G403600 chr1D 468257114 468258028 914 False 523.00 730 87.7615 1342 2633 2 chr1D.!!$F3 1291
2 TraesCS1D01G403600 chr1D 468359980 468360644 664 False 507.00 507 80.7690 2667 3330 1 chr1D.!!$F2 663
3 TraesCS1D01G403600 chr1A 561279198 561282603 3405 False 2663.75 5271 95.8935 1 3389 2 chr1A.!!$F4 3388
4 TraesCS1D01G403600 chr1A 561202001 561204835 2834 False 584.50 915 85.2420 1056 2633 2 chr1A.!!$F2 1577
5 TraesCS1D01G403600 chr1A 561290445 561291100 655 False 460.00 460 79.7640 2667 3330 1 chr1A.!!$F1 663
6 TraesCS1D01G403600 chr1B 647141283 647144613 3330 False 2032.00 3506 91.4750 168 3207 2 chr1B.!!$F2 3039

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
756 1041 0.033504 CAGACCAACACCAGCTACGT 59.966 55.0 0.0 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2673 4350 0.833287 GGGGCTTCTCTGATGCACTA 59.167 55.0 7.45 0.0 36.54 2.74 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
42 43 6.894682 TCTACAATATGTGCACCAAAGGATA 58.105 36.000 15.69 4.52 0.00 2.59
97 98 4.338964 TGGCCTGCATACAAATTACTGATG 59.661 41.667 3.32 0.00 0.00 3.07
104 105 7.922837 TGCATACAAATTACTGATGATGAGTG 58.077 34.615 0.00 0.00 0.00 3.51
129 130 5.532406 CCCCCACATAACACATAATCTGAAG 59.468 44.000 0.00 0.00 0.00 3.02
154 155 5.399013 GGAAAACATAGCTAAACGCACAAT 58.601 37.500 0.00 0.00 42.61 2.71
204 206 3.767131 ACCCCACATACAAATTACTTGGC 59.233 43.478 0.00 0.00 39.56 4.52
254 257 7.436933 TGCTGAACTATGAATCAAGACGATAT 58.563 34.615 0.00 0.00 32.51 1.63
278 281 5.643664 TGTGAAATTAGTGCAAGCATGATC 58.356 37.500 0.00 0.00 0.00 2.92
279 282 4.731961 GTGAAATTAGTGCAAGCATGATCG 59.268 41.667 0.00 0.00 0.00 3.69
286 289 1.332686 TGCAAGCATGATCGAGCAATC 59.667 47.619 7.76 2.04 0.00 2.67
291 294 0.952497 CATGATCGAGCAATCCCCCG 60.952 60.000 7.76 0.00 0.00 5.73
353 356 6.371595 TGCAGGGAATGAAACCAAAAATAT 57.628 33.333 0.00 0.00 0.00 1.28
361 364 7.600752 GGAATGAAACCAAAAATATTGTCCGAA 59.399 33.333 0.00 0.00 0.00 4.30
384 391 4.750021 AAATACTCAGATGAGAGCTGCA 57.250 40.909 16.52 0.00 44.74 4.41
394 401 3.650950 GAGCTGCAGGGTTGGGGA 61.651 66.667 17.12 0.00 0.00 4.81
441 449 0.722282 CGACGTCGATGACTGACTCT 59.278 55.000 33.35 0.00 43.02 3.24
462 470 0.893727 ACCTCATTGGCGAAACACCC 60.894 55.000 0.00 0.00 40.22 4.61
635 643 4.057428 GCCAGCGACGGTGACTCT 62.057 66.667 27.42 0.00 32.22 3.24
636 644 2.126307 CCAGCGACGGTGACTCTG 60.126 66.667 27.42 9.56 32.22 3.35
738 1023 3.181453 TGGTCAAAACTGATTCGGGTACA 60.181 43.478 0.00 0.00 0.00 2.90
756 1041 0.033504 CAGACCAACACCAGCTACGT 59.966 55.000 0.00 0.00 0.00 3.57
786 1101 1.872952 CGCCACATGAGACAAACAGAA 59.127 47.619 0.00 0.00 0.00 3.02
791 1106 3.185188 CACATGAGACAAACAGAACGAGG 59.815 47.826 0.00 0.00 0.00 4.63
859 1176 5.298276 TGAAGTGAAAATAGAAACAGCCGTT 59.702 36.000 0.00 0.00 36.73 4.44
900 1217 6.371389 GTGGGAAACGTCTGAAATTTAGAAG 58.629 40.000 0.00 0.00 0.00 2.85
941 1258 7.267128 ACAATTCATGCGTGGATAAATGAAAT 58.733 30.769 5.98 0.00 41.11 2.17
949 1266 9.725019 ATGCGTGGATAAATGAAATATTCTCTA 57.275 29.630 0.00 0.00 0.00 2.43
1077 1402 2.575993 CACGTCAGCCTCTCCCTG 59.424 66.667 0.00 0.00 0.00 4.45
1907 2247 0.904865 TGGAACGCCCTGATCTCAGT 60.905 55.000 6.46 0.00 42.27 3.41
2127 3591 3.379445 GTTGACCTCCTCGGCCGA 61.379 66.667 29.03 29.03 35.61 5.54
2397 4073 1.066716 CGGTTGTCAAAGATACCCGGA 60.067 52.381 0.73 0.00 0.00 5.14
2606 4283 8.593679 TCTTTTTGGTGAGATACAGATGAGTTA 58.406 33.333 0.00 0.00 0.00 2.24
2661 4338 3.221389 GCCATCGCCACATGCCAT 61.221 61.111 0.00 0.00 36.24 4.40
2673 4350 4.519213 CCACATGCCATGAAAAATGGAAT 58.481 39.130 12.53 0.01 41.64 3.01
2950 4652 9.368674 CAGATTGTTGGTTGATGCAATATTTAA 57.631 29.630 0.00 0.00 32.47 1.52
3011 4713 2.806945 TTTGGGCCATAGGTGAAGAG 57.193 50.000 7.26 0.00 0.00 2.85
3323 5026 8.366359 AGTGATATTTTGCTACAATTTTCCCT 57.634 30.769 0.00 0.00 0.00 4.20
3324 5027 8.815912 AGTGATATTTTGCTACAATTTTCCCTT 58.184 29.630 0.00 0.00 0.00 3.95
3325 5028 9.435688 GTGATATTTTGCTACAATTTTCCCTTT 57.564 29.630 0.00 0.00 0.00 3.11
3326 5029 9.651913 TGATATTTTGCTACAATTTTCCCTTTC 57.348 29.630 0.00 0.00 0.00 2.62
3343 5046 3.371380 CCTTTCTTCTTGCCTAGCCAGAT 60.371 47.826 0.00 0.00 30.58 2.90
3364 5067 2.166870 TGCTAATGCCTTCCTTGCAATG 59.833 45.455 0.00 0.00 42.92 2.82
3389 5092 9.803315 TGTGTACTCATCTTATAGCTAACTTTG 57.197 33.333 0.00 0.00 0.00 2.77
3390 5093 8.756864 GTGTACTCATCTTATAGCTAACTTTGC 58.243 37.037 0.00 0.00 0.00 3.68
3391 5094 8.474831 TGTACTCATCTTATAGCTAACTTTGCA 58.525 33.333 0.00 0.00 0.00 4.08
3392 5095 9.482627 GTACTCATCTTATAGCTAACTTTGCAT 57.517 33.333 0.00 0.00 0.00 3.96
3393 5096 8.375608 ACTCATCTTATAGCTAACTTTGCATG 57.624 34.615 0.00 0.00 0.00 4.06
3394 5097 7.989741 ACTCATCTTATAGCTAACTTTGCATGT 59.010 33.333 0.00 0.00 0.00 3.21
3395 5098 8.370493 TCATCTTATAGCTAACTTTGCATGTC 57.630 34.615 0.00 0.00 0.00 3.06
3396 5099 8.206867 TCATCTTATAGCTAACTTTGCATGTCT 58.793 33.333 0.00 0.00 0.00 3.41
3397 5100 8.834465 CATCTTATAGCTAACTTTGCATGTCTT 58.166 33.333 0.00 0.00 0.00 3.01
3398 5101 8.792830 TCTTATAGCTAACTTTGCATGTCTTT 57.207 30.769 0.00 0.00 0.00 2.52
3399 5102 9.231297 TCTTATAGCTAACTTTGCATGTCTTTT 57.769 29.630 0.00 0.00 0.00 2.27
3400 5103 9.846248 CTTATAGCTAACTTTGCATGTCTTTTT 57.154 29.630 0.00 0.00 0.00 1.94
3419 5122 4.314740 TTTTTGCCAGACGCTATTTTGT 57.685 36.364 0.00 0.00 38.78 2.83
3420 5123 4.314740 TTTTGCCAGACGCTATTTTGTT 57.685 36.364 0.00 0.00 38.78 2.83
3421 5124 4.314740 TTTGCCAGACGCTATTTTGTTT 57.685 36.364 0.00 0.00 38.78 2.83
3422 5125 4.314740 TTGCCAGACGCTATTTTGTTTT 57.685 36.364 0.00 0.00 38.78 2.43
3423 5126 3.637432 TGCCAGACGCTATTTTGTTTTG 58.363 40.909 0.00 0.00 38.78 2.44
3424 5127 2.408368 GCCAGACGCTATTTTGTTTTGC 59.592 45.455 0.00 0.00 0.00 3.68
3425 5128 2.986479 CCAGACGCTATTTTGTTTTGCC 59.014 45.455 0.00 0.00 0.00 4.52
3426 5129 3.551863 CCAGACGCTATTTTGTTTTGCCA 60.552 43.478 0.00 0.00 0.00 4.92
3427 5130 3.425193 CAGACGCTATTTTGTTTTGCCAC 59.575 43.478 0.00 0.00 0.00 5.01
3428 5131 3.317993 AGACGCTATTTTGTTTTGCCACT 59.682 39.130 0.00 0.00 0.00 4.00
3429 5132 4.048504 GACGCTATTTTGTTTTGCCACTT 58.951 39.130 0.00 0.00 0.00 3.16
3430 5133 4.048504 ACGCTATTTTGTTTTGCCACTTC 58.951 39.130 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.456380 ACCTTATCCTTTGGTGCACAT 57.544 42.857 20.43 4.67 32.16 3.21
52 53 7.338449 GGCCAGGTTTCAATTTGTATAGAACTA 59.662 37.037 0.00 0.00 0.00 2.24
60 61 2.298729 GCAGGCCAGGTTTCAATTTGTA 59.701 45.455 5.01 0.00 0.00 2.41
62 63 1.070445 TGCAGGCCAGGTTTCAATTTG 59.930 47.619 5.01 0.00 0.00 2.32
75 76 4.580167 TCATCAGTAATTTGTATGCAGGCC 59.420 41.667 0.00 0.00 0.00 5.19
76 77 5.756195 TCATCAGTAATTTGTATGCAGGC 57.244 39.130 0.00 0.00 0.00 4.85
97 98 1.064758 TGTTATGTGGGGGCACTCATC 60.065 52.381 0.00 0.00 0.00 2.92
104 105 3.569701 CAGATTATGTGTTATGTGGGGGC 59.430 47.826 0.00 0.00 0.00 5.80
129 130 3.416119 GCGTTTAGCTATGTTTTCCCC 57.584 47.619 0.00 0.00 44.04 4.81
154 155 9.559732 CTCATTATCAGTAATTTGTATGTGGGA 57.440 33.333 0.00 0.00 0.00 4.37
204 206 1.135972 CGTGGAGCTCAATGTTTTCGG 60.136 52.381 17.19 0.00 0.00 4.30
254 257 5.450592 TCATGCTTGCACTAATTTCACAA 57.549 34.783 0.00 0.00 0.00 3.33
278 281 4.776322 TGTGCGGGGGATTGCTCG 62.776 66.667 0.00 0.00 0.00 5.03
279 282 2.361104 TTGTGCGGGGGATTGCTC 60.361 61.111 0.00 0.00 0.00 4.26
286 289 2.339712 CTTTTGCTTGTGCGGGGG 59.660 61.111 0.00 0.00 43.34 5.40
291 294 3.188460 TCGTTAGATCCTTTTGCTTGTGC 59.812 43.478 0.00 0.00 40.20 4.57
361 364 5.494724 TGCAGCTCTCATCTGAGTATTTTT 58.505 37.500 7.07 0.00 42.60 1.94
383 389 1.747206 CGAGCTATTTCCCCAACCCTG 60.747 57.143 0.00 0.00 0.00 4.45
384 391 0.546598 CGAGCTATTTCCCCAACCCT 59.453 55.000 0.00 0.00 0.00 4.34
394 401 1.679032 GGGAGGCACAACGAGCTATTT 60.679 52.381 0.00 0.00 0.00 1.40
421 429 0.247735 GAGTCAGTCATCGACGTCGG 60.248 60.000 35.05 21.47 38.46 4.79
427 435 2.290323 TGAGGTCAGAGTCAGTCATCGA 60.290 50.000 0.00 0.00 0.00 3.59
431 439 2.564504 CCAATGAGGTCAGAGTCAGTCA 59.435 50.000 0.00 0.00 0.00 3.41
441 449 1.234821 GTGTTTCGCCAATGAGGTCA 58.765 50.000 0.00 0.00 40.61 4.02
462 470 2.973600 TTTTTCGTCCCGCCACCG 60.974 61.111 0.00 0.00 0.00 4.94
485 493 1.077858 GTACGGAGAGGAGGTCGGT 60.078 63.158 0.00 0.00 0.00 4.69
663 671 7.651027 AAATCATTTCTGTAATGGAGAAGGG 57.349 36.000 7.09 0.00 43.19 3.95
726 1011 1.972075 TGTTGGTCTGTACCCGAATCA 59.028 47.619 0.00 0.00 46.16 2.57
738 1023 0.317479 GACGTAGCTGGTGTTGGTCT 59.683 55.000 0.00 0.00 0.00 3.85
786 1101 0.029567 CGAATCTTAGCGCTCCTCGT 59.970 55.000 16.34 0.00 41.07 4.18
791 1106 2.793933 TGTACACGAATCTTAGCGCTC 58.206 47.619 16.34 0.00 0.00 5.03
831 1147 5.048434 GCTGTTTCTATTTTCACTTCAGGCT 60.048 40.000 0.00 0.00 0.00 4.58
848 1165 5.966636 AAAAAGAATCAAACGGCTGTTTC 57.033 34.783 20.80 10.04 44.94 2.78
900 1217 7.566709 CATGAATTGTTTTGCAGTTTTCCTAC 58.433 34.615 0.00 0.00 0.00 3.18
941 1258 3.429822 CCCGCACCTCGTTTTAGAGAATA 60.430 47.826 0.00 0.00 40.57 1.75
949 1266 1.670083 GTAGCCCGCACCTCGTTTT 60.670 57.895 0.00 0.00 36.19 2.43
1313 1638 1.078528 TGGGAGAAGAAGGCGAGGA 59.921 57.895 0.00 0.00 0.00 3.71
1781 2120 3.727258 TGCCAAGGATCACCCCCG 61.727 66.667 0.00 0.00 36.73 5.73
2127 3591 2.239907 GGCCTCCAATAGAAGTCCACTT 59.760 50.000 0.00 0.00 39.23 3.16
2397 4073 2.816958 CCAGCAACAGCGCTCGAT 60.817 61.111 7.13 0.00 41.38 3.59
2606 4283 2.302587 ATTTGGTCCCAACGGTGAAT 57.697 45.000 0.00 0.00 35.46 2.57
2653 4330 6.342906 CACTATTCCATTTTTCATGGCATGT 58.657 36.000 25.62 4.50 39.01 3.21
2661 4338 6.885918 TCTCTGATGCACTATTCCATTTTTCA 59.114 34.615 0.00 0.00 0.00 2.69
2673 4350 0.833287 GGGGCTTCTCTGATGCACTA 59.167 55.000 7.45 0.00 36.54 2.74
2801 4482 4.525487 ACACATGGCAAGATCTGAACATTT 59.475 37.500 0.00 0.00 0.00 2.32
2908 4609 8.663911 CCAACAATCTGCAAAAGAAACTAAAAA 58.336 29.630 0.00 0.00 38.79 1.94
2909 4610 7.821846 ACCAACAATCTGCAAAAGAAACTAAAA 59.178 29.630 0.00 0.00 38.79 1.52
2950 4652 8.812513 TGGAGACAATCAATCAGAATACAAAT 57.187 30.769 0.00 0.00 37.44 2.32
2983 4685 8.644374 TTCACCTATGGCCCAAAATATATTAC 57.356 34.615 0.00 0.00 0.00 1.89
2993 4695 0.255890 GCTCTTCACCTATGGCCCAA 59.744 55.000 0.00 0.00 0.00 4.12
3323 5026 3.614092 CATCTGGCTAGGCAAGAAGAAA 58.386 45.455 20.64 0.71 42.33 2.52
3324 5027 2.681976 GCATCTGGCTAGGCAAGAAGAA 60.682 50.000 20.64 2.41 42.33 2.52
3325 5028 1.134280 GCATCTGGCTAGGCAAGAAGA 60.134 52.381 20.64 13.90 42.33 2.87
3326 5029 1.307097 GCATCTGGCTAGGCAAGAAG 58.693 55.000 20.64 15.98 42.33 2.85
3343 5046 1.921982 TTGCAAGGAAGGCATTAGCA 58.078 45.000 0.00 0.00 44.61 3.49
3364 5067 8.756864 GCAAAGTTAGCTATAAGATGAGTACAC 58.243 37.037 0.00 0.00 0.00 2.90
3403 5106 2.408368 GCAAAACAAAATAGCGTCTGGC 59.592 45.455 0.00 0.00 44.05 4.85
3404 5107 2.986479 GGCAAAACAAAATAGCGTCTGG 59.014 45.455 0.00 0.00 0.00 3.86
3405 5108 3.425193 GTGGCAAAACAAAATAGCGTCTG 59.575 43.478 0.00 0.00 0.00 3.51
3406 5109 3.317993 AGTGGCAAAACAAAATAGCGTCT 59.682 39.130 0.00 0.00 0.00 4.18
3407 5110 3.638484 AGTGGCAAAACAAAATAGCGTC 58.362 40.909 0.00 0.00 0.00 5.19
3408 5111 3.726291 AGTGGCAAAACAAAATAGCGT 57.274 38.095 0.00 0.00 0.00 5.07
3409 5112 4.629527 GAAGTGGCAAAACAAAATAGCG 57.370 40.909 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.