Multiple sequence alignment - TraesCS2B01G288700

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 TraesCS2B01G288700 chr2B 100.000 3185 0 0 1 3185 399336923 399340107 0.000000e+00 5882
1 TraesCS2B01G288700 chr2D 97.084 3189 71 12 1 3185 330735994 330739164 0.000000e+00 5354
2 TraesCS2B01G288700 chr2A 97.659 2478 53 5 711 3185 437966005 437968480 0.000000e+00 4250
3 TraesCS2B01G288700 chr2A 94.173 532 17 6 1 528 437964889 437965410 0.000000e+00 798
4 TraesCS2B01G288700 chr2A 96.032 126 4 1 526 651 437965494 437965618 1.500000e-48 204


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 TraesCS2B01G288700 chr2B 399336923 399340107 3184 False 5882.000000 5882 100.000000 1 3185 1 chr2B.!!$F1 3184
1 TraesCS2B01G288700 chr2D 330735994 330739164 3170 False 5354.000000 5354 97.084000 1 3185 1 chr2D.!!$F1 3184
2 TraesCS2B01G288700 chr2A 437964889 437968480 3591 False 1750.666667 4250 95.954667 1 3185 3 chr2A.!!$F1 3184

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
686 780 0.029300 GATGGTGTGTGTGTGTGTGC 59.971 55.0 0.0 0.0 0.00 4.57 F
1543 1970 0.179179 GCTTCGGCAAAGTGAGCATC 60.179 55.0 0.0 0.0 41.33 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2425 0.611714 CTACCTTACGGCCCAACTGT 59.388 55.000 0.0 0.0 42.04 3.55 R
3137 3567 1.134491 ACCTTCCCGCTACTACAATGC 60.134 52.381 0.0 0.0 0.00 3.56 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
27 28 1.198637 GATGTGGCTGCTGACTTGTTC 59.801 52.381 0.00 0.00 0.00 3.18
58 61 9.793259 TTGAATTGATTACTTAAGGTCTTCAGT 57.207 29.630 7.53 3.49 32.45 3.41
64 67 7.665559 TGATTACTTAAGGTCTTCAGTGCAAAT 59.334 33.333 7.53 1.30 30.55 2.32
91 95 7.231519 CCCCCATTTTACTCATTTCTAGGAATC 59.768 40.741 0.00 0.00 0.00 2.52
159 165 7.014808 TGGTTTGAAGATATTCCTTTTCGGTTT 59.985 33.333 0.00 0.00 0.00 3.27
160 166 7.870954 GGTTTGAAGATATTCCTTTTCGGTTTT 59.129 33.333 0.00 0.00 0.00 2.43
227 233 8.748412 TGGTTTGAGTTCCAGGATTATTATTTG 58.252 33.333 0.00 0.00 0.00 2.32
321 328 3.054287 TCAGGGGAACTTGTGTTTGTGTA 60.054 43.478 0.00 0.00 38.80 2.90
411 418 7.606456 ACCATTTCAGTATAACCAGTAACACAG 59.394 37.037 0.00 0.00 0.00 3.66
424 431 5.463724 CCAGTAACACAGTTCTGTTTCTCTC 59.536 44.000 2.47 0.00 35.87 3.20
465 472 5.416639 AGTGTTGAGCTCATGATGCATAAAA 59.583 36.000 19.04 0.00 0.00 1.52
497 504 9.178758 GTCTCTTGTCCTGTATTTCCATAAATT 57.821 33.333 0.00 0.00 36.67 1.82
654 748 6.683974 AGTGCATTCACAGATTTATACCAC 57.316 37.500 0.00 0.00 45.49 4.16
666 760 9.975218 ACAGATTTATACCACAAGGAGTTTATT 57.025 29.630 0.00 0.00 38.69 1.40
680 774 4.518970 GGAGTTTATTGATGGTGTGTGTGT 59.481 41.667 0.00 0.00 0.00 3.72
682 776 4.887071 AGTTTATTGATGGTGTGTGTGTGT 59.113 37.500 0.00 0.00 0.00 3.72
684 778 2.121291 TTGATGGTGTGTGTGTGTGT 57.879 45.000 0.00 0.00 0.00 3.72
685 779 1.377536 TGATGGTGTGTGTGTGTGTG 58.622 50.000 0.00 0.00 0.00 3.82
686 780 0.029300 GATGGTGTGTGTGTGTGTGC 59.971 55.000 0.00 0.00 0.00 4.57
687 781 1.713937 ATGGTGTGTGTGTGTGTGCG 61.714 55.000 0.00 0.00 0.00 5.34
688 782 2.395360 GGTGTGTGTGTGTGTGCGT 61.395 57.895 0.00 0.00 0.00 5.24
689 783 1.084935 GGTGTGTGTGTGTGTGCGTA 61.085 55.000 0.00 0.00 0.00 4.42
901 1328 2.558795 AGTGGGCTGCATACGTAGATAG 59.441 50.000 0.08 0.03 0.00 2.08
1067 1494 2.579873 ACCATTACCATCATCTGCAGC 58.420 47.619 9.47 0.00 0.00 5.25
1248 1675 3.911719 GGAGAACCTCCCATTGCAT 57.088 52.632 1.60 0.00 44.36 3.96
1362 1789 6.071447 CCAATTCAGAACATACAATGGTTCCA 60.071 38.462 0.00 0.00 43.37 3.53
1543 1970 0.179179 GCTTCGGCAAAGTGAGCATC 60.179 55.000 0.00 0.00 41.33 3.91
1545 1972 1.808945 CTTCGGCAAAGTGAGCATCTT 59.191 47.619 0.00 0.00 34.92 2.40
1595 2022 3.253230 GGAAGGCACCATTGAATTTTCG 58.747 45.455 0.00 0.00 0.00 3.46
1641 2068 7.310361 GGACCTTCTGCTATAAATGCTAGAGAT 60.310 40.741 0.00 0.00 0.00 2.75
1711 2138 2.609350 CAATTGGGATTCAGTTTGGCG 58.391 47.619 0.00 0.00 0.00 5.69
1712 2139 1.185315 ATTGGGATTCAGTTTGGCGG 58.815 50.000 0.00 0.00 0.00 6.13
1998 2425 1.215912 CCATGCGGCATTGAAGCAA 59.784 52.632 13.81 0.00 44.51 3.91
2142 2569 2.750350 CCTCGTCTGCTTGGGGTT 59.250 61.111 0.00 0.00 0.00 4.11
2225 2652 5.277442 GGGTTTTTCACATTGCAAGATTGTG 60.277 40.000 20.65 20.65 41.60 3.33
2262 2689 2.298163 CTCTTGCTTCATGGCCTTTGTT 59.702 45.455 3.32 0.00 0.00 2.83
2488 2915 4.215399 GTGCTTAACAGAACTATGGTGCAA 59.785 41.667 0.00 0.00 0.00 4.08
2769 3196 6.400568 AGGAACAAATTGGCAGATGTTTATG 58.599 36.000 13.44 0.00 36.22 1.90
2783 3211 7.414429 GCAGATGTTTATGATGCACAGAAGTTA 60.414 37.037 0.00 0.00 36.88 2.24
2948 3377 3.561143 TGTTCTGCAATTGGTACTTGGT 58.439 40.909 7.72 0.00 0.00 3.67
2959 3388 5.585820 TTGGTACTTGGTTGTTTTCCTTC 57.414 39.130 0.00 0.00 0.00 3.46
3002 3431 5.452078 TTAACTGGCCATTTGTCAAGAAG 57.548 39.130 18.05 0.00 0.00 2.85
3012 3441 5.819901 CCATTTGTCAAGAAGAGGAGGTATC 59.180 44.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.944422 TTCAAACTCGAACAAGTCAGC 57.056 42.857 0.00 0.00 0.00 4.26
27 28 8.936864 AGACCTTAAGTAATCAATTCAAACTCG 58.063 33.333 0.97 0.00 0.00 4.18
58 61 3.784178 TGAGTAAAATGGGGGATTTGCA 58.216 40.909 0.00 0.00 34.30 4.08
64 67 5.734140 TCCTAGAAATGAGTAAAATGGGGGA 59.266 40.000 0.00 0.00 0.00 4.81
91 95 3.187227 CGATTCCAACACAGTTTCTCCTG 59.813 47.826 0.00 0.00 38.45 3.86
159 165 4.142403 GCAACATTGAGCTTATGCCTACAA 60.142 41.667 9.07 3.05 40.80 2.41
160 166 3.378112 GCAACATTGAGCTTATGCCTACA 59.622 43.478 9.07 0.00 40.80 2.74
227 233 4.010349 ACTCAATTCCGACCCAGAAATTC 58.990 43.478 0.00 0.00 0.00 2.17
362 369 3.784338 TGCAGGTCAGCAAAAGAAAAAG 58.216 40.909 0.00 0.00 42.46 2.27
363 370 3.883830 TGCAGGTCAGCAAAAGAAAAA 57.116 38.095 0.00 0.00 42.46 1.94
465 472 6.431234 GGAAATACAGGACAAGAGACATTTGT 59.569 38.462 0.00 0.00 41.21 2.83
568 662 4.702131 ACTTGTTACATTCTGGATTCAGGC 59.298 41.667 0.00 0.00 41.23 4.85
651 745 4.766891 ACACCATCAATAAACTCCTTGTGG 59.233 41.667 0.00 0.00 33.53 4.17
654 748 5.241506 ACACACACCATCAATAAACTCCTTG 59.758 40.000 0.00 0.00 0.00 3.61
666 760 1.377536 CACACACACACACACCATCA 58.622 50.000 0.00 0.00 0.00 3.07
668 762 1.713937 CGCACACACACACACACCAT 61.714 55.000 0.00 0.00 0.00 3.55
901 1328 0.907230 ACTCTTCCTCCAGTCCTGCC 60.907 60.000 0.00 0.00 0.00 4.85
1248 1675 1.646912 TGGAACGGATGAGGTGGTTA 58.353 50.000 0.00 0.00 0.00 2.85
1320 1747 0.994247 TGGTGACATCCTCAGCCATT 59.006 50.000 0.00 0.00 45.45 3.16
1362 1789 2.373169 AGTGTCACCATTCCAGACATGT 59.627 45.455 0.00 0.00 43.35 3.21
1543 1970 2.083774 TCGCTTGGTAAATGGCTCAAG 58.916 47.619 0.00 0.00 39.46 3.02
1545 1972 2.288666 GATCGCTTGGTAAATGGCTCA 58.711 47.619 0.00 0.00 0.00 4.26
1595 2022 3.070159 TCCATTGCTATGTAGAGAGCCAC 59.930 47.826 3.82 0.00 35.40 5.01
1641 2068 5.947663 TGTGTAATTTCTTCTCCCAAGGAA 58.052 37.500 0.00 0.00 0.00 3.36
1711 2138 1.276138 AGCCTGGCAAAAATTAGCACC 59.724 47.619 22.65 0.00 0.00 5.01
1712 2139 2.749280 AGCCTGGCAAAAATTAGCAC 57.251 45.000 22.65 0.00 0.00 4.40
1998 2425 0.611714 CTACCTTACGGCCCAACTGT 59.388 55.000 0.00 0.00 42.04 3.55
2014 2441 6.978343 TTGCAGTGATACACCATTTACTAC 57.022 37.500 0.00 0.00 34.49 2.73
2142 2569 1.828595 TCAAGTAGCCCTGATGCGTTA 59.171 47.619 0.00 0.00 36.02 3.18
2225 2652 2.191128 AGAGACACCATCAAGTTGGC 57.809 50.000 2.34 0.00 40.68 4.52
2262 2689 5.546499 ACCCTCAGTAAGTTATGACCTGAAA 59.454 40.000 3.39 0.00 32.23 2.69
2488 2915 3.383825 GCTCATCAATTCATTTGGAGCCT 59.616 43.478 0.00 0.00 40.71 4.58
2769 3196 9.534565 TGTCTTATCTTATAACTTCTGTGCATC 57.465 33.333 0.00 0.00 0.00 3.91
2783 3211 5.487488 TGGTGTTCCCACTGTCTTATCTTAT 59.513 40.000 0.00 0.00 41.53 1.73
2880 3309 5.801380 AGCCCTCGAAACTAAATAAACTCA 58.199 37.500 0.00 0.00 0.00 3.41
2927 3356 3.561143 ACCAAGTACCAATTGCAGAACA 58.439 40.909 0.00 0.00 0.00 3.18
2948 3377 5.828299 ACAACTTCATCGAAGGAAAACAA 57.172 34.783 8.49 0.00 43.25 2.83
2959 3388 3.067106 AGCACAGGTTACAACTTCATCG 58.933 45.455 0.00 0.00 0.00 3.84
3090 3520 5.804639 TGGTTGCTAAAAGAGAGCTCATAA 58.195 37.500 17.77 0.00 40.76 1.90
3136 3566 1.583054 CTTCCCGCTACTACAATGCC 58.417 55.000 0.00 0.00 0.00 4.40
3137 3567 1.134491 ACCTTCCCGCTACTACAATGC 60.134 52.381 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.