Multiple sequence alignment - TraesCS5D01G115700

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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 TraesCS5D01G115700 chr5D 100.000 2499 0 0 1 2499 135520681 135523179 0 4615
1 TraesCS5D01G115700 chr5B 94.589 2532 83 15 2 2499 147155901 147158412 0 3868
2 TraesCS5D01G115700 chr5A 96.369 1928 54 5 585 2499 169624920 169622996 0 3158
3 TraesCS5D01G115700 chr5A 92.674 546 31 2 1 546 169625460 169624924 0 778


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 TraesCS5D01G115700 chr5D 135520681 135523179 2498 False 4615 4615 100.0000 1 2499 1 chr5D.!!$F1 2498
1 TraesCS5D01G115700 chr5B 147155901 147158412 2511 False 3868 3868 94.5890 2 2499 1 chr5B.!!$F1 2497
2 TraesCS5D01G115700 chr5A 169622996 169625460 2464 True 1968 3158 94.5215 1 2499 2 chr5A.!!$R1 2498

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
909 913 1.268283 GGTTGGGGAGGAGAGAGGTG 61.268 65.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 2496 0.393808 ACGTATTCGGCTTGGGCATT 60.394 50.0 0.0 0.0 41.85 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
84 85 4.090819 GGGAAGAACTTACTCTCCACTCT 58.909 47.826 0.00 0.00 0.00 3.24
149 151 1.450531 GCACCACAGCTATGCATCCC 61.451 60.000 0.19 0.00 39.23 3.85
189 193 4.330250 CCATACCCTCCATTATTCTGCTG 58.670 47.826 0.00 0.00 0.00 4.41
191 195 5.456619 CCATACCCTCCATTATTCTGCTGAA 60.457 44.000 8.59 8.59 36.54 3.02
207 211 6.598503 TCTGCTGAAGGATCATTAATGATGT 58.401 36.000 30.86 17.24 46.84 3.06
209 213 8.380867 TCTGCTGAAGGATCATTAATGATGTAT 58.619 33.333 30.86 17.69 46.84 2.29
252 256 1.833630 GGATCAGGTCATGAGACACCA 59.166 52.381 0.00 0.00 46.80 4.17
405 409 3.699025 TCTATCACTGGGGTCCACATA 57.301 47.619 0.00 0.00 0.00 2.29
408 412 2.262266 TCACTGGGGTCCACATATCA 57.738 50.000 0.00 0.00 0.00 2.15
421 425 6.283694 GTCCACATATCAGTTGCTTCTCATA 58.716 40.000 0.00 0.00 0.00 2.15
438 442 7.868415 GCTTCTCATACGTATTAAGGAGTTCAT 59.132 37.037 18.14 0.00 0.00 2.57
489 493 3.611057 GCAACCAGACAAGCAGAGATTTG 60.611 47.826 0.00 0.00 0.00 2.32
492 496 3.326006 ACCAGACAAGCAGAGATTTGAGA 59.674 43.478 0.00 0.00 0.00 3.27
493 497 4.202398 ACCAGACAAGCAGAGATTTGAGAA 60.202 41.667 0.00 0.00 0.00 2.87
496 500 3.990469 GACAAGCAGAGATTTGAGAACGA 59.010 43.478 0.00 0.00 0.00 3.85
503 507 5.797434 GCAGAGATTTGAGAACGAAAATTCC 59.203 40.000 0.00 0.00 0.00 3.01
508 512 7.295930 AGATTTGAGAACGAAAATTCCGTAAC 58.704 34.615 6.32 4.94 39.57 2.50
532 536 3.067320 GCTTTTCTTCAAGCTGTGTTCCT 59.933 43.478 0.00 0.00 45.03 3.36
538 542 3.895232 TCAAGCTGTGTTCCTATCTCC 57.105 47.619 0.00 0.00 0.00 3.71
553 557 5.102870 TCCTATCTCCTCTCCCTTTCTTCAT 60.103 44.000 0.00 0.00 0.00 2.57
555 559 3.796111 TCTCCTCTCCCTTTCTTCATGT 58.204 45.455 0.00 0.00 0.00 3.21
556 560 3.517100 TCTCCTCTCCCTTTCTTCATGTG 59.483 47.826 0.00 0.00 0.00 3.21
557 561 3.517100 CTCCTCTCCCTTTCTTCATGTGA 59.483 47.826 0.00 0.00 0.00 3.58
558 562 3.517100 TCCTCTCCCTTTCTTCATGTGAG 59.483 47.826 0.00 0.00 0.00 3.51
635 639 7.009179 TCATGATTCTCCAAGTAGAAACAGT 57.991 36.000 0.00 0.00 40.31 3.55
909 913 1.268283 GGTTGGGGAGGAGAGAGGTG 61.268 65.000 0.00 0.00 0.00 4.00
944 948 2.747460 GCCATCGGCTGCTTGACA 60.747 61.111 0.00 0.00 46.69 3.58
967 971 3.243535 CCAAGGAGGAAAGAACAAACAGC 60.244 47.826 0.00 0.00 41.22 4.40
1077 1081 4.079787 AGCATCCCTCTAAACCTGCAATAA 60.080 41.667 0.00 0.00 32.18 1.40
1204 1208 6.015772 TGCAACATCATTATGCTGATATGCTT 60.016 34.615 18.30 0.00 42.41 3.91
1450 1454 2.099431 CGCAGAGACAGCAAGCTCC 61.099 63.158 0.00 0.00 0.00 4.70
1456 1460 3.177884 ACAGCAAGCTCCCCCACA 61.178 61.111 0.00 0.00 0.00 4.17
1512 1516 3.920231 TCTGTGAATGCATAAGAGGCT 57.080 42.857 0.00 0.00 0.00 4.58
1604 1608 3.641434 ATGATAAACCAGCTGCTCAGT 57.359 42.857 8.66 0.00 0.00 3.41
1666 1670 8.506437 CAGTGTTAAACTCTGCATTAATCTTCA 58.494 33.333 0.00 0.00 36.83 3.02
1775 1779 3.848726 ACTGTCAACCTTGTTGCAAAAG 58.151 40.909 0.00 7.50 0.00 2.27
1901 1905 8.071368 CAGTGCTCAATGTTTTTATGCATTTTT 58.929 29.630 3.54 0.00 33.55 1.94
1938 1951 5.311265 ACCATATCCAGACATAATGCACTG 58.689 41.667 0.00 0.00 0.00 3.66
1954 1971 1.277739 CTGCACACACTGAACTGCG 59.722 57.895 0.00 0.00 31.96 5.18
2090 2107 8.109634 ACCATGGATTATCCTCATTATGTTACC 58.890 37.037 21.47 0.00 37.46 2.85
2430 2468 9.254133 CAGTACCAATTTACTCTAGATGATGTG 57.746 37.037 0.00 0.00 29.30 3.21
2431 2469 8.982723 AGTACCAATTTACTCTAGATGATGTGT 58.017 33.333 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.664649 CTTGTCTCTTCGTGCGGCA 60.665 57.895 0.00 0.00 0.00 5.69
149 151 5.186797 GGTATGGGATCTGATACTCCTTGAG 59.813 48.000 0.00 0.00 35.52 3.02
209 213 8.518720 TCCATCTTCCCCATATATTTTCTGTA 57.481 34.615 0.00 0.00 0.00 2.74
213 217 7.559170 CCTGATCCATCTTCCCCATATATTTTC 59.441 40.741 0.00 0.00 0.00 2.29
217 221 5.617888 ACCTGATCCATCTTCCCCATATAT 58.382 41.667 0.00 0.00 0.00 0.86
252 256 2.363788 TCAGAAGAACTTGCGCGTAT 57.636 45.000 8.43 0.00 0.00 3.06
405 409 7.653713 CCTTAATACGTATGAGAAGCAACTGAT 59.346 37.037 9.24 0.00 0.00 2.90
408 412 7.108841 TCCTTAATACGTATGAGAAGCAACT 57.891 36.000 9.24 0.00 0.00 3.16
438 442 6.072175 GGATGTTGTCTGCCACAAACTTATTA 60.072 38.462 0.09 0.00 46.90 0.98
447 451 1.955778 CAAAGGATGTTGTCTGCCACA 59.044 47.619 0.00 0.00 0.00 4.17
448 452 1.336240 GCAAAGGATGTTGTCTGCCAC 60.336 52.381 0.00 0.00 0.00 5.01
489 493 4.151867 AGCAGTTACGGAATTTTCGTTCTC 59.848 41.667 8.24 0.13 41.38 2.87
492 496 4.823790 AAGCAGTTACGGAATTTTCGTT 57.176 36.364 8.24 0.00 41.38 3.85
493 497 4.823790 AAAGCAGTTACGGAATTTTCGT 57.176 36.364 8.01 8.01 43.64 3.85
496 500 6.801575 TGAAGAAAAGCAGTTACGGAATTTT 58.198 32.000 0.00 0.00 0.00 1.82
532 536 5.365025 CACATGAAGAAAGGGAGAGGAGATA 59.635 44.000 0.00 0.00 0.00 1.98
538 542 4.815533 TCTCACATGAAGAAAGGGAGAG 57.184 45.455 0.00 0.00 0.00 3.20
553 557 4.866508 ACGAAGGAATACAGTTCTCACA 57.133 40.909 0.00 0.00 0.00 3.58
555 559 3.994392 GCAACGAAGGAATACAGTTCTCA 59.006 43.478 0.00 0.00 0.00 3.27
556 560 4.246458 AGCAACGAAGGAATACAGTTCTC 58.754 43.478 0.00 0.00 0.00 2.87
557 561 4.273148 AGCAACGAAGGAATACAGTTCT 57.727 40.909 0.00 0.00 0.00 3.01
558 562 5.407387 TGTTAGCAACGAAGGAATACAGTTC 59.593 40.000 0.00 0.00 0.00 3.01
635 639 4.161565 CCAAGTACTGTCCTATGGCAGTAA 59.838 45.833 13.19 0.00 45.94 2.24
909 913 1.527433 GCAGTTCCCTCTTGGTTGGC 61.527 60.000 0.00 0.00 34.77 4.52
935 939 0.397941 TCCTCCTTGGTGTCAAGCAG 59.602 55.000 0.96 0.00 46.69 4.24
944 948 3.954258 CTGTTTGTTCTTTCCTCCTTGGT 59.046 43.478 0.00 0.00 37.07 3.67
967 971 0.659957 GGAGGCGCTAAAATCTGCTG 59.340 55.000 7.64 0.00 0.00 4.41
1026 1030 2.606378 ACTTACCGGAGAAGACCAGTT 58.394 47.619 22.28 1.94 0.00 3.16
1077 1081 7.178983 TGGAATCTACCAAATTGAAAGCTTCAT 59.821 33.333 0.00 0.00 36.93 2.57
1204 1208 5.647658 CACAATCCAGGCAGTTACTTTATGA 59.352 40.000 0.00 0.00 0.00 2.15
1450 1454 2.435938 CCGTCGGTTGATGTGGGG 60.436 66.667 2.08 0.00 0.00 4.96
1456 1460 2.742372 GCTGTGCCGTCGGTTGAT 60.742 61.111 13.94 0.00 0.00 2.57
1512 1516 4.687901 TCAGTGATTCTTCCAGTGTGAA 57.312 40.909 0.00 0.00 36.58 3.18
1604 1608 1.544724 GGTGCCTACATGCTGGAAAA 58.455 50.000 8.57 0.00 0.00 2.29
1666 1670 7.692460 TCAGTGAAAATGAGAATGCAATAGT 57.308 32.000 0.00 0.00 35.16 2.12
1901 1905 9.778741 GTCTGGATATGGTTAATCACAATCTAA 57.221 33.333 10.98 2.70 0.00 2.10
1910 1923 8.454106 GTGCATTATGTCTGGATATGGTTAATC 58.546 37.037 0.00 0.00 0.00 1.75
1938 1951 2.633657 CCGCAGTTCAGTGTGTGC 59.366 61.111 4.62 4.62 0.00 4.57
1993 2010 5.949354 CCATTAACATTCTCTTGGTTGGGTA 59.051 40.000 0.00 0.00 0.00 3.69
2090 2107 5.107109 TGATGAACTTGGACGTTTTCATG 57.893 39.130 12.23 6.83 38.51 3.07
2458 2496 0.393808 ACGTATTCGGCTTGGGCATT 60.394 50.000 0.00 0.00 41.85 3.56


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

AutoCloner maintained by Alex Coulton.