Multiple sequence alignment - TraesCS4A01G169000

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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 TraesCS4A01G169000 chr4A 100.000 4190 0 0 676 4865 423894626 423890437 0.000000e+00 7738
1 TraesCS4A01G169000 chr4A 100.000 220 0 0 1 220 423895301 423895082 1.630000e-109 407
2 TraesCS4A01G169000 chr4D 96.388 3821 91 16 676 4469 137768133 137764333 0.000000e+00 6248
3 TraesCS4A01G169000 chr4D 91.727 278 20 2 4589 4865 137763998 137763723 2.750000e-102 383
4 TraesCS4A01G169000 chr4D 92.857 224 6 6 1 220 137768793 137768576 2.830000e-82 316
5 TraesCS4A01G169000 chr4B 93.336 4217 192 48 676 4865 230011736 230007582 0.000000e+00 6148
6 TraesCS4A01G169000 chr4B 93.333 225 10 3 1 220 230012351 230012127 1.310000e-85 327


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 TraesCS4A01G169000 chr4A 423890437 423895301 4864 True 4072.500000 7738 100.000000 1 4865 2 chr4A.!!$R1 4864
1 TraesCS4A01G169000 chr4D 137763723 137768793 5070 True 2315.666667 6248 93.657333 1 4865 3 chr4D.!!$R1 4864
2 TraesCS4A01G169000 chr4B 230007582 230012351 4769 True 3237.500000 6148 93.334500 1 4865 2 chr4B.!!$R1 4864

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
891 897 2.125952 CATGCTCCACTGCGACGA 60.126 61.111 0.0 0.0 35.36 4.20 F
1989 1996 1.674441 GGCTCCGGGTAATTTTGCTAC 59.326 52.381 0.0 0.0 0.00 3.58 F
3140 3151 1.843421 CTCAGGGGTGGTTGGTCAA 59.157 57.895 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2719 2728 0.036164 AGCCGGTTATGCTGAACACA 59.964 50.0 1.9 0.0 37.76 3.72 R
3649 3672 0.463474 GATGGACAGGCTCTTCAGGC 60.463 60.0 0.0 0.0 45.92 4.85 R
4817 5075 0.320421 TTTACTGGAGCACGACAGGC 60.320 55.0 0.0 0.0 39.00 4.85 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
89 92 7.726216 TGGTATAGATACATGAAGGTGTGAAG 58.274 38.462 0.00 0.00 34.98 3.02
147 153 4.674281 AGAAAACGAGTCTGGAGAAACT 57.326 40.909 0.00 0.00 0.00 2.66
799 805 3.307059 CCTGTTTCCTGGTTCGATCTCTT 60.307 47.826 0.00 0.00 0.00 2.85
819 825 5.276270 TCTTAGACCGATTCGATTTTACCG 58.724 41.667 7.83 0.00 0.00 4.02
891 897 2.125952 CATGCTCCACTGCGACGA 60.126 61.111 0.00 0.00 35.36 4.20
985 991 7.858879 GTGTGACGTTAAGACATAATTTTGGTT 59.141 33.333 0.00 0.00 0.00 3.67
1113 1119 5.198602 AGGCCAAAGAGTTATCCATTCTT 57.801 39.130 5.01 0.00 32.80 2.52
1197 1203 4.500035 GGCGACAAAAGGTAATGGTTTTGA 60.500 41.667 13.05 0.00 43.42 2.69
1206 1212 6.780457 AGGTAATGGTTTTGATTCATCTGG 57.220 37.500 0.00 0.00 0.00 3.86
1224 1230 6.544931 TCATCTGGGTTGATTCATTCAGATTC 59.455 38.462 17.05 0.00 39.17 2.52
1335 1341 4.976987 CAATTTTGCCATTGAATTGCTCC 58.023 39.130 2.85 0.00 36.39 4.70
1366 1372 9.474920 CTTGGCTGATTAGTTAATTGAAACAAA 57.525 29.630 0.00 0.00 0.00 2.83
1410 1416 7.603784 GCATTTCACCAATTCTGAAATTTACCT 59.396 33.333 14.19 0.00 42.97 3.08
1496 1503 9.691362 TTCTTTCATTTTTGCAATAGTAGTTCC 57.309 29.630 0.00 0.00 0.00 3.62
1576 1583 6.065976 TCTGTCATGTTTTCAGATATGGGT 57.934 37.500 0.00 0.00 34.00 4.51
1584 1591 8.849168 CATGTTTTCAGATATGGGTTGCTAATA 58.151 33.333 0.00 0.00 0.00 0.98
1807 1814 3.391296 TGTTTAACAGGAAGCTGGAGAGT 59.609 43.478 0.00 0.00 0.00 3.24
1989 1996 1.674441 GGCTCCGGGTAATTTTGCTAC 59.326 52.381 0.00 0.00 0.00 3.58
2146 2153 3.070076 GGCGATGAGCACTTCATGA 57.930 52.632 0.00 0.00 46.51 3.07
2169 2176 6.475402 TGAAATTTCTTCTTTCTGGTTTTCGC 59.525 34.615 18.64 0.00 34.43 4.70
2311 2318 2.517959 AGCAGCTCCACAAATTTGCTA 58.482 42.857 18.12 3.06 39.85 3.49
2426 2433 6.428465 TGCCGTCTAAAGTAATGTTTTCATGA 59.572 34.615 0.00 0.00 40.79 3.07
2450 2457 5.047306 ACACGTGATCTTCACTTCATAAGGA 60.047 40.000 25.01 0.00 44.85 3.36
2500 2508 9.649167 GGTAGAGTTAATTGTAGCTCTTTACAA 57.351 33.333 2.40 2.40 43.25 2.41
2543 2551 6.680810 TGAAAATTGAGGAGCATAACAGTTG 58.319 36.000 0.00 0.00 0.00 3.16
3041 3052 2.904866 TTGTGGTTCCACAGCGGC 60.905 61.111 21.36 0.00 45.90 6.53
3140 3151 1.843421 CTCAGGGGTGGTTGGTCAA 59.157 57.895 0.00 0.00 0.00 3.18
3154 3165 4.443063 GGTTGGTCAAGAATTTTGTTACGC 59.557 41.667 0.00 0.00 0.00 4.42
3156 3167 4.602995 TGGTCAAGAATTTTGTTACGCAC 58.397 39.130 0.00 0.00 0.00 5.34
3157 3168 4.336993 TGGTCAAGAATTTTGTTACGCACT 59.663 37.500 0.00 0.00 0.00 4.40
3159 3170 5.849604 GGTCAAGAATTTTGTTACGCACTAC 59.150 40.000 0.00 0.00 0.00 2.73
3535 3558 2.279517 GTCGGCGGCCACTATGAG 60.280 66.667 20.71 0.11 0.00 2.90
3621 3644 1.887344 TACGATCACCAGCAGCAGCA 61.887 55.000 3.17 0.00 45.49 4.41
3646 3669 4.999950 CCATCTGCCCAAGTGAGTAATATC 59.000 45.833 0.00 0.00 0.00 1.63
3648 3671 3.069586 TCTGCCCAAGTGAGTAATATCCG 59.930 47.826 0.00 0.00 0.00 4.18
3649 3672 2.104111 TGCCCAAGTGAGTAATATCCGG 59.896 50.000 0.00 0.00 0.00 5.14
3650 3673 2.767505 CCCAAGTGAGTAATATCCGGC 58.232 52.381 0.00 0.00 0.00 6.13
3651 3674 2.550208 CCCAAGTGAGTAATATCCGGCC 60.550 54.545 0.00 0.00 0.00 6.13
3652 3675 2.368875 CCAAGTGAGTAATATCCGGCCT 59.631 50.000 0.00 0.00 0.00 5.19
3655 3678 3.305720 AGTGAGTAATATCCGGCCTGAA 58.694 45.455 0.00 0.00 0.00 3.02
3656 3679 3.322254 AGTGAGTAATATCCGGCCTGAAG 59.678 47.826 0.00 0.00 0.00 3.02
3657 3680 3.321111 GTGAGTAATATCCGGCCTGAAGA 59.679 47.826 0.00 0.00 0.00 2.87
3658 3681 3.574396 TGAGTAATATCCGGCCTGAAGAG 59.426 47.826 0.00 0.00 0.00 2.85
3659 3682 2.300437 AGTAATATCCGGCCTGAAGAGC 59.700 50.000 0.00 0.00 0.00 4.09
3668 3706 0.463474 GCCTGAAGAGCCTGTCCATC 60.463 60.000 0.00 0.00 0.00 3.51
3676 3714 2.703007 AGAGCCTGTCCATCAAGTATCC 59.297 50.000 0.00 0.00 0.00 2.59
3814 3854 7.936847 TCTGGTCTTCTTTTCAGCTTATTGTTA 59.063 33.333 0.00 0.00 0.00 2.41
3875 3915 1.875009 CAACTCTGACAGCAGCTTCA 58.125 50.000 0.00 0.00 42.01 3.02
3879 3919 2.008329 CTCTGACAGCAGCTTCATTCC 58.992 52.381 0.00 0.00 42.01 3.01
3916 3956 4.746611 CGTACATCAGCAGCTCATGATTTA 59.253 41.667 14.08 0.00 33.91 1.40
3964 4004 2.484889 CTAAAGGCCTTACCATCGCTC 58.515 52.381 20.84 0.00 43.14 5.03
4346 4388 8.376270 AGCATGTAGTTAAACTTCTCTACCTTT 58.624 33.333 0.00 0.00 33.91 3.11
4380 4422 4.227134 CATGCTAGGCGCCGGTCT 62.227 66.667 23.20 5.85 38.05 3.85
4398 4440 1.205417 TCTACCGGCTAAAACTTCGGG 59.795 52.381 0.00 0.00 45.97 5.14
4455 4497 3.645660 TGCGATTCCTGGGTGCCA 61.646 61.111 0.00 0.00 0.00 4.92
4466 4508 0.548031 TGGGTGCCATCCTCATCTTC 59.452 55.000 0.00 0.00 0.00 2.87
4469 4511 2.621407 GGGTGCCATCCTCATCTTCAAA 60.621 50.000 0.00 0.00 0.00 2.69
4477 4519 5.453903 CCATCCTCATCTTCAAATACTCCGT 60.454 44.000 0.00 0.00 0.00 4.69
4482 4524 6.288941 TCATCTTCAAATACTCCGTGGTAA 57.711 37.500 0.00 0.00 0.00 2.85
4483 4525 6.703319 TCATCTTCAAATACTCCGTGGTAAA 58.297 36.000 0.00 0.00 0.00 2.01
4533 4575 1.916777 ACCCCCAACCTCGTCGAAT 60.917 57.895 0.00 0.00 0.00 3.34
4541 4583 2.395690 CTCGTCGAATTGCCGCAC 59.604 61.111 0.00 0.00 0.00 5.34
4572 4614 2.436646 CTCCTCGCCACCGCATTT 60.437 61.111 0.00 0.00 34.03 2.32
4573 4615 2.435938 TCCTCGCCACCGCATTTC 60.436 61.111 0.00 0.00 34.03 2.17
4574 4616 3.508840 CCTCGCCACCGCATTTCC 61.509 66.667 0.00 0.00 34.03 3.13
4575 4617 3.864686 CTCGCCACCGCATTTCCG 61.865 66.667 0.00 0.00 34.03 4.30
4576 4618 4.690719 TCGCCACCGCATTTCCGT 62.691 61.111 0.00 0.00 34.03 4.69
4577 4619 4.459331 CGCCACCGCATTTCCGTG 62.459 66.667 0.00 0.00 34.03 4.94
4578 4620 4.776647 GCCACCGCATTTCCGTGC 62.777 66.667 0.00 0.00 41.65 5.34
4579 4621 3.055719 CCACCGCATTTCCGTGCT 61.056 61.111 0.00 0.00 42.88 4.40
4580 4622 2.625823 CCACCGCATTTCCGTGCTT 61.626 57.895 0.00 0.00 42.88 3.91
4581 4623 1.442520 CACCGCATTTCCGTGCTTG 60.443 57.895 0.00 0.00 42.88 4.01
4582 4624 2.179018 CCGCATTTCCGTGCTTGG 59.821 61.111 0.00 0.00 42.88 3.61
4583 4625 2.179018 CGCATTTCCGTGCTTGGG 59.821 61.111 0.00 0.00 42.88 4.12
4584 4626 2.125952 GCATTTCCGTGCTTGGGC 60.126 61.111 0.00 0.00 41.82 5.36
4610 4867 2.202824 CGCCGCTACATTTCCGGA 60.203 61.111 0.00 0.00 44.55 5.14
4613 4870 0.743345 GCCGCTACATTTCCGGACTT 60.743 55.000 1.83 0.00 44.55 3.01
4617 4874 0.373716 CTACATTTCCGGACTTGCGC 59.626 55.000 1.83 0.00 0.00 6.09
4636 4893 3.114616 CGCTCCTCACCGCACTTG 61.115 66.667 0.00 0.00 0.00 3.16
4796 5054 1.007271 CACGTTCACTGCGGTCTCT 60.007 57.895 0.00 0.00 0.00 3.10
4817 5075 0.955428 AGCGTACACCATGGCTTGTG 60.955 55.000 13.04 4.93 38.44 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 92 2.125773 TTCTCCTCGTCCTAGTGTCC 57.874 55.000 0.00 0.00 0.00 4.02
98 101 6.359883 GTGCTTTTGTTTATTTTCTCCTCGTC 59.640 38.462 0.00 0.00 0.00 4.20
136 141 7.889873 TGGAAATGTTTTTAGTTTCTCCAGA 57.110 32.000 0.00 0.00 33.51 3.86
147 153 5.506649 GCTCGGACAGTTGGAAATGTTTTTA 60.507 40.000 0.00 0.00 0.00 1.52
799 805 3.374745 GCGGTAAAATCGAATCGGTCTA 58.625 45.455 1.76 0.00 0.00 2.59
819 825 0.318955 AATGCTTCCTTGTTGTGCGC 60.319 50.000 0.00 0.00 0.00 6.09
985 991 2.307392 TCCCCATGTCGAAGAATTTCCA 59.693 45.455 0.00 0.00 39.69 3.53
1113 1119 7.945134 TGAGAAGAATGAGATCGATATCACAA 58.055 34.615 23.97 2.89 36.48 3.33
1197 1203 6.429151 TCTGAATGAATCAACCCAGATGAAT 58.571 36.000 7.98 0.00 37.67 2.57
1206 1212 5.649395 TGACCTGAATCTGAATGAATCAACC 59.351 40.000 0.00 0.00 37.67 3.77
1224 1230 5.009010 GTCATATTATGGGCTTGTTGACCTG 59.991 44.000 3.89 0.00 46.68 4.00
1335 1341 9.859427 TTCAATTAACTAATCAGCCAAGAAATG 57.141 29.630 0.00 0.00 0.00 2.32
1366 1372 8.508875 GTGAAATGCATTGAAAAATCAATTCCT 58.491 29.630 13.82 0.00 38.16 3.36
1410 1416 3.383505 CAGTCGGAACATAGGACCATACA 59.616 47.826 0.00 0.00 0.00 2.29
1496 1503 6.564499 CGATTTCACCCAAAAGAAAAAGCATG 60.564 38.462 0.00 0.00 37.30 4.06
1576 1583 9.453572 CTCTGCCATCCTAAATATTATTAGCAA 57.546 33.333 0.00 0.00 32.62 3.91
1584 1591 9.866655 TGATTTAACTCTGCCATCCTAAATATT 57.133 29.630 0.00 0.00 0.00 1.28
1595 1602 4.766373 TGCAATTCTGATTTAACTCTGCCA 59.234 37.500 0.00 0.00 0.00 4.92
2060 2067 7.122650 CCCCTGCAATAGATTGAAAAGAACTAA 59.877 37.037 6.43 0.00 40.14 2.24
2104 2111 7.445121 CCCTAGCTGTGATATATGTTGAAGAA 58.555 38.462 0.00 0.00 0.00 2.52
2146 2153 6.573434 AGCGAAAACCAGAAAGAAGAAATTT 58.427 32.000 0.00 0.00 0.00 1.82
2169 2176 3.982475 TGAGCCAACGAGCATTAGATAG 58.018 45.455 0.00 0.00 34.23 2.08
2500 2508 5.948742 TTCATGGTTTCCCTTCAAGTTTT 57.051 34.783 0.00 0.00 0.00 2.43
2719 2728 0.036164 AGCCGGTTATGCTGAACACA 59.964 50.000 1.90 0.00 37.76 3.72
2720 2729 1.933853 CTAGCCGGTTATGCTGAACAC 59.066 52.381 1.90 0.00 39.91 3.32
3063 3074 2.945668 GGTCTTCAGGTAACATCATGGC 59.054 50.000 0.00 0.00 41.41 4.40
3140 3151 6.128634 GCTACAGTAGTGCGTAACAAAATTCT 60.129 38.462 9.42 0.00 0.00 2.40
3154 3165 8.479313 TTCTTCACATAAATGCTACAGTAGTG 57.521 34.615 9.42 0.00 0.00 2.74
3156 3167 8.932945 TCTTCTTCACATAAATGCTACAGTAG 57.067 34.615 2.85 2.85 0.00 2.57
3157 3168 9.719355 TTTCTTCTTCACATAAATGCTACAGTA 57.281 29.630 0.00 0.00 0.00 2.74
3159 3170 8.506437 TGTTTCTTCTTCACATAAATGCTACAG 58.494 33.333 0.00 0.00 0.00 2.74
3328 3339 3.770040 TGCTGATGTACCGCCGCT 61.770 61.111 0.00 0.00 0.00 5.52
3621 3644 1.302285 CTCACTTGGGCAGATGGCT 59.698 57.895 6.34 0.00 44.01 4.75
3648 3671 1.919600 ATGGACAGGCTCTTCAGGCC 61.920 60.000 0.00 0.00 46.80 5.19
3649 3672 0.463474 GATGGACAGGCTCTTCAGGC 60.463 60.000 0.00 0.00 45.92 4.85
3650 3673 0.907486 TGATGGACAGGCTCTTCAGG 59.093 55.000 0.00 0.00 0.00 3.86
3651 3674 2.027377 ACTTGATGGACAGGCTCTTCAG 60.027 50.000 0.00 0.00 0.00 3.02
3652 3675 1.980765 ACTTGATGGACAGGCTCTTCA 59.019 47.619 0.00 0.00 0.00 3.02
3655 3678 2.703007 GGATACTTGATGGACAGGCTCT 59.297 50.000 0.00 0.00 0.00 4.09
3656 3679 3.118905 GGATACTTGATGGACAGGCTC 57.881 52.381 0.00 0.00 0.00 4.70
3814 3854 4.566488 GGTCAGGGATTCAGTCATGTTCTT 60.566 45.833 0.00 0.00 0.00 2.52
3875 3915 2.672996 GCAGTGGCGTGGTGGAAT 60.673 61.111 0.00 0.00 0.00 3.01
3916 3956 4.142687 CGGTTCGTTGGCTAAAGAATCATT 60.143 41.667 18.70 0.00 35.84 2.57
4284 4326 9.722056 GTCATGTATTTTGGAACATAGATTGTC 57.278 33.333 0.00 0.00 39.30 3.18
4313 4355 8.324163 AGAAGTTTAACTACATGCTTTACAGG 57.676 34.615 0.00 0.00 35.74 4.00
4380 4422 0.391528 GCCCGAAGTTTTAGCCGGTA 60.392 55.000 1.90 0.00 40.30 4.02
4455 4497 5.453903 CCACGGAGTATTTGAAGATGAGGAT 60.454 44.000 0.00 0.00 41.61 3.24
4506 4548 3.828023 GTTGGGGGTGGTGGTGGT 61.828 66.667 0.00 0.00 0.00 4.16
4509 4551 3.182996 GAGGTTGGGGGTGGTGGT 61.183 66.667 0.00 0.00 0.00 4.16
4510 4552 4.344865 CGAGGTTGGGGGTGGTGG 62.345 72.222 0.00 0.00 0.00 4.61
4512 4554 3.246880 GACGAGGTTGGGGGTGGT 61.247 66.667 0.00 0.00 0.00 4.16
4555 4597 2.436646 AAATGCGGTGGCGAGGAG 60.437 61.111 0.00 0.00 44.10 3.69
4556 4598 2.435938 GAAATGCGGTGGCGAGGA 60.436 61.111 0.00 0.00 44.10 3.71
4557 4599 3.508840 GGAAATGCGGTGGCGAGG 61.509 66.667 0.00 0.00 44.10 4.63
4558 4600 3.864686 CGGAAATGCGGTGGCGAG 61.865 66.667 0.00 0.00 44.10 5.03
4559 4601 4.690719 ACGGAAATGCGGTGGCGA 62.691 61.111 0.00 0.00 44.10 5.54
4560 4602 4.459331 CACGGAAATGCGGTGGCG 62.459 66.667 0.00 0.00 42.30 5.69
4561 4603 4.776647 GCACGGAAATGCGGTGGC 62.777 66.667 1.00 0.00 45.09 5.01
4567 4609 2.125952 GCCCAAGCACGGAAATGC 60.126 61.111 0.00 0.00 46.50 3.56
4568 4610 3.364442 TGCCCAAGCACGGAAATG 58.636 55.556 0.00 0.00 46.52 2.32
4599 4856 1.355796 CGCGCAAGTCCGGAAATGTA 61.356 55.000 5.23 0.00 41.68 2.29
4762 5020 2.027073 GTGCGCCATGAGTTCGACA 61.027 57.895 4.18 0.00 0.00 4.35
4796 5054 0.673333 CAAGCCATGGTGTACGCTCA 60.673 55.000 14.67 3.31 0.00 4.26
4817 5075 0.320421 TTTACTGGAGCACGACAGGC 60.320 55.000 0.00 0.00 39.00 4.85


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

AutoCloner maintained by Alex Coulton.