Multiple sequence alignment - TraesCS4B01G145700

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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 TraesCS4B01G145700 chr4B 100.000 3005 0 0 1 3005 209077439 209074435 0 5550
1 TraesCS4B01G145700 chr4D 98.536 3006 43 1 1 3005 123299969 123302974 0 5306
2 TraesCS4B01G145700 chr7B 98.303 3006 49 2 1 3005 644467523 644470527 0 5267
3 TraesCS4B01G145700 chr7D 98.238 3008 50 2 1 3005 203515555 203518562 0 5258
4 TraesCS4B01G145700 chr3A 98.037 3005 56 2 1 3005 633111333 633114334 0 5219
5 TraesCS4B01G145700 chr6B 97.773 3009 62 2 1 3005 306995911 306992904 0 5180
6 TraesCS4B01G145700 chr2A 97.539 3007 68 4 1 3005 332944218 332941216 0 5138


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 TraesCS4B01G145700 chr4B 209074435 209077439 3004 True 5550 5550 100.000 1 3005 1 chr4B.!!$R1 3004
1 TraesCS4B01G145700 chr4D 123299969 123302974 3005 False 5306 5306 98.536 1 3005 1 chr4D.!!$F1 3004
2 TraesCS4B01G145700 chr7B 644467523 644470527 3004 False 5267 5267 98.303 1 3005 1 chr7B.!!$F1 3004
3 TraesCS4B01G145700 chr7D 203515555 203518562 3007 False 5258 5258 98.238 1 3005 1 chr7D.!!$F1 3004
4 TraesCS4B01G145700 chr3A 633111333 633114334 3001 False 5219 5219 98.037 1 3005 1 chr3A.!!$F1 3004
5 TraesCS4B01G145700 chr6B 306992904 306995911 3007 True 5180 5180 97.773 1 3005 1 chr6B.!!$R1 3004
6 TraesCS4B01G145700 chr2A 332941216 332944218 3002 True 5138 5138 97.539 1 3005 1 chr2A.!!$R1 3004

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
860 868 0.237498 GACCAGAAAACGCCTTTCGG 59.763 55.0 14.27 14.27 46.89 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2742 2753 1.065854 CCTCCTGGAAAGAGCGATGTT 60.066 52.381 0.0 0.0 34.57 2.71 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
227 228 1.202154 CGCTCACAGTAGTTCTACCCG 60.202 57.143 6.39 1.94 0.00 5.28
253 254 5.296283 AGAAAAGATCATGAAAGAGGCGATG 59.704 40.000 0.00 0.00 0.00 3.84
355 356 3.133721 CCCTCAGACGGATCAAAGAAGAT 59.866 47.826 0.00 0.00 0.00 2.40
611 612 3.053693 CGATCAGGAGATAGGGAGGATCT 60.054 52.174 0.00 0.00 36.33 2.75
729 730 2.335712 GCTTCAACGCTCCCCAAGG 61.336 63.158 0.00 0.00 0.00 3.61
798 799 3.243737 GCGACCTTTCATTCCCTTGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
860 868 0.237498 GACCAGAAAACGCCTTTCGG 59.763 55.000 14.27 14.27 46.89 4.30
1036 1045 2.888212 AGTATTGCAAAAGAAGGGGCA 58.112 42.857 1.71 0.00 0.00 5.36
1055 1064 3.133014 GCTGATAGAGCTGGGCGA 58.867 61.111 0.00 0.00 45.21 5.54
1180 1189 4.341235 CCGATGACTTACTACTGGGAATCA 59.659 45.833 0.00 0.00 0.00 2.57
1366 1375 3.197766 TCCCATACAATTCTTGCGAGAGT 59.802 43.478 3.32 0.00 32.44 3.24
1376 1385 0.392706 TTGCGAGAGTTGGAGAAGCA 59.607 50.000 0.00 0.00 0.00 3.91
1382 1391 3.129462 CGAGAGTTGGAGAAGCATCTACA 59.871 47.826 0.00 0.00 45.07 2.74
1739 1748 2.345991 CTTTGGTCGGAAGGCGGA 59.654 61.111 0.00 0.00 35.76 5.54
1851 1861 2.158652 TCGGGATCGAGGTCTCATTAGT 60.159 50.000 0.00 0.00 40.88 2.24
1988 1998 4.070009 GACAACCTTTACCAAGTCCGAAT 58.930 43.478 0.00 0.00 0.00 3.34
2002 2012 5.407407 AGTCCGAATGATTGTCAACTACT 57.593 39.130 0.00 0.00 0.00 2.57
2010 2020 6.716934 ATGATTGTCAACTACTAGATCCGT 57.283 37.500 0.00 0.00 0.00 4.69
2073 2083 3.869246 CGGCGCGGAATATAATCCTAAAT 59.131 43.478 9.72 0.00 37.34 1.40
2495 2505 1.153568 CCGGAAGATCGCTGCTTCA 60.154 57.895 0.00 0.00 42.68 3.02
2520 2530 3.949031 GCGACTAGCTTCTACCCAG 57.051 57.895 0.00 0.00 44.04 4.45
2742 2753 1.133575 CCCTACTCACCCGGTCTATGA 60.134 57.143 0.00 0.00 0.00 2.15
2878 2889 1.315257 GGTCCGTGCAGCATTTCCAT 61.315 55.000 0.00 0.00 0.00 3.41
2912 2923 3.464720 TCAATTAATGGGACTTGGCCA 57.535 42.857 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.305922 CAATCATTCCGAAGAGCCGC 59.694 55.000 0.00 0.00 0.00 6.53
117 118 3.055328 TCAATTGATAGATCAGGGCCCA 58.945 45.455 27.56 3.72 38.19 5.36
227 228 5.812642 TCGCCTCTTTCATGATCTTTTCTAC 59.187 40.000 0.00 0.00 0.00 2.59
355 356 2.592993 CCAGCGAGAGGTTCCCCAA 61.593 63.158 0.00 0.00 41.81 4.12
611 612 0.881118 GGAATTTCGTGCTTCTGCCA 59.119 50.000 0.00 0.00 38.71 4.92
729 730 1.661341 CACTATGAGGGCTCTGTTGC 58.339 55.000 0.00 0.00 0.00 4.17
962 971 7.865706 TTAAAGCCTTCTCTACCATTGAATC 57.134 36.000 0.00 0.00 0.00 2.52
1055 1064 4.202588 ACCTGATAACTAGTATCGCCTCCT 60.203 45.833 0.00 0.00 41.51 3.69
1180 1189 2.238646 TGAGAAGAAATACGGCACCCAT 59.761 45.455 0.00 0.00 0.00 4.00
1366 1375 5.734720 CTTTACCTGTAGATGCTTCTCCAA 58.265 41.667 5.22 0.00 33.17 3.53
1618 1627 2.337583 TGAGCTATGCAACAACGAGAC 58.662 47.619 0.00 0.00 0.00 3.36
1669 1678 1.513158 CCGATCGTGAGACTGCCTT 59.487 57.895 15.09 0.00 46.97 4.35
1739 1748 2.127528 GTCCCCTTCCTTCCCCCT 59.872 66.667 0.00 0.00 0.00 4.79
1851 1861 1.125093 TTGGCCTGGGTCTTCTTCGA 61.125 55.000 3.32 0.00 0.00 3.71
1899 1909 6.370442 CGGACCAATTTACTATGTCTTTGTCA 59.630 38.462 0.00 0.00 0.00 3.58
1988 1998 6.330278 CAACGGATCTAGTAGTTGACAATCA 58.670 40.000 13.11 0.00 44.64 2.57
2002 2012 1.991121 ATAGCGGACCAACGGATCTA 58.009 50.000 0.00 0.00 0.00 1.98
2010 2020 2.404559 AGGGTGAATATAGCGGACCAA 58.595 47.619 0.00 0.00 0.00 3.67
2073 2083 8.153221 TGACTATATTTGAGTCTTTGGGGTAA 57.847 34.615 5.86 0.00 43.19 2.85
2495 2505 1.551452 AGAAGCTAGTCGCCAGAAGT 58.449 50.000 0.00 0.00 40.39 3.01
2520 2530 5.590259 TGATTCAAGGTAGCTTTAGCCATTC 59.410 40.000 3.96 0.00 43.38 2.67
2716 2727 1.622607 CCGGGTGAGTAGGGATGCAA 61.623 60.000 0.00 0.00 0.00 4.08
2742 2753 1.065854 CCTCCTGGAAAGAGCGATGTT 60.066 52.381 0.00 0.00 34.57 2.71
2912 2923 5.489792 TGATAGAGGCAAGAACACTTTCT 57.510 39.130 0.00 0.00 44.53 2.52


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

AutoCloner maintained by Alex Coulton.