Multiple sequence alignment - TraesCS6B01G246200

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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 TraesCS6B01G246200 chr6B 100.000 4772 0 0 1 4772 438917401 438912630 0.000000e+00 8813.0
1 TraesCS6B01G246200 chr6A 93.994 4695 153 41 64 4689 398637533 398642167 0.000000e+00 6988.0
2 TraesCS6B01G246200 chr6A 93.333 60 4 0 4713 4772 398974442 398974501 6.580000e-14 89.8
3 TraesCS6B01G246200 chr6D 94.190 2599 77 21 25 2583 277023781 277021217 0.000000e+00 3895.0
4 TraesCS6B01G246200 chr6D 94.991 2196 84 9 2586 4772 277021131 277018953 0.000000e+00 3422.0
5 TraesCS6B01G246200 chr3B 81.921 177 24 8 2212 2385 413032621 413032450 4.980000e-30 143.0
6 TraesCS6B01G246200 chr5B 76.639 244 33 13 2161 2389 281627779 281627545 3.900000e-21 113.0
7 TraesCS6B01G246200 chr5B 86.667 75 6 4 3124 3195 11043577 11043504 3.960000e-11 80.5
8 TraesCS6B01G246200 chr7D 86.000 100 12 2 2212 2310 598431028 598431126 6.530000e-19 106.0


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 TraesCS6B01G246200 chr6B 438912630 438917401 4771 True 8813.0 8813 100.0000 1 4772 1 chr6B.!!$R1 4771
1 TraesCS6B01G246200 chr6A 398637533 398642167 4634 False 6988.0 6988 93.9940 64 4689 1 chr6A.!!$F1 4625
2 TraesCS6B01G246200 chr6D 277018953 277023781 4828 True 3658.5 3895 94.5905 25 4772 2 chr6D.!!$R1 4747

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
547 572 0.104120 CCATCCATCTGGTTCGCGTA 59.896 55.000 5.77 0.00 36.34 4.42 F
725 751 1.202200 TGCCTTTTCGAAACAACGTGG 60.202 47.619 10.79 7.35 34.70 4.94 F
1123 1172 1.531149 CTGTTGTAAGCGTGTTCCTGG 59.469 52.381 0.00 0.00 0.00 4.45 F
2450 2513 0.250727 TACACCCCTTGCAGCACTTC 60.251 55.000 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2407 0.610509 TAAGGCGCCCATGCTTTTCA 60.611 50.000 26.15 0.0 35.6 2.69 R
2434 2497 1.529244 GTGAAGTGCTGCAAGGGGT 60.529 57.895 2.77 0.0 0.0 4.95 R
3078 3226 4.329545 GGCTGCCGGTTCACTCCA 62.330 66.667 1.35 0.0 0.0 3.86 R
4033 4183 0.029300 CAAACCCGCACAGTTCACAG 59.971 55.000 0.00 0.0 0.0 3.66 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
32 33 2.210711 CCCCAGGGCTCTATCCGTC 61.211 68.421 0.00 0.00 0.00 4.79
247 250 1.264288 GAACACGGACAAGCCAAGAAG 59.736 52.381 0.00 0.00 35.94 2.85
315 318 2.752238 CCTCTCGCGTCCTGACCT 60.752 66.667 5.77 0.00 0.00 3.85
442 467 6.129179 CCATAGGGTTTTGATTGAGGTATGT 58.871 40.000 0.00 0.00 0.00 2.29
516 541 2.270850 GGGCGCACCACCATCTAA 59.729 61.111 10.83 0.00 39.85 2.10
546 571 1.153369 CCATCCATCTGGTTCGCGT 60.153 57.895 5.77 0.00 36.34 6.01
547 572 0.104120 CCATCCATCTGGTTCGCGTA 59.896 55.000 5.77 0.00 36.34 4.42
548 573 1.270305 CCATCCATCTGGTTCGCGTAT 60.270 52.381 5.77 0.00 36.34 3.06
658 683 2.093625 TCTGAACACGCGTTGCATATTC 59.906 45.455 10.22 7.55 34.75 1.75
725 751 1.202200 TGCCTTTTCGAAACAACGTGG 60.202 47.619 10.79 7.35 34.70 4.94
756 793 5.009631 TGTAAGCTGCAATTTCTACACCAT 58.990 37.500 1.02 0.00 0.00 3.55
842 879 5.525199 ACAATGTGGTCCGATGTTAAAAAC 58.475 37.500 0.00 0.00 0.00 2.43
888 926 5.283060 AGTTTCTTTACAGCACAATAGCG 57.717 39.130 0.00 0.00 40.15 4.26
1101 1139 8.122952 CGAAACTAATTCATGGTATGGAAGTTC 58.877 37.037 0.00 0.00 37.96 3.01
1123 1172 1.531149 CTGTTGTAAGCGTGTTCCTGG 59.469 52.381 0.00 0.00 0.00 4.45
1139 1188 2.401699 CTGGTGTGCAGGCAAGAGGA 62.402 60.000 0.00 0.00 0.00 3.71
1530 1579 4.601019 CGGACCTTTTCAATATGTGCATC 58.399 43.478 0.00 0.00 0.00 3.91
2075 2124 9.267084 TCCTTTTACCACAAAAGAAATATTTGC 57.733 29.630 5.17 0.00 40.58 3.68
2208 2259 4.760683 CGCACACATTTCAAAAATCAACC 58.239 39.130 0.00 0.00 0.00 3.77
2284 2347 9.695526 TCATATTCAAAAGAACTTTCAATGGTG 57.304 29.630 0.21 6.56 31.45 4.17
2449 2512 0.405585 ATACACCCCTTGCAGCACTT 59.594 50.000 0.00 0.00 0.00 3.16
2450 2513 0.250727 TACACCCCTTGCAGCACTTC 60.251 55.000 0.00 0.00 0.00 3.01
2683 2829 9.665264 GTCCTGTTTCAGTTTATTTACTTTGAG 57.335 33.333 0.00 0.00 0.00 3.02
2733 2880 7.010697 TGCATACTCGTATTAAACAATGGTG 57.989 36.000 0.00 0.00 0.00 4.17
2898 3046 8.666129 TTCTTCTCCTCTACTTATTCTTTGGA 57.334 34.615 0.00 0.00 0.00 3.53
3078 3226 2.848694 ACCTTGATCTGTGTCATCCCAT 59.151 45.455 0.00 0.00 0.00 4.00
3204 3354 6.613153 AACTAGCTAAGGGATTATAGGCTG 57.387 41.667 0.00 0.00 0.00 4.85
3246 3396 5.191426 TGCTTAGTCGTCTAGTATGTTCCT 58.809 41.667 0.00 0.00 0.00 3.36
3259 3409 9.537852 TCTAGTATGTTCCTGTTCCTTAGTTTA 57.462 33.333 0.00 0.00 0.00 2.01
3263 3413 6.999705 TGTTCCTGTTCCTTAGTTTACCTA 57.000 37.500 0.00 0.00 0.00 3.08
3331 3481 1.466856 TGTCATTTGCTCATGCTCCC 58.533 50.000 0.00 0.00 40.48 4.30
3535 3685 1.135046 CTCGCACATTCATAGGCTCG 58.865 55.000 0.00 0.00 0.00 5.03
3735 3885 3.119531 AGTTTCAGCTGAGAGACGAGATG 60.120 47.826 17.43 0.00 0.00 2.90
3824 3974 2.670934 CCACTGCTGTCACTGCCC 60.671 66.667 3.95 0.00 0.00 5.36
3863 4013 1.813786 AGGAGCAGTCGACTGTAGAAC 59.186 52.381 38.11 24.79 45.45 3.01
3869 4019 4.154556 AGCAGTCGACTGTAGAACTAGAAC 59.845 45.833 38.11 21.18 45.45 3.01
3921 4071 4.000325 TGTTGTGATGGATGAACCTAACG 59.000 43.478 0.00 0.00 39.86 3.18
4025 4175 4.506654 GTGTAAATGGTCGCATAAGATCGT 59.493 41.667 0.00 0.00 0.00 3.73
4033 4183 4.220572 GTCGCATAAGATCGTTCCTCTAC 58.779 47.826 0.00 0.00 0.00 2.59
4134 4289 7.356089 TCATATACACGGTTTTATGGAGAGT 57.644 36.000 0.00 0.00 0.00 3.24
4348 4504 5.426833 AGCATCTCTAACCTTGTCCTACAAT 59.573 40.000 0.00 0.00 37.48 2.71
4354 4510 6.472887 TCTAACCTTGTCCTACAATTCCTTG 58.527 40.000 0.00 0.00 37.48 3.61
4357 4514 5.892348 ACCTTGTCCTACAATTCCTTGAAT 58.108 37.500 0.00 0.00 37.48 2.57
4360 4517 7.290014 ACCTTGTCCTACAATTCCTTGAATTTT 59.710 33.333 0.00 0.00 39.82 1.82
4372 4529 6.840780 TCCTTGAATTTTCTCCCAAATCTC 57.159 37.500 0.00 0.00 0.00 2.75
4490 4648 6.991485 ACTTCAGCACAAATATTTCAAACG 57.009 33.333 0.00 0.00 0.00 3.60
4552 4710 7.657336 TCCAACAATTCAGCTAAAAACCTAAG 58.343 34.615 0.00 0.00 0.00 2.18
4566 4724 2.119495 ACCTAAGCATAGTCCACCCAG 58.881 52.381 0.00 0.00 0.00 4.45
4620 4779 3.153130 TCATCGAAAAGCCACCAAATCA 58.847 40.909 0.00 0.00 0.00 2.57
4623 4782 4.392921 TCGAAAAGCCACCAAATCAAAA 57.607 36.364 0.00 0.00 0.00 2.44
4671 4830 4.142093 GGCACATACTTCATCAAAAGCCAT 60.142 41.667 0.00 0.00 38.27 4.40
4676 4835 4.627611 ACTTCATCAAAAGCCATCATCG 57.372 40.909 0.00 0.00 0.00 3.84
4710 4869 3.099141 TCATGCACTCTCATGGTCACTA 58.901 45.455 0.00 0.00 42.96 2.74
4711 4870 3.118992 TCATGCACTCTCATGGTCACTAC 60.119 47.826 0.00 0.00 42.96 2.73
4712 4871 1.550524 TGCACTCTCATGGTCACTACC 59.449 52.381 0.00 0.00 46.98 3.18
4759 4919 3.457234 CCGATCCTCGATTTTGTCATGA 58.543 45.455 0.00 0.00 43.74 3.07
4769 4929 5.756833 TCGATTTTGTCATGATCTCTCCATG 59.243 40.000 0.00 0.00 41.93 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.623834 GGATAGAGCCCTGGGGATAGG 60.624 61.905 16.03 0.00 37.50 2.57
10 11 1.872773 GGATAGAGCCCTGGGGATAG 58.127 60.000 16.03 0.00 37.50 2.08
11 12 0.041238 CGGATAGAGCCCTGGGGATA 59.959 60.000 16.03 0.00 37.50 2.59
12 13 1.229336 CGGATAGAGCCCTGGGGAT 60.229 63.158 16.03 2.12 37.50 3.85
13 14 2.201490 CGGATAGAGCCCTGGGGA 59.799 66.667 16.03 0.00 37.50 4.81
14 15 2.122813 ACGGATAGAGCCCTGGGG 60.123 66.667 16.03 4.75 38.57 4.96
15 16 1.152440 AGACGGATAGAGCCCTGGG 60.152 63.158 8.86 8.86 0.00 4.45
16 17 1.519751 CGAGACGGATAGAGCCCTGG 61.520 65.000 0.00 0.00 0.00 4.45
17 18 1.953017 CGAGACGGATAGAGCCCTG 59.047 63.158 0.00 0.00 0.00 4.45
18 19 4.484987 CGAGACGGATAGAGCCCT 57.515 61.111 0.00 0.00 0.00 5.19
39 40 1.864082 GTTTTCATTTGTTGTGGCCCG 59.136 47.619 0.00 0.00 0.00 6.13
137 140 2.670148 CGGTGGGAAGGAAGAGGGG 61.670 68.421 0.00 0.00 0.00 4.79
247 250 0.670854 GAGACGCTGGGGAGTTGTTC 60.671 60.000 0.00 0.00 0.00 3.18
315 318 5.222171 GGAGGTAGGAGAGATTTAGAGCCTA 60.222 48.000 0.00 0.00 0.00 3.93
516 541 1.355718 ATGGATGGACAGGGCGGATT 61.356 55.000 0.00 0.00 0.00 3.01
546 571 6.628398 GCCCGAGAAGAAGAAGAAGAAGAATA 60.628 42.308 0.00 0.00 0.00 1.75
547 572 5.729510 CCCGAGAAGAAGAAGAAGAAGAAT 58.270 41.667 0.00 0.00 0.00 2.40
548 573 4.561734 GCCCGAGAAGAAGAAGAAGAAGAA 60.562 45.833 0.00 0.00 0.00 2.52
725 751 4.691860 AATTGCAGCTTACACATCAGAC 57.308 40.909 0.00 0.00 0.00 3.51
888 926 3.608474 GCAATACACAACGAGTTCCCAAC 60.608 47.826 0.00 0.00 0.00 3.77
947 985 4.398044 TCGAAAGCCTGGATGGAATTAAAC 59.602 41.667 0.00 0.00 38.35 2.01
953 991 0.253044 CCTCGAAAGCCTGGATGGAA 59.747 55.000 0.00 0.00 38.35 3.53
1101 1139 0.872388 GGAACACGCTTACAACAGGG 59.128 55.000 0.00 0.00 0.00 4.45
1123 1172 1.072159 AGTCCTCTTGCCTGCACAC 59.928 57.895 0.00 0.00 0.00 3.82
1139 1188 2.434884 CGCGTTCAGCCCATCAGT 60.435 61.111 0.00 0.00 44.76 3.41
1530 1579 6.986231 TGCACAGACATGATATAACCAGTTAG 59.014 38.462 0.00 0.00 0.00 2.34
2075 2124 4.054780 AGCTTGCAGCAATCAATAATGG 57.945 40.909 8.67 0.00 45.56 3.16
2182 2231 2.132740 TTTTGAAATGTGTGCGCCTC 57.867 45.000 4.18 0.00 0.00 4.70
2327 2390 5.584251 GCTTTTCAAAATCCAACTTTGACCA 59.416 36.000 0.00 0.00 41.32 4.02
2344 2407 0.610509 TAAGGCGCCCATGCTTTTCA 60.611 50.000 26.15 0.00 35.60 2.69
2434 2497 1.529244 GTGAAGTGCTGCAAGGGGT 60.529 57.895 2.77 0.00 0.00 4.95
2449 2512 9.419297 CACAAGTTTAACTATAGCTAGTTGTGA 57.581 33.333 23.59 1.39 45.61 3.58
2450 2513 8.656849 CCACAAGTTTAACTATAGCTAGTTGTG 58.343 37.037 22.38 22.38 45.61 3.33
2683 2829 6.811253 TCCATATAATCATTGCGGGTAAAC 57.189 37.500 0.00 0.00 0.00 2.01
3078 3226 4.329545 GGCTGCCGGTTCACTCCA 62.330 66.667 1.35 0.00 0.00 3.86
3204 3354 5.376854 AGCAATGACTGTTGGTTTATGTC 57.623 39.130 0.00 0.00 36.49 3.06
3246 3396 9.317827 AGAACATACTAGGTAAACTAAGGAACA 57.682 33.333 0.00 0.00 0.00 3.18
3259 3409 5.937111 ACCAACAACAAGAACATACTAGGT 58.063 37.500 0.00 0.00 0.00 3.08
3263 3413 7.554835 TGTAAAGACCAACAACAAGAACATACT 59.445 33.333 0.00 0.00 0.00 2.12
3279 3429 9.494271 GATATCTTCATTAGCATGTAAAGACCA 57.506 33.333 0.00 0.00 0.00 4.02
3535 3685 3.976942 TGACACGTTAAACGAACTAGAGC 59.023 43.478 0.00 0.00 46.05 4.09
3576 3726 8.134905 AGAAAACTGAAACAAAATTGCAGATC 57.865 30.769 1.56 0.00 0.00 2.75
3735 3885 3.495806 CCAGGCTCCATGGATAAAGACTC 60.496 52.174 16.63 0.00 40.51 3.36
3921 4071 3.370061 GCAACACTGAAACCCGATAGTAC 59.630 47.826 0.00 0.00 0.00 2.73
4025 4175 2.288213 CGCACAGTTCACAGTAGAGGAA 60.288 50.000 0.00 0.00 0.00 3.36
4033 4183 0.029300 CAAACCCGCACAGTTCACAG 59.971 55.000 0.00 0.00 0.00 3.66
4134 4289 8.485578 AACCAAAGTTCTATTCCAAAACCATA 57.514 30.769 0.00 0.00 0.00 2.74
4348 4504 6.782000 TGAGATTTGGGAGAAAATTCAAGGAA 59.218 34.615 0.00 0.00 29.89 3.36
4354 4510 7.890515 AGAAGTTGAGATTTGGGAGAAAATTC 58.109 34.615 0.00 0.00 29.89 2.17
4357 4514 8.760980 TTTAGAAGTTGAGATTTGGGAGAAAA 57.239 30.769 0.00 0.00 0.00 2.29
4387 4544 1.448985 CGCCCAGCTTTTAACTGCTA 58.551 50.000 1.63 0.00 37.81 3.49
4432 4590 5.392165 CCGTCGCAAAATTGTTATTAGGGAA 60.392 40.000 0.00 0.00 0.00 3.97
4490 4648 7.769719 CAATTGCTTAAATTGTTGTGCAATC 57.230 32.000 10.68 0.00 46.81 2.67
4508 4666 1.391144 GAAGCGGTGCATTTCAATTGC 59.609 47.619 0.00 0.00 0.00 3.56
4552 4710 0.618458 TTGGACTGGGTGGACTATGC 59.382 55.000 0.00 0.00 0.00 3.14
4597 4756 4.220382 TGATTTGGTGGCTTTTCGATGAAT 59.780 37.500 0.00 0.00 0.00 2.57
4623 4782 4.223923 TGTGGTGGTTTTTGGATGAACTTT 59.776 37.500 0.00 0.00 0.00 2.66
4671 4830 3.694043 TGATTTGGTGGAGTTCGATGA 57.306 42.857 0.00 0.00 0.00 2.92
4676 4835 2.821969 AGTGCATGATTTGGTGGAGTTC 59.178 45.455 0.00 0.00 0.00 3.01
4710 4869 4.183858 CGTGGTGGTGGTGGTGGT 62.184 66.667 0.00 0.00 0.00 4.16
4711 4870 3.825160 CTCGTGGTGGTGGTGGTGG 62.825 68.421 0.00 0.00 0.00 4.61
4712 4871 2.280797 CTCGTGGTGGTGGTGGTG 60.281 66.667 0.00 0.00 0.00 4.17
4713 4872 4.250305 GCTCGTGGTGGTGGTGGT 62.250 66.667 0.00 0.00 0.00 4.16
4714 4873 4.248842 TGCTCGTGGTGGTGGTGG 62.249 66.667 0.00 0.00 0.00 4.61
4715 4874 2.972505 GTGCTCGTGGTGGTGGTG 60.973 66.667 0.00 0.00 0.00 4.17
4742 4902 5.452496 GGAGAGATCATGACAAAATCGAGGA 60.452 44.000 0.00 0.00 0.00 3.71
4745 4905 5.343307 TGGAGAGATCATGACAAAATCGA 57.657 39.130 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.