Multiple sequence alignment - TraesCS2D01G375000

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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 TraesCS2D01G375000 chr2D 100.000 5692 0 0 1 5692 478708796 478703105 0.00 10512.0
1 TraesCS2D01G375000 chr2B 95.298 3190 99 15 1 3171 561224067 561227224 0.00 5012.0
2 TraesCS2D01G375000 chr2B 92.451 2477 98 35 3267 5692 561227241 561229679 0.00 3456.0
3 TraesCS2D01G375000 chr2B 100.000 28 0 0 3175 3202 561227217 561227244 0.01 52.8
4 TraesCS2D01G375000 chr2A 93.634 3330 119 40 1 3275 621476574 621479865 0.00 4889.0
5 TraesCS2D01G375000 chr2A 93.242 1746 69 11 3272 4974 621479987 621481726 0.00 2525.0
6 TraesCS2D01G375000 chr2A 95.168 683 30 3 5013 5692 621481726 621482408 0.00 1075.0


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 TraesCS2D01G375000 chr2D 478703105 478708796 5691 True 10512.000000 10512 100.000000 1 5692 1 chr2D.!!$R1 5691
1 TraesCS2D01G375000 chr2B 561224067 561229679 5612 False 2840.266667 5012 95.916333 1 5692 3 chr2B.!!$F1 5691
2 TraesCS2D01G375000 chr2A 621476574 621482408 5834 False 2829.666667 4889 94.014667 1 5692 3 chr2A.!!$F1 5691

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
866 900 0.032615 AAAACTTGCCCAGGGTGTGA 60.033 50.0 7.55 0.0 0.00 3.58 F
867 901 0.032615 AAACTTGCCCAGGGTGTGAA 60.033 50.0 7.55 0.0 0.00 3.18 F
1574 1612 0.108138 CCAAGACGGTGAGGGATGTC 60.108 60.0 0.00 0.0 0.00 3.06 F
2232 2275 1.731720 ACTCGCCTGAGCTTTTGATC 58.268 50.0 0.00 0.0 46.69 2.92 F
3445 3635 1.071314 AATGGGGTGGAGTGGGTTGA 61.071 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2259 0.371645 GTCGATCAAAAGCTCAGGCG 59.628 55.000 0.00 0.0 44.37 5.52 R
2232 2275 2.688507 ACAGCACAGAACTATTGGTCG 58.311 47.619 0.00 0.0 0.00 4.79 R
3421 3611 1.324740 CCACTCCACCCCATTGCATG 61.325 60.000 0.00 0.0 0.00 4.06 R
4200 4441 1.132453 TCACGCGATTGAAGAGATCGT 59.868 47.619 15.93 0.0 45.99 3.73 R
5084 5326 0.109723 TAGTGACCGGCAAAAAGGCT 59.890 50.000 0.00 0.0 41.46 4.58 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
68 71 3.312736 TTTCTGGATAAGATTGGGGGC 57.687 47.619 0.00 0.00 33.93 5.80
176 183 0.478072 TGTGTTGATTGGTCAGGCCT 59.522 50.000 0.00 0.00 38.35 5.19
273 287 2.879233 GCTCGGGTCCTTGTCCACA 61.879 63.158 0.00 0.00 0.00 4.17
285 299 5.531287 GTCCTTGTCCACATGTTACTTTCTT 59.469 40.000 0.00 0.00 0.00 2.52
290 304 6.969366 TGTCCACATGTTACTTTCTTGATTG 58.031 36.000 0.00 0.00 0.00 2.67
387 418 3.067106 ACTGCCGACTCTGTTTAACATG 58.933 45.455 0.00 0.00 0.00 3.21
568 599 4.512944 GTCATGCAGTTGAGAAGAGTTTGA 59.487 41.667 0.00 0.00 0.00 2.69
619 650 3.531538 AGCGTCTTTGACAAGTGAAAGA 58.468 40.909 10.16 10.16 39.76 2.52
637 668 9.578439 AGTGAAAGAAAAATTCTGTTTCTGAAG 57.422 29.630 4.73 0.00 43.00 3.02
638 669 9.358872 GTGAAAGAAAAATTCTGTTTCTGAAGT 57.641 29.630 4.73 0.00 43.00 3.01
721 752 4.974399 AGGAAATTTCGAGTTCTTCCTGT 58.026 39.130 11.95 0.00 43.34 4.00
722 753 4.757149 AGGAAATTTCGAGTTCTTCCTGTG 59.243 41.667 11.95 0.00 43.34 3.66
732 763 6.153851 TCGAGTTCTTCCTGTGTATTGGATTA 59.846 38.462 0.00 0.00 31.76 1.75
866 900 0.032615 AAAACTTGCCCAGGGTGTGA 60.033 50.000 7.55 0.00 0.00 3.58
867 901 0.032615 AAACTTGCCCAGGGTGTGAA 60.033 50.000 7.55 0.00 0.00 3.18
1078 1112 4.821805 AGAATGTGGTTTCATTTCAGACGT 59.178 37.500 0.00 0.00 38.03 4.34
1323 1357 6.128138 AGGTAAGCTATTTCCACTTGTCTT 57.872 37.500 0.00 0.00 0.00 3.01
1574 1612 0.108138 CCAAGACGGTGAGGGATGTC 60.108 60.000 0.00 0.00 0.00 3.06
1656 1694 7.770801 ATTTGTTCTTGTTTTTCTGCTTACC 57.229 32.000 0.00 0.00 0.00 2.85
1976 2017 6.038997 AGTGGAAGGTACACTTATTCTCAC 57.961 41.667 0.00 0.00 46.38 3.51
2216 2259 6.743575 ACAACAGCTGAATTGGTAATACTC 57.256 37.500 23.35 0.00 0.00 2.59
2232 2275 1.731720 ACTCGCCTGAGCTTTTGATC 58.268 50.000 0.00 0.00 46.69 2.92
2363 2423 5.693961 TGAAGATATAAGGCTGGCATTTGA 58.306 37.500 3.38 0.00 0.00 2.69
2784 2849 7.312154 TGTTATGTGCATATTTTTGTCTGGTC 58.688 34.615 0.00 0.00 0.00 4.02
2856 2921 2.329267 ACCACTCATCCTGTTCAGACA 58.671 47.619 1.00 0.00 0.00 3.41
3028 3093 5.123027 CCTATTTTGCTTATAGCTAGCTGCC 59.877 44.000 27.68 10.64 42.97 4.85
3162 3227 6.096141 ACCAACCGTATGATTTGCAATCAATA 59.904 34.615 0.00 0.00 31.33 1.90
3293 3483 7.979444 AAAGTAGCAACTAATAAGTCTTGCA 57.021 32.000 4.22 0.00 37.24 4.08
3355 3545 5.365619 CACTGGTTTCTTGGTAGTTACTGT 58.634 41.667 0.00 0.00 0.00 3.55
3421 3611 6.039616 TGATACAAAATAATGCGAAAAGGCC 58.960 36.000 0.00 0.00 0.00 5.19
3445 3635 1.071314 AATGGGGTGGAGTGGGTTGA 61.071 55.000 0.00 0.00 0.00 3.18
3523 3742 1.704628 TGACCACCATGACCAGTTGAT 59.295 47.619 0.00 0.00 0.00 2.57
3619 3838 5.450818 AATTTAACTCACATAGGCAGGGA 57.549 39.130 0.00 0.00 0.00 4.20
3649 3868 7.706100 TTAATAAAAGGCACGGGATTACTTT 57.294 32.000 0.00 0.00 33.19 2.66
3650 3869 6.599356 AATAAAAGGCACGGGATTACTTTT 57.401 33.333 12.24 12.24 42.18 2.27
3674 3893 6.774673 TGACTCCATTGGAACTTGTTATGTA 58.225 36.000 6.88 0.00 0.00 2.29
3719 3938 5.063944 TGCAAGAAATGATTAAGAGAGTCGC 59.936 40.000 0.00 0.00 0.00 5.19
3723 3942 5.988561 AGAAATGATTAAGAGAGTCGCCATC 59.011 40.000 0.00 0.00 0.00 3.51
3735 3954 4.279671 AGAGTCGCCATCTTAGAAATCGAT 59.720 41.667 0.00 0.00 0.00 3.59
3752 3979 7.704472 AGAAATCGATCTCTGAACATTGAGTAC 59.296 37.037 0.00 0.00 0.00 2.73
3970 4197 5.886609 TCCATAAACTGACCATCTTTTCCA 58.113 37.500 0.00 0.00 0.00 3.53
3983 4210 2.912956 TCTTTTCCACCATGTAGCCTCT 59.087 45.455 0.00 0.00 0.00 3.69
4035 4262 6.127897 ACTGGAAGAAAATAATCGGCTTCTTG 60.128 38.462 0.00 0.00 38.05 3.02
4103 4331 4.180817 TCATGTGCAATTACTCGTACAGG 58.819 43.478 0.00 0.00 31.14 4.00
4118 4359 6.071334 ACTCGTACAGGAGAATGATTTTCTCA 60.071 38.462 15.13 0.00 45.01 3.27
4200 4441 6.723298 TTTCTTCCAGGCTCAAAATAACAA 57.277 33.333 0.00 0.00 0.00 2.83
4463 4704 3.118261 TGCTCCCAGATCTTACAATGGTC 60.118 47.826 0.00 0.00 0.00 4.02
4490 4731 6.911250 TCTTCCAGTTGATGTCACTACTTA 57.089 37.500 0.00 0.00 0.00 2.24
4749 4990 4.022589 ACTGAAACTTCATCGGTAGTTCGA 60.023 41.667 0.00 0.00 43.61 3.71
4790 5031 2.703409 GCTTCAGCATGTACGCCG 59.297 61.111 0.00 0.00 41.59 6.46
5025 5267 8.934023 CTCCTCCAGAGAGTAGAGTAAATATT 57.066 38.462 0.00 0.00 46.50 1.28
5028 5270 9.802039 CCTCCAGAGAGTAGAGTAAATATTAGT 57.198 37.037 0.00 0.00 38.58 2.24
5053 5295 6.291377 AGAAGATGTAGCAACAACAAGAAGA 58.709 36.000 0.00 0.00 39.58 2.87
5100 5342 0.827368 AAAAGCCTTTTTGCCGGTCA 59.173 45.000 1.90 0.00 35.26 4.02
5101 5343 0.104120 AAAGCCTTTTTGCCGGTCAC 59.896 50.000 1.90 0.00 0.00 3.67
5106 5348 2.750712 GCCTTTTTGCCGGTCACTATTA 59.249 45.455 1.90 0.00 0.00 0.98
5112 5354 4.364415 TTGCCGGTCACTATTAATTTGC 57.636 40.909 1.90 0.00 0.00 3.68
5147 5389 3.485216 GCAAACGTAAATCCGGATGTCTG 60.485 47.826 19.95 9.63 0.00 3.51
5163 5408 4.028993 TGTCTGGTTTTACCCAATCTCC 57.971 45.455 0.00 0.00 37.50 3.71
5367 5612 1.478105 GGCTCAAAAGGCGGATTGATT 59.522 47.619 3.73 0.00 38.44 2.57
5389 5634 1.068250 GTGCGATCCCCTACTCTGC 59.932 63.158 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.074752 GAGAGAAGCGCACAAAGGAG 58.925 55.000 11.47 0.00 0.00 3.69
68 71 1.374758 GGAACAGACCTGGCTCGTG 60.375 63.158 0.00 0.00 34.19 4.35
142 149 4.320456 ACACAGTGAGGCGGGCAG 62.320 66.667 7.81 0.00 0.00 4.85
143 150 4.624364 CACACAGTGAGGCGGGCA 62.624 66.667 7.81 0.00 35.23 5.36
176 183 6.537301 CCTGTAGAAATGATTACGTAAAGCCA 59.463 38.462 12.81 10.92 0.00 4.75
257 271 1.125093 ACATGTGGACAAGGACCCGA 61.125 55.000 0.00 0.00 0.00 5.14
285 299 8.827832 AATAACTCCATGAAAGAATCCAATCA 57.172 30.769 0.00 0.00 0.00 2.57
290 304 8.084684 GCCAATAATAACTCCATGAAAGAATCC 58.915 37.037 0.00 0.00 0.00 3.01
387 418 8.621286 CAAAGTATGTTTATCTATGGGACCAAC 58.379 37.037 0.00 0.00 0.00 3.77
443 474 3.064900 GGTGAGTTCAGAAATCAGCCT 57.935 47.619 25.46 0.31 35.86 4.58
474 505 8.040132 AGACACTCAGATTCTTTCATTTCCTAG 58.960 37.037 0.00 0.00 0.00 3.02
482 513 6.931281 CCTTACAAGACACTCAGATTCTTTCA 59.069 38.462 0.00 0.00 0.00 2.69
552 583 7.775561 ACCTAAAACATCAAACTCTTCTCAACT 59.224 33.333 0.00 0.00 0.00 3.16
568 599 5.217978 TGTCAGTTCCGTACCTAAAACAT 57.782 39.130 0.00 0.00 0.00 2.71
619 650 8.293699 AGGTACACTTCAGAAACAGAATTTTT 57.706 30.769 0.00 0.00 0.00 1.94
732 763 8.708378 AGAACCTTGAAATTTTGGAGAAAAGAT 58.292 29.630 11.20 0.00 34.53 2.40
804 838 4.386413 CAAGTGTGGACTCCTGGC 57.614 61.111 0.00 0.00 0.00 4.85
832 866 0.442699 GTTTTTCGCCTACTGCTCCG 59.557 55.000 0.00 0.00 38.05 4.63
847 881 0.032615 TCACACCCTGGGCAAGTTTT 60.033 50.000 14.08 0.00 0.00 2.43
866 900 7.897575 TGTTTCAAGTTTTACTGCATTTGTT 57.102 28.000 0.00 0.00 0.00 2.83
867 901 7.816995 TCTTGTTTCAAGTTTTACTGCATTTGT 59.183 29.630 8.93 0.00 0.00 2.83
1408 1445 5.714333 TGGTAGCATAAACCAACATGACAAT 59.286 36.000 0.00 0.00 43.99 2.71
1446 1484 4.095610 CGAACGCAAAAATCAAGGGATAC 58.904 43.478 0.00 0.00 32.09 2.24
1574 1612 0.881600 TCCATTGGCATCTCATCGCG 60.882 55.000 0.00 0.00 0.00 5.87
1656 1694 2.022195 CCTCAAACAGATGGCATCCAG 58.978 52.381 23.33 18.17 36.75 3.86
1677 1715 2.489971 TGTAGCACTTCCAAAGGAACG 58.510 47.619 0.00 0.00 36.71 3.95
1683 1721 6.899393 ATTTTCTGATGTAGCACTTCCAAA 57.101 33.333 0.00 0.00 0.00 3.28
1928 1968 9.424319 CTCGTCCTAATATATGCAACATTTAGT 57.576 33.333 0.00 0.00 0.00 2.24
2216 2259 0.371645 GTCGATCAAAAGCTCAGGCG 59.628 55.000 0.00 0.00 44.37 5.52
2232 2275 2.688507 ACAGCACAGAACTATTGGTCG 58.311 47.619 0.00 0.00 0.00 4.79
2606 2669 7.322664 ACAATTTTGACTGAAAGCTTTCTTCA 58.677 30.769 33.03 29.63 37.60 3.02
2856 2921 5.186797 CACAAAGGAAGAGACTCCTGTATCT 59.813 44.000 0.00 0.00 45.59 1.98
2966 3031 4.097892 ACGGAATAAATCAATTGGACCTGC 59.902 41.667 5.42 0.00 0.00 4.85
3106 3171 4.735369 AGGGTAAATGAACCATCAACACA 58.265 39.130 0.00 0.00 41.67 3.72
3162 3227 6.127196 GGGAGTATCTCAACTCAATCTCAACT 60.127 42.308 6.37 0.00 46.40 3.16
3323 3513 3.256631 CCAAGAAACCAGTGCTTTGCTAT 59.743 43.478 0.00 0.00 0.00 2.97
3355 3545 7.680113 GCCAGTTAACTAGCACTTTGTGTTTTA 60.680 37.037 19.39 0.00 35.75 1.52
3387 3577 7.536964 CGCATTATTTTGTATCAACACACAGAA 59.463 33.333 0.00 0.00 34.61 3.02
3421 3611 1.324740 CCACTCCACCCCATTGCATG 61.325 60.000 0.00 0.00 0.00 4.06
3445 3635 1.964373 CGGTAGTTTTGTGCCGCCT 60.964 57.895 0.00 0.00 37.69 5.52
3649 3868 6.068010 ACATAACAAGTTCCAATGGAGTCAA 58.932 36.000 0.86 0.00 31.21 3.18
3650 3869 5.630121 ACATAACAAGTTCCAATGGAGTCA 58.370 37.500 0.86 0.00 31.21 3.41
3674 3893 8.487313 TTGCAAGTACAACGATACATATTTCT 57.513 30.769 0.00 0.00 0.00 2.52
3719 3938 7.205992 TGTTCAGAGATCGATTTCTAAGATGG 58.794 38.462 17.29 5.44 0.00 3.51
3723 3942 8.640091 TCAATGTTCAGAGATCGATTTCTAAG 57.360 34.615 17.29 7.43 0.00 2.18
3735 3954 4.021104 CCACAGGTACTCAATGTTCAGAGA 60.021 45.833 0.00 0.00 34.60 3.10
3752 3979 2.168521 ACAGGTTCGACATATCCACAGG 59.831 50.000 0.00 0.00 0.00 4.00
3970 4197 2.045524 CCATCTCAGAGGCTACATGGT 58.954 52.381 6.85 0.00 0.00 3.55
3983 4210 5.561679 AGCTGTACTATACGATCCATCTCA 58.438 41.667 0.00 0.00 0.00 3.27
4035 4262 8.668353 TGTTTGAATATTTGTGTCTATCTGAGC 58.332 33.333 0.00 0.00 0.00 4.26
4103 4331 4.940046 TGGCTGACTGAGAAAATCATTCTC 59.060 41.667 10.49 10.49 43.85 2.87
4200 4441 1.132453 TCACGCGATTGAAGAGATCGT 59.868 47.619 15.93 0.00 45.99 3.73
4463 4704 4.384056 AGTGACATCAACTGGAAGAACTG 58.616 43.478 0.00 0.00 37.43 3.16
4554 4795 2.095567 CGAACTCCAAAGCAGTTCATGG 60.096 50.000 12.69 0.19 46.99 3.66
4720 4961 4.759782 ACCGATGAAGTTTCAGTATCTGG 58.240 43.478 0.74 3.23 41.08 3.86
4749 4990 9.080097 AGCAGTATTTATCTTCCTATAACTCGT 57.920 33.333 0.00 0.00 0.00 4.18
4790 5031 1.337071 TGACTCTATTCGTCGCCATCC 59.663 52.381 0.00 0.00 34.17 3.51
5024 5266 8.364894 TCTTGTTGTTGCTACATCTTCTACTAA 58.635 33.333 0.81 0.00 33.44 2.24
5025 5267 7.892609 TCTTGTTGTTGCTACATCTTCTACTA 58.107 34.615 0.81 0.00 33.44 1.82
5026 5268 6.759272 TCTTGTTGTTGCTACATCTTCTACT 58.241 36.000 0.81 0.00 33.44 2.57
5027 5269 7.385205 TCTTCTTGTTGTTGCTACATCTTCTAC 59.615 37.037 0.81 0.00 33.44 2.59
5028 5270 7.441836 TCTTCTTGTTGTTGCTACATCTTCTA 58.558 34.615 0.81 0.00 33.44 2.10
5029 5271 6.291377 TCTTCTTGTTGTTGCTACATCTTCT 58.709 36.000 0.81 0.00 33.44 2.85
5030 5272 6.545504 TCTTCTTGTTGTTGCTACATCTTC 57.454 37.500 0.81 0.00 33.44 2.87
5031 5273 8.621532 TTATCTTCTTGTTGTTGCTACATCTT 57.378 30.769 0.81 0.00 33.44 2.40
5032 5274 8.798859 ATTATCTTCTTGTTGTTGCTACATCT 57.201 30.769 0.81 0.00 33.44 2.90
5035 5277 9.719355 TCTTATTATCTTCTTGTTGTTGCTACA 57.281 29.630 0.00 0.00 0.00 2.74
5084 5326 0.109723 TAGTGACCGGCAAAAAGGCT 59.890 50.000 0.00 0.00 41.46 4.58
5100 5342 8.624776 GCATACAAGGAGAAGCAAATTAATAGT 58.375 33.333 0.00 0.00 0.00 2.12
5101 5343 8.623903 TGCATACAAGGAGAAGCAAATTAATAG 58.376 33.333 0.00 0.00 0.00 1.73
5106 5348 5.726980 TTGCATACAAGGAGAAGCAAATT 57.273 34.783 0.00 0.00 38.82 1.82
5112 5354 5.856126 TTACGTTTGCATACAAGGAGAAG 57.144 39.130 8.06 0.00 37.04 2.85
5147 5389 1.644337 AGGGGGAGATTGGGTAAAACC 59.356 52.381 0.00 0.00 37.60 3.27
5154 5399 1.153132 AGGATAGAGGGGGAGATTGGG 59.847 57.143 0.00 0.00 0.00 4.12
5342 5587 2.042831 CCGCCTTTTGAGCCTCTGG 61.043 63.158 0.00 0.00 0.00 3.86
5359 5604 2.223572 GGGATCGCACACAAATCAATCC 60.224 50.000 4.64 0.00 0.00 3.01
5367 5612 0.535335 GAGTAGGGGATCGCACACAA 59.465 55.000 12.32 0.00 0.00 3.33
5389 5634 1.787155 CGACCTCTTCAACAACGTCAG 59.213 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.