Multiple sequence alignment - TraesCS6B01G380100

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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 TraesCS6B01G380100 chr6B 100.000 3565 0 0 1 3565 655034541 655038105 0 6584
1 TraesCS6B01G380100 chr2A 98.152 3572 56 3 3 3565 509596842 509593272 0 6222
2 TraesCS6B01G380100 chr2A 97.762 3574 70 8 1 3565 525341416 525337844 0 6148
3 TraesCS6B01G380100 chr1B 98.097 3574 59 2 1 3565 259400780 259404353 0 6215
4 TraesCS6B01G380100 chr1B 98.014 3575 57 5 1 3565 245469169 245465599 0 6196
5 TraesCS6B01G380100 chr7A 98.041 3574 60 3 1 3565 199149599 199146027 0 6204
6 TraesCS6B01G380100 chr5A 97.846 3574 68 2 1 3565 99056370 99052797 0 6165
7 TraesCS6B01G380100 chr7B 97.706 3574 72 3 1 3565 157298800 157295228 0 6137
8 TraesCS6B01G380100 chr5B 97.678 3575 72 4 1 3565 349334460 349330887 0 6131
9 TraesCS6B01G380100 chr3B 97.594 3574 77 2 1 3565 354102670 354106243 0 6115


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 TraesCS6B01G380100 chr6B 655034541 655038105 3564 False 6584 6584 100.000 1 3565 1 chr6B.!!$F1 3564
1 TraesCS6B01G380100 chr2A 509593272 509596842 3570 True 6222 6222 98.152 3 3565 1 chr2A.!!$R1 3562
2 TraesCS6B01G380100 chr2A 525337844 525341416 3572 True 6148 6148 97.762 1 3565 1 chr2A.!!$R2 3564
3 TraesCS6B01G380100 chr1B 259400780 259404353 3573 False 6215 6215 98.097 1 3565 1 chr1B.!!$F1 3564
4 TraesCS6B01G380100 chr1B 245465599 245469169 3570 True 6196 6196 98.014 1 3565 1 chr1B.!!$R1 3564
5 TraesCS6B01G380100 chr7A 199146027 199149599 3572 True 6204 6204 98.041 1 3565 1 chr7A.!!$R1 3564
6 TraesCS6B01G380100 chr5A 99052797 99056370 3573 True 6165 6165 97.846 1 3565 1 chr5A.!!$R1 3564
7 TraesCS6B01G380100 chr7B 157295228 157298800 3572 True 6137 6137 97.706 1 3565 1 chr7B.!!$R1 3564
8 TraesCS6B01G380100 chr5B 349330887 349334460 3573 True 6131 6131 97.678 1 3565 1 chr5B.!!$R1 3564
9 TraesCS6B01G380100 chr3B 354102670 354106243 3573 False 6115 6115 97.594 1 3565 1 chr3B.!!$F1 3564

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
796 807 0.536006 GCTTCCGATGCTTAGGCCAT 60.536 55.0 5.01 0.0 37.74 4.40 F
1388 1399 0.687354 ACTGAATTCACTGACGGCCT 59.313 50.0 3.38 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1827 0.400213 AGGTGCTCCGGTTCATTCAA 59.600 50.0 0.00 0.0 39.05 2.69 R
2716 2727 1.075601 TCTGGGGCCACATCTTCTTT 58.924 50.0 8.98 0.0 0.00 2.52 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
126 127 9.396022 GTCTTGGATATCTTCTGTTTAATTGGA 57.604 33.333 2.05 0.00 0.00 3.53
293 294 5.758784 GCTCGGTTGCCTTATAAATAAGACT 59.241 40.000 10.64 0.00 41.72 3.24
448 457 1.134965 CGTCTTTCCGCATCTTCTCCT 60.135 52.381 0.00 0.00 0.00 3.69
520 529 7.148086 GGTTCCATGTTCTTGCTATGTTCATTA 60.148 37.037 0.00 0.00 0.00 1.90
522 531 6.883756 TCCATGTTCTTGCTATGTTCATTACA 59.116 34.615 0.00 0.00 41.97 2.41
572 582 1.204704 CATCTGTGGACTCTTGCCGTA 59.795 52.381 0.00 0.00 0.00 4.02
796 807 0.536006 GCTTCCGATGCTTAGGCCAT 60.536 55.000 5.01 0.00 37.74 4.40
824 835 8.512138 CGGTTTAACTTCACCATAGAGAAAAAT 58.488 33.333 0.00 0.00 31.84 1.82
858 869 7.064866 CCGGTATATATGTCATTAGTCCCCTA 58.935 42.308 0.00 0.00 0.00 3.53
1275 1286 3.637273 GGCCCCAACTCCGTCACT 61.637 66.667 0.00 0.00 0.00 3.41
1388 1399 0.687354 ACTGAATTCACTGACGGCCT 59.313 50.000 3.38 0.00 0.00 5.19
1467 1478 2.233922 CGTCAAACTCCATACTCACCCT 59.766 50.000 0.00 0.00 0.00 4.34
2431 2442 2.027003 AACAGTCCGGTTCGAAAACA 57.973 45.000 0.00 0.00 37.10 2.83
2562 2573 1.224592 GGTGAATCATCGGCCACCT 59.775 57.895 2.24 0.00 44.13 4.00
2716 2727 2.268802 CGCCTGGATAGAGCGGCTA 61.269 63.158 0.60 0.00 45.88 3.93
2809 2820 0.539669 TCCTCCTCTGCAAGACGACA 60.540 55.000 0.00 0.00 38.67 4.35
2818 2829 3.958147 TCTGCAAGACGACATTATCCCTA 59.042 43.478 0.00 0.00 38.67 3.53
3535 3549 3.347958 TTTCTTGGATCGTTTGTGCAC 57.652 42.857 10.75 10.75 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 6.790232 AAATAATGACGACATGGGGATTTT 57.210 33.333 0.05 0.00 36.79 1.82
132 133 6.472163 GCAACTAAAAATAATGACGACATGGG 59.528 38.462 0.05 0.00 36.79 4.00
293 294 5.316987 GAAGAGAAAGGAAATGACCCTTCA 58.683 41.667 0.00 0.00 42.82 3.02
448 457 2.454538 GAGAGAGGACTTACCGGGAAA 58.545 52.381 6.32 0.00 44.74 3.13
520 529 3.255888 TCAGAGAACAGCTATGAACGTGT 59.744 43.478 0.00 0.00 41.59 4.49
522 531 3.367498 GGTCAGAGAACAGCTATGAACGT 60.367 47.826 0.00 0.00 45.63 3.99
572 582 3.958798 TGCTAAAGGGATCGCTACTAAGT 59.041 43.478 13.34 0.00 0.00 2.24
796 807 4.020928 TCTCTATGGTGAAGTTAAACCGCA 60.021 41.667 3.42 0.00 39.47 5.69
824 835 8.911918 AATGACATATATACCGGTTTAGCAAA 57.088 30.769 15.04 0.00 0.00 3.68
858 869 0.400213 TGGATTCTGGCGGTTCAACT 59.600 50.000 0.00 0.00 0.00 3.16
943 954 5.450818 AGGACATGCTGGATAAAAAGGTA 57.549 39.130 0.00 0.00 0.00 3.08
956 967 0.620556 ATCCGGTTCAAGGACATGCT 59.379 50.000 0.00 0.00 41.10 3.79
1325 1336 9.179909 AGAGATCTCTAAATAACTCGACTGAAA 57.820 33.333 23.98 0.00 38.35 2.69
1467 1478 2.817258 CCAAGTTGCGTTCCATTCCTTA 59.183 45.455 0.00 0.00 0.00 2.69
1816 1827 0.400213 AGGTGCTCCGGTTCATTCAA 59.600 50.000 0.00 0.00 39.05 2.69
2562 2573 5.043737 ACTGTTTTCAAAGGTGGTAGCTA 57.956 39.130 0.00 0.00 0.00 3.32
2716 2727 1.075601 TCTGGGGCCACATCTTCTTT 58.924 50.000 8.98 0.00 0.00 2.52
2818 2829 7.001073 GCTGGAATATGAATAGGACCTTCTTT 58.999 38.462 0.00 0.00 0.00 2.52
2973 2984 1.452108 GGCAGGATTCCCAGGTTCG 60.452 63.158 0.00 0.00 33.88 3.95
3207 3218 1.474330 CTTGGGGGTTACAAGGATGC 58.526 55.000 0.00 0.00 41.16 3.91
3528 3542 2.102084 TGGCATTTTAAGCTGTGCACAA 59.898 40.909 21.98 4.04 39.27 3.33
3535 3549 4.980434 GCATACAGATGGCATTTTAAGCTG 59.020 41.667 0.00 5.74 33.26 4.24


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

AutoCloner maintained by Alex Coulton.