Multiple sequence alignment - TraesCS1B01G419200

Loading Multiple Alignment...

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 TraesCS1B01G419200 chr1B 100.000 4370 0 0 1 4370 642702379 642698010 0.000000e+00 8070.0
1 TraesCS1B01G419200 chr1B 83.766 462 46 18 3447 3880 621606171 621605711 1.130000e-110 411.0
2 TraesCS1B01G419200 chr1D 97.405 4393 77 9 3 4370 465904051 465899671 0.000000e+00 7446.0
3 TraesCS1B01G419200 chr3D 89.780 4315 297 51 159 4370 121342753 121338480 0.000000e+00 5393.0
4 TraesCS1B01G419200 chr3D 92.916 2555 162 8 836 3390 120142429 120144964 0.000000e+00 3698.0
5 TraesCS1B01G419200 chr3D 89.726 146 13 1 10 155 613710011 613710154 7.460000e-43 185.0
6 TraesCS1B01G419200 chr3A 89.434 4221 302 64 165 4272 127859699 127855510 0.000000e+00 5192.0
7 TraesCS1B01G419200 chr3A 79.873 472 42 19 3462 3880 735448339 735448810 3.300000e-76 296.0
8 TraesCS1B01G419200 chr3B 90.768 3607 234 38 155 3679 173008619 173005030 0.000000e+00 4724.0
9 TraesCS1B01G419200 chr3B 93.697 2602 147 10 836 3431 172170449 172173039 0.000000e+00 3880.0
10 TraesCS1B01G419200 chr3B 93.537 2584 151 10 854 3431 172052107 172054680 0.000000e+00 3832.0
11 TraesCS1B01G419200 chr3B 93.094 2534 159 9 901 3430 146982458 146979937 0.000000e+00 3696.0
12 TraesCS1B01G419200 chr3B 89.140 709 41 7 3693 4370 173004933 173004230 0.000000e+00 850.0
13 TraesCS1B01G419200 chr3B 83.621 464 45 20 3447 3880 18022507 18022045 1.460000e-109 407.0
14 TraesCS1B01G419200 chr3B 87.085 271 22 6 4096 4356 172055687 172055954 1.190000e-75 294.0
15 TraesCS1B01G419200 chr6D 91.704 2688 178 21 836 3496 452128075 452125406 0.000000e+00 3687.0
16 TraesCS1B01G419200 chr5B 91.112 2644 190 24 887 3524 507803038 507800434 0.000000e+00 3539.0
17 TraesCS1B01G419200 chr5B 89.116 147 13 2 10 155 601445540 601445684 3.470000e-41 180.0
18 TraesCS1B01G419200 chrUn 84.632 462 42 18 3447 3880 219069292 219068832 2.410000e-117 433.0
19 TraesCS1B01G419200 chr7B 84.416 462 43 18 3447 3880 733237148 733236688 1.120000e-115 427.0
20 TraesCS1B01G419200 chr2D 86.667 165 18 4 3 165 459840427 459840265 3.470000e-41 180.0
21 TraesCS1B01G419200 chr6B 87.821 156 14 4 3 155 297533817 297533664 1.250000e-40 178.0
22 TraesCS1B01G419200 chr6B 94.231 52 3 0 3987 4038 490499900 490499951 3.620000e-11 80.5
23 TraesCS1B01G419200 chr2B 87.821 156 14 4 3 155 551247820 551247973 1.250000e-40 178.0
24 TraesCS1B01G419200 chr1A 87.821 156 14 4 3 155 474249082 474249235 1.250000e-40 178.0
25 TraesCS1B01G419200 chr6A 88.435 147 14 2 10 155 605355443 605355587 1.620000e-39 174.0
26 TraesCS1B01G419200 chr2A 86.076 158 14 6 3 156 763348614 763348461 3.500000e-36 163.0


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 TraesCS1B01G419200 chr1B 642698010 642702379 4369 True 8070 8070 100.000 1 4370 1 chr1B.!!$R2 4369
1 TraesCS1B01G419200 chr1D 465899671 465904051 4380 True 7446 7446 97.405 3 4370 1 chr1D.!!$R1 4367
2 TraesCS1B01G419200 chr3D 121338480 121342753 4273 True 5393 5393 89.780 159 4370 1 chr3D.!!$R1 4211
3 TraesCS1B01G419200 chr3D 120142429 120144964 2535 False 3698 3698 92.916 836 3390 1 chr3D.!!$F1 2554
4 TraesCS1B01G419200 chr3A 127855510 127859699 4189 True 5192 5192 89.434 165 4272 1 chr3A.!!$R1 4107
5 TraesCS1B01G419200 chr3B 172170449 172173039 2590 False 3880 3880 93.697 836 3431 1 chr3B.!!$F1 2595
6 TraesCS1B01G419200 chr3B 146979937 146982458 2521 True 3696 3696 93.094 901 3430 1 chr3B.!!$R2 2529
7 TraesCS1B01G419200 chr3B 173004230 173008619 4389 True 2787 4724 89.954 155 4370 2 chr3B.!!$R3 4215
8 TraesCS1B01G419200 chr3B 172052107 172055954 3847 False 2063 3832 90.311 854 4356 2 chr3B.!!$F2 3502
9 TraesCS1B01G419200 chr6D 452125406 452128075 2669 True 3687 3687 91.704 836 3496 1 chr6D.!!$R1 2660
10 TraesCS1B01G419200 chr5B 507800434 507803038 2604 True 3539 3539 91.112 887 3524 1 chr5B.!!$R1 2637

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
816 878 0.736325 CCACGGGCAAAGAGTACGAG 60.736 60.0 0.0 0.0 0.0 4.18 F
1004 1089 0.108615 CGAGAGTTGAAGGCGATGGT 60.109 55.0 0.0 0.0 0.0 3.55 F
2697 2786 0.732880 CGTGCGTCCTGTTCTTCGAT 60.733 55.0 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 2873 0.179100 CGTTCATGCCGTCCATCTCT 60.179 55.000 0.0 0.0 29.71 3.10 R
3115 3204 4.838152 CCCGCCGTCCACATCCAG 62.838 72.222 0.0 0.0 0.00 3.86 R
4269 4939 2.630098 TCAAATTGCCACCGATTTCCAA 59.370 40.909 0.0 0.0 33.69 3.53 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
92 93 7.816995 AGATCTGTGTCTGAGTTTTTCTATCAC 59.183 37.037 0.00 0.00 0.00 3.06
96 97 5.179555 GTGTCTGAGTTTTTCTATCACCACC 59.820 44.000 0.00 0.00 0.00 4.61
117 118 6.404734 CCACCCTTAAAATACTTAGCTTGCTG 60.405 42.308 5.26 0.00 0.00 4.41
118 119 6.151144 CACCCTTAAAATACTTAGCTTGCTGT 59.849 38.462 5.26 0.00 0.00 4.40
130 131 4.927782 TGCTGTCGGCCTTTGCGT 62.928 61.111 0.00 0.00 40.92 5.24
381 408 1.827789 CTCCTCTCGAGCTCCCTGG 60.828 68.421 7.81 5.78 0.00 4.45
706 757 2.404789 CGCCATTGTTAGCGCAGG 59.595 61.111 11.47 0.19 46.50 4.85
816 878 0.736325 CCACGGGCAAAGAGTACGAG 60.736 60.000 0.00 0.00 0.00 4.18
1004 1089 0.108615 CGAGAGTTGAAGGCGATGGT 60.109 55.000 0.00 0.00 0.00 3.55
1299 1387 2.660552 CACGACGCCAAGTTCGGT 60.661 61.111 0.00 0.00 0.00 4.69
1638 1726 2.259818 CTCGTCGAGCTGCCACTT 59.740 61.111 9.74 0.00 0.00 3.16
1855 1943 0.891373 CGAGGAGGCTGAGAAGAACA 59.109 55.000 0.00 0.00 0.00 3.18
2601 2690 1.831286 CATCAGCATCAAGGGGCCC 60.831 63.158 17.12 17.12 0.00 5.80
2697 2786 0.732880 CGTGCGTCCTGTTCTTCGAT 60.733 55.000 0.00 0.00 0.00 3.59
2784 2873 1.070758 GTCCTGAACCAGCTTCTCACA 59.929 52.381 0.00 0.00 0.00 3.58
2946 3035 1.004044 CACCAGATCTTCAAGGCCTGT 59.996 52.381 5.69 0.00 0.00 4.00
3115 3204 2.093235 CAGAGGATGGAGAAAGACACCC 60.093 54.545 0.00 0.00 0.00 4.61
3331 3420 2.429058 CTGCTGCTGACACCACCT 59.571 61.111 0.00 0.00 0.00 4.00
3628 4159 0.843309 TCCCTCTGTTCCTGCACAAA 59.157 50.000 0.00 0.00 0.00 2.83
3982 4624 4.993584 CACAGACAAGAACAATCTGCTACT 59.006 41.667 0.47 0.00 43.04 2.57
3983 4625 5.468072 CACAGACAAGAACAATCTGCTACTT 59.532 40.000 0.47 0.00 43.04 2.24
3984 4626 6.646653 CACAGACAAGAACAATCTGCTACTTA 59.353 38.462 0.47 0.00 43.04 2.24
3985 4627 7.171508 CACAGACAAGAACAATCTGCTACTTAA 59.828 37.037 0.47 0.00 43.04 1.85
4047 4689 3.251729 CAGAGTGTTGTTCTTGATGGTGG 59.748 47.826 0.00 0.00 0.00 4.61
4278 4948 2.097466 CCGAGGGACAAATTGGAAATCG 59.903 50.000 0.00 2.31 0.00 3.34
4349 5021 5.391312 AAAAATACATGGCAGACAAGACC 57.609 39.130 0.00 0.00 0.00 3.85
4350 5022 2.717639 ATACATGGCAGACAAGACCC 57.282 50.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.862371 GATAGAAAAACTCAGACACAGATCTAA 57.138 33.333 0.00 0.00 0.00 2.10
65 66 9.025041 TGATAGAAAAACTCAGACACAGATCTA 57.975 33.333 0.00 0.00 0.00 1.98
92 93 5.652452 AGCAAGCTAAGTATTTTAAGGGTGG 59.348 40.000 0.00 0.00 0.00 4.61
96 97 6.456988 CCGACAGCAAGCTAAGTATTTTAAGG 60.457 42.308 0.00 0.00 0.00 2.69
109 110 2.113986 AAAGGCCGACAGCAAGCT 59.886 55.556 0.00 0.00 46.50 3.74
117 118 1.154225 CAATGACGCAAAGGCCGAC 60.154 57.895 0.00 0.00 36.38 4.79
118 119 2.331893 CCAATGACGCAAAGGCCGA 61.332 57.895 0.00 0.00 36.38 5.54
130 131 0.673333 ATGACTCGTTGCGCCAATGA 60.673 50.000 4.18 9.46 37.09 2.57
139 140 5.048153 TCTTCACACTAGATGACTCGTTG 57.952 43.478 0.00 0.00 0.00 4.10
140 141 5.707242 TTCTTCACACTAGATGACTCGTT 57.293 39.130 0.00 0.00 0.00 3.85
141 142 5.707242 TTTCTTCACACTAGATGACTCGT 57.293 39.130 0.00 0.00 0.00 4.18
142 143 7.462069 CGATTTTTCTTCACACTAGATGACTCG 60.462 40.741 0.00 0.00 0.00 4.18
143 144 7.542477 TCGATTTTTCTTCACACTAGATGACTC 59.458 37.037 0.00 0.00 0.00 3.36
218 220 0.033796 CCTGATGAGCAATGGGTGGT 60.034 55.000 0.00 0.00 41.89 4.16
409 436 1.729838 GAAGTGCGCGAGAAGACGT 60.730 57.895 12.10 0.00 35.59 4.34
706 757 2.017049 ACTCGGAATATTTGCACCTGC 58.983 47.619 0.00 0.00 42.50 4.85
879 954 3.391382 GAGGTGGAGACGTGGGGG 61.391 72.222 0.00 0.00 0.00 5.40
1299 1387 1.809619 GAGGATGTGCACGCGCTTA 60.810 57.895 13.13 0.00 39.64 3.09
1363 1451 2.468915 GAAGTAGGGCTTGAGGTAGGT 58.531 52.381 0.00 0.00 37.59 3.08
1638 1726 1.413118 TGAAGATCTGCGGATGCCTA 58.587 50.000 14.17 0.00 41.78 3.93
1855 1943 2.230025 CGATGAAGATGATAGAGGGCGT 59.770 50.000 0.00 0.00 0.00 5.68
2043 2131 3.056107 TCTCACGATCAAACCTTCCGAAT 60.056 43.478 0.00 0.00 0.00 3.34
2601 2690 2.759783 CCACATGGTGAGAAGCTCG 58.240 57.895 0.00 0.00 35.23 5.03
2784 2873 0.179100 CGTTCATGCCGTCCATCTCT 60.179 55.000 0.00 0.00 29.71 3.10
3115 3204 4.838152 CCCGCCGTCCACATCCAG 62.838 72.222 0.00 0.00 0.00 3.86
3331 3420 1.044790 TCATCCTCATCAGCTGCCGA 61.045 55.000 9.47 6.79 0.00 5.54
3417 3886 6.827586 AGAGGAAACACAACAAAAACAGTA 57.172 33.333 0.00 0.00 0.00 2.74
3430 3900 4.983671 AAAGTGGACAAAGAGGAAACAC 57.016 40.909 0.00 0.00 0.00 3.32
3817 4443 8.638565 GCATTGACTGAAATTACAACAATACAC 58.361 33.333 0.00 0.00 31.45 2.90
3982 4624 8.038351 TGATTGTCTTCGACACCATCTAATTAA 58.962 33.333 8.46 0.00 42.60 1.40
3983 4625 7.552459 TGATTGTCTTCGACACCATCTAATTA 58.448 34.615 8.46 0.00 42.60 1.40
3984 4626 6.406370 TGATTGTCTTCGACACCATCTAATT 58.594 36.000 8.46 0.00 42.60 1.40
3985 4627 5.977635 TGATTGTCTTCGACACCATCTAAT 58.022 37.500 8.46 0.00 42.60 1.73
4269 4939 2.630098 TCAAATTGCCACCGATTTCCAA 59.370 40.909 0.00 0.00 33.69 3.53
4278 4948 6.557291 TTTCATTCATTTCAAATTGCCACC 57.443 33.333 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.