Multiple sequence alignment - TraesCS6A01G041400

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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 TraesCS6A01G041400 chr6A 100.000 4679 0 0 1 4679 21695454 21690776 0 8641
1 TraesCS6A01G041400 chr6A 94.667 4688 234 11 1 4679 37317813 37313133 0 7258
2 TraesCS6A01G041400 chr6A 94.604 4689 230 16 1 4679 611901122 611896447 0 7236
3 TraesCS6A01G041400 chr6A 92.964 4690 275 28 1 4676 26737231 26741879 0 6782
4 TraesCS6A01G041400 chr6A 91.516 2982 233 15 1 2973 609543449 609540479 0 4087
5 TraesCS6A01G041400 chr6A 91.473 2932 230 16 1 2922 30236079 30239000 0 4012
6 TraesCS6A01G041400 chr6A 92.668 1814 126 6 2872 4679 609540529 609538717 0 2606
7 TraesCS6A01G041400 chr6A 93.345 1758 111 6 2926 4679 26849183 26847428 0 2593
8 TraesCS6A01G041400 chr6A 93.223 1756 114 4 2926 4679 615352115 615350363 0 2579
9 TraesCS6A01G041400 chr6A 92.999 1757 117 6 2926 4679 21027148 21025395 0 2558
10 TraesCS6A01G041400 chr6A 92.796 1763 116 9 2922 4679 30238949 30240705 0 2542
11 TraesCS6A01G041400 chr2A 94.471 2930 140 12 1 2922 778366022 778363107 0 4494
12 TraesCS6A01G041400 chr2A 92.260 2933 200 15 1 2922 765255959 765253043 0 4133
13 TraesCS6A01G041400 chr2A 90.408 2940 249 25 1 2922 780352262 780349338 0 3836
14 TraesCS6A01G041400 chr2A 96.066 1754 67 2 2927 4679 778363153 778361401 0 2856
15 TraesCS6A01G041400 chr2A 93.530 1762 108 6 2922 4679 765253094 765251335 0 2617
16 TraesCS6A01G041400 chrUn 88.586 2935 307 24 1 2922 31244061 31246980 0 3539


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 TraesCS6A01G041400 chr6A 21690776 21695454 4678 True 8641.0 8641 100.0000 1 4679 1 chr6A.!!$R2 4678
1 TraesCS6A01G041400 chr6A 37313133 37317813 4680 True 7258.0 7258 94.6670 1 4679 1 chr6A.!!$R4 4678
2 TraesCS6A01G041400 chr6A 611896447 611901122 4675 True 7236.0 7236 94.6040 1 4679 1 chr6A.!!$R5 4678
3 TraesCS6A01G041400 chr6A 26737231 26741879 4648 False 6782.0 6782 92.9640 1 4676 1 chr6A.!!$F1 4675
4 TraesCS6A01G041400 chr6A 609538717 609543449 4732 True 3346.5 4087 92.0920 1 4679 2 chr6A.!!$R7 4678
5 TraesCS6A01G041400 chr6A 30236079 30240705 4626 False 3277.0 4012 92.1345 1 4679 2 chr6A.!!$F2 4678
6 TraesCS6A01G041400 chr6A 26847428 26849183 1755 True 2593.0 2593 93.3450 2926 4679 1 chr6A.!!$R3 1753
7 TraesCS6A01G041400 chr6A 615350363 615352115 1752 True 2579.0 2579 93.2230 2926 4679 1 chr6A.!!$R6 1753
8 TraesCS6A01G041400 chr6A 21025395 21027148 1753 True 2558.0 2558 92.9990 2926 4679 1 chr6A.!!$R1 1753
9 TraesCS6A01G041400 chr2A 780349338 780352262 2924 True 3836.0 3836 90.4080 1 2922 1 chr2A.!!$R1 2921
10 TraesCS6A01G041400 chr2A 778361401 778366022 4621 True 3675.0 4494 95.2685 1 4679 2 chr2A.!!$R3 4678
11 TraesCS6A01G041400 chr2A 765251335 765255959 4624 True 3375.0 4133 92.8950 1 4679 2 chr2A.!!$R2 4678
12 TraesCS6A01G041400 chrUn 31244061 31246980 2919 False 3539.0 3539 88.5860 1 2922 1 chrUn.!!$F1 2921

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
580 588 0.108615 CAGTCGCCTTGATCCGTTCT 60.109 55.0 0.00 0.00 0.00 3.01 F
1665 1681 0.546747 TTCCACCCTTCACCCTCGAT 60.547 55.0 0.00 0.00 0.00 3.59 F
2642 2670 0.102481 CTCCAACCCTGGTACGATCG 59.898 60.0 14.88 14.88 43.97 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 2519 0.035598 TGTCCTCCAATCGGCGAAAA 59.964 50.0 15.93 0.0 0.0 2.29 R
3378 3470 0.389391 CGACAGGACACAGACCACTT 59.611 55.0 0.00 0.0 0.0 3.16 R
4486 4583 0.039165 GGCGGCCAGTTTTTCTTCTG 60.039 55.0 15.62 0.0 0.0 3.02 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
28 29 3.755628 GCCCTACGTCTCGGTGCA 61.756 66.667 0.00 0.00 0.00 4.57
73 75 2.159226 CGTGAGTAAGATGACAGGGGTC 60.159 54.545 0.00 0.00 44.57 4.46
120 122 4.479619 GGTGGTTTATATAGAGTACGCCG 58.520 47.826 0.00 0.00 0.00 6.46
239 242 2.004017 CTTAATAGCCGACCGTTTGCA 58.996 47.619 0.00 0.00 0.00 4.08
263 267 1.273098 GGAGTGACTTGAGGTCCCCTA 60.273 57.143 0.00 0.00 43.89 3.53
346 351 4.275196 CGTCGAGTGGGATATCTTCAAGTA 59.725 45.833 2.05 0.00 0.00 2.24
347 352 5.220989 CGTCGAGTGGGATATCTTCAAGTAA 60.221 44.000 2.05 0.00 0.00 2.24
383 388 6.457351 ACTTCCTCTAAGGATGTCCTATGGC 61.457 48.000 1.21 0.00 46.21 4.40
541 549 3.282745 CTGGGTCGACTGTCACGGG 62.283 68.421 16.46 0.00 0.00 5.28
580 588 0.108615 CAGTCGCCTTGATCCGTTCT 60.109 55.000 0.00 0.00 0.00 3.01
614 622 3.242739 CGAATGGATTTCTTTACCTGCGG 60.243 47.826 0.00 0.00 31.73 5.69
764 773 1.762460 GAAGGCTCCTCGATCCCCA 60.762 63.158 0.00 0.00 0.00 4.96
915 924 2.357637 GCGTGCTCATCTCTTCTACTCT 59.642 50.000 0.00 0.00 0.00 3.24
1470 1486 0.671796 TTCGCTCTCAGTCGGTGAAA 59.328 50.000 0.00 0.00 33.60 2.69
1665 1681 0.546747 TTCCACCCTTCACCCTCGAT 60.547 55.000 0.00 0.00 0.00 3.59
2147 2169 2.359967 GGGGTCGACTGAGGAAGGG 61.360 68.421 16.46 0.00 0.00 3.95
2195 2217 2.681778 CAGGGCGAGTGGGAGTCT 60.682 66.667 0.00 0.00 0.00 3.24
2204 2226 3.062466 TGGGAGTCTGACGGCGAG 61.062 66.667 16.62 0.25 0.00 5.03
2254 2282 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
2255 2283 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
2256 2284 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
2257 2285 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
2258 2286 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
2259 2287 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
2267 2295 3.471806 GAGGAGGAGGCCGAACCC 61.472 72.222 11.88 6.18 40.58 4.11
2268 2296 3.986116 GAGGAGGAGGCCGAACCCT 62.986 68.421 9.12 9.12 40.58 4.34
2372 2400 3.068691 CGCCCTCGGACCTCTTCA 61.069 66.667 0.00 0.00 0.00 3.02
2472 2500 2.030027 AACTGTCCCTGTCATCTCCA 57.970 50.000 0.00 0.00 0.00 3.86
2491 2519 3.117663 TCCAGGTAACAAGCCTTGTCTTT 60.118 43.478 11.11 0.00 44.59 2.52
2532 2560 4.750598 CAGATCCTCAGTCGACTCGTTATA 59.249 45.833 16.96 0.00 0.00 0.98
2642 2670 0.102481 CTCCAACCCTGGTACGATCG 59.898 60.000 14.88 14.88 43.97 3.69
2653 2681 3.894920 TGGTACGATCGTTGACGTTTTA 58.105 40.909 27.88 1.08 42.61 1.52
2671 2705 5.558083 CGTTTTATTTTTGAGTTGGCTTGGC 60.558 40.000 0.00 0.00 0.00 4.52
2924 3012 0.109086 CGACTGTCAATCCGACTGCT 60.109 55.000 8.73 0.00 45.01 4.24
2991 3079 1.719780 CTTCACTCTTTGTCGCGTACC 59.280 52.381 5.77 0.00 0.00 3.34
3038 3126 0.251916 CGAAGGAGGCCATACACCAA 59.748 55.000 5.01 0.00 0.00 3.67
3071 3159 1.377856 GGAGCAGGTGAAGAAGGCC 60.378 63.158 0.00 0.00 0.00 5.19
3109 3197 0.801067 GCTTACGATGCGAGTTCGGT 60.801 55.000 3.50 0.00 40.83 4.69
3125 3213 1.338973 TCGGTGCTTCAGAGTAACGTT 59.661 47.619 5.88 5.88 46.87 3.99
3140 3228 2.510768 ACGTTCAGGTCAGTTGACTC 57.489 50.000 11.67 3.08 44.20 3.36
3372 3464 0.468226 TTCACTCGGTTTGGTCTGCT 59.532 50.000 0.00 0.00 0.00 4.24
3378 3470 0.320374 CGGTTTGGTCTGCTAGGTCA 59.680 55.000 0.00 0.00 0.00 4.02
3386 3479 1.896465 GTCTGCTAGGTCAAGTGGTCT 59.104 52.381 0.00 0.00 0.00 3.85
3781 3877 0.165079 TTCGATCGCCGTTTCTTTGC 59.835 50.000 11.09 0.00 39.75 3.68
3977 4073 4.413851 AGTTGGAAGAAGAAGAACCTCCTT 59.586 41.667 0.00 0.00 0.00 3.36
4198 4295 2.108362 GACCGGGCGGATCGAAAT 59.892 61.111 6.32 0.00 38.96 2.17
4356 4453 2.587194 CAGAATCCGCGCTCCAGG 60.587 66.667 5.56 0.00 0.00 4.45
4395 4492 2.844946 TGGCTCGACTTGACAAAATCA 58.155 42.857 0.00 0.00 34.65 2.57
4486 4583 4.704833 TCACTGCAAGGAGGCGCC 62.705 66.667 21.89 21.89 39.30 6.53
4496 4593 0.110486 AGGAGGCGCCAGAAGAAAAA 59.890 50.000 31.54 0.00 40.02 1.94
4521 4618 1.434696 GCCATCCAAGTCGCCAATG 59.565 57.895 0.00 0.00 0.00 2.82
4608 4705 2.168521 GGAATCGACCTGGATGAGTTCA 59.831 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.143333 CCAATCGACCGCCTCCGT 62.143 66.667 0.00 0.00 0.00 4.69
73 75 2.101582 CTCCTCAGTATCAAGGGTTCGG 59.898 54.545 0.00 0.00 33.21 4.30
103 105 2.493278 GGGCCGGCGTACTCTATATAAA 59.507 50.000 22.54 0.00 0.00 1.40
239 242 0.247736 GACCTCAAGTCACTCCGCAT 59.752 55.000 0.00 0.00 45.55 4.73
346 351 6.717084 CCTTAGAGGAAGTCACCTTTCAAATT 59.283 38.462 0.00 0.00 40.73 1.82
347 352 6.044404 TCCTTAGAGGAAGTCACCTTTCAAAT 59.956 38.462 0.00 0.00 42.51 2.32
383 388 3.537874 CCCGTCCTAAGAGCCCCG 61.538 72.222 0.00 0.00 0.00 5.73
384 389 2.365237 ACCCGTCCTAAGAGCCCC 60.365 66.667 0.00 0.00 0.00 5.80
510 518 2.742372 CCCAGAACGAAGCACCCG 60.742 66.667 0.00 0.00 0.00 5.28
541 549 4.989168 ACTGAAAGAGGTTAATGACGTCAC 59.011 41.667 22.71 7.96 43.81 3.67
580 588 4.730949 AATCCATTCGACGAAAGACCTA 57.269 40.909 15.22 0.00 0.00 3.08
856 865 3.073356 TCCGGGCCAACTATTTATAAGGG 59.927 47.826 4.39 0.00 0.00 3.95
915 924 1.728068 CGACGGAGAGACAGAGAGAA 58.272 55.000 0.00 0.00 0.00 2.87
1204 1219 0.719015 ATCTCTCCCCCTGGAAGACA 59.281 55.000 0.00 0.00 41.17 3.41
1470 1486 1.884579 TCGTCACTCGACTTAGCCTTT 59.115 47.619 0.00 0.00 44.01 3.11
1764 1780 2.610859 AGCAGGTCCATCCCCGTT 60.611 61.111 0.00 0.00 36.75 4.44
2147 2169 2.683933 TCACCTCCGCTCCCTTCC 60.684 66.667 0.00 0.00 0.00 3.46
2204 2226 2.123251 TCATCGCCTCCCTCTCCC 60.123 66.667 0.00 0.00 0.00 4.30
2276 2304 2.209838 CGAGCTTAGATCGCCTTTCA 57.790 50.000 7.02 0.00 32.81 2.69
2337 2365 1.673009 GTTTCAACGATGGCCCGGA 60.673 57.895 0.73 0.00 0.00 5.14
2350 2378 2.920912 AGGTCCGAGGGCGTTTCA 60.921 61.111 0.00 0.00 35.23 2.69
2372 2400 0.974383 CCTTCCTAGTCGGTGTTGGT 59.026 55.000 0.00 0.00 0.00 3.67
2491 2519 0.035598 TGTCCTCCAATCGGCGAAAA 59.964 50.000 15.93 0.00 0.00 2.29
2497 2525 3.997672 GGATCTGTCCTCCAATCGG 57.002 57.895 0.00 0.00 41.60 4.18
2532 2560 2.300152 TCGAAGAATCAGCCAGTTCAGT 59.700 45.455 0.00 0.00 0.00 3.41
2584 2612 3.524648 TTGGTCGTCGTCCTTGGCC 62.525 63.158 9.90 0.00 0.00 5.36
2642 2670 6.254804 AGCCAACTCAAAAATAAAACGTCAAC 59.745 34.615 0.00 0.00 0.00 3.18
2671 2705 2.665519 CGACCAGAATTGCAAGAAACGG 60.666 50.000 4.94 4.26 0.00 4.44
2911 2948 3.068732 CAGAGGATTAGCAGTCGGATTGA 59.931 47.826 4.52 0.00 0.00 2.57
2966 3054 1.795286 GCGACAAAGAGTGAAGTCAGG 59.205 52.381 0.00 0.00 0.00 3.86
2968 3056 1.202371 ACGCGACAAAGAGTGAAGTCA 60.202 47.619 15.93 0.00 0.00 3.41
2991 3079 0.605589 ACTTCGTCTTCAGGAGCAGG 59.394 55.000 0.00 0.00 0.00 4.85
3017 3105 1.883084 GTGTATGGCCTCCTTCGCG 60.883 63.158 3.32 0.00 0.00 5.87
3038 3126 1.992519 GCTCCATCATGACCCCTGCT 61.993 60.000 0.00 0.00 0.00 4.24
3109 3197 2.364324 ACCTGAACGTTACTCTGAAGCA 59.636 45.455 0.00 0.00 0.00 3.91
3125 3213 3.687125 AGTATCGAGTCAACTGACCTGA 58.313 45.455 6.23 5.34 45.85 3.86
3140 3228 7.178712 AGACTCTTCAAACAAACAAGTATCG 57.821 36.000 0.00 0.00 0.00 2.92
3234 3324 2.235016 CCCCACTGATTCGACCAAAAA 58.765 47.619 0.00 0.00 0.00 1.94
3372 3464 1.968493 GGACACAGACCACTTGACCTA 59.032 52.381 0.00 0.00 0.00 3.08
3378 3470 0.389391 CGACAGGACACAGACCACTT 59.611 55.000 0.00 0.00 0.00 3.16
3676 3772 1.381327 CGCCCTCCCTGACCTTCTA 60.381 63.158 0.00 0.00 0.00 2.10
3781 3877 4.082354 CCAAAGCTCTTTCCAATTCTCCTG 60.082 45.833 0.00 0.00 0.00 3.86
3929 4025 1.610522 GTCAGCTTGTTGGCATCAGTT 59.389 47.619 0.00 0.00 34.17 3.16
3977 4073 0.253044 CTTCCATCTCCTCGCCCAAA 59.747 55.000 0.00 0.00 0.00 3.28
4356 4453 3.364565 GCCATAAGAGACTCGAGATCGTC 60.365 52.174 21.68 6.96 40.80 4.20
4395 4492 1.679305 ACTCCTGCACTCGATCGGT 60.679 57.895 16.41 9.34 0.00 4.69
4454 4551 0.526662 AGTGAACGCGGACTAAGGAG 59.473 55.000 12.47 0.00 0.00 3.69
4486 4583 0.039165 GGCGGCCAGTTTTTCTTCTG 60.039 55.000 15.62 0.00 0.00 3.02
4496 4593 3.628646 GACTTGGATGGCGGCCAGT 62.629 63.158 27.62 18.64 36.75 4.00
4586 4683 1.866015 ACTCATCCAGGTCGATTCCA 58.134 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.