Multiple sequence alignment - TraesCS2D01G191700

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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 TraesCS2D01G191700 chr2D 100.000 2540 0 0 1 2540 135605672 135603133 0 4691
1 TraesCS2D01G191700 chr2B 96.973 2544 71 6 1 2540 193395191 193392650 0 4266
2 TraesCS2D01G191700 chr2A 94.192 2548 112 11 1 2540 143727996 143725477 0 3853


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 TraesCS2D01G191700 chr2D 135603133 135605672 2539 True 4691 4691 100.000 1 2540 1 chr2D.!!$R1 2539
1 TraesCS2D01G191700 chr2B 193392650 193395191 2541 True 4266 4266 96.973 1 2540 1 chr2B.!!$R1 2539
2 TraesCS2D01G191700 chr2A 143725477 143727996 2519 True 3853 3853 94.192 1 2540 1 chr2A.!!$R1 2539

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
428 429 0.463116 ATGGGGTTAATCCACGCGAC 60.463 55.0 15.93 0.0 43.99 5.19 F
995 1000 0.754957 TGTGCCACTCCCAACAAAGG 60.755 55.0 0.00 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1325 0.181350 CTGGCCCTCATAGGTTGGAC 59.819 60.0 0.00 0.0 31.93 4.02 R
1832 1839 0.467384 AGAGCAGCGCTAATCACCAT 59.533 50.0 10.99 0.0 39.88 3.55 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
426 427 1.099689 AAATGGGGTTAATCCACGCG 58.900 50.000 7.18 3.53 43.99 6.01
428 429 0.463116 ATGGGGTTAATCCACGCGAC 60.463 55.000 15.93 0.00 43.99 5.19
462 463 2.146342 GCTGAACAAAGTCTAGCAGCA 58.854 47.619 0.00 0.00 45.78 4.41
524 526 6.681777 ACTTCTTTTCCACATACATTTCTGC 58.318 36.000 0.00 0.00 0.00 4.26
530 532 7.517614 TTTCCACATACATTTCTGCACTAAA 57.482 32.000 0.00 0.00 0.00 1.85
531 533 7.517614 TTCCACATACATTTCTGCACTAAAA 57.482 32.000 0.00 0.00 0.00 1.52
566 568 9.722056 GAAATATACAAACATGAACAGTGGATC 57.278 33.333 0.00 0.00 0.00 3.36
575 577 3.041211 TGAACAGTGGATCCCTAGATGG 58.959 50.000 9.90 0.00 30.90 3.51
596 598 3.311966 GCAGGTGAGCAAATCAGAAAAC 58.688 45.455 0.00 0.00 39.07 2.43
640 642 8.715088 GGTTTTTCAAACTGTACTACGTCATAT 58.285 33.333 0.00 0.00 0.00 1.78
744 748 5.871396 ACGGGACAGTATACATGAAAGAT 57.129 39.130 5.50 0.00 0.00 2.40
785 789 2.738521 CCAACGAGCTGACCACCG 60.739 66.667 0.00 0.00 0.00 4.94
995 1000 0.754957 TGTGCCACTCCCAACAAAGG 60.755 55.000 0.00 0.00 0.00 3.11
998 1003 1.342474 TGCCACTCCCAACAAAGGAAA 60.342 47.619 0.00 0.00 31.49 3.13
999 1004 1.760029 GCCACTCCCAACAAAGGAAAA 59.240 47.619 0.00 0.00 31.49 2.29
1041 1048 9.255304 GAAGCAGAAGAACAGATATTAGGTAAG 57.745 37.037 0.00 0.00 0.00 2.34
1059 1066 1.509923 GCAAGGTGATGAAGCTGGC 59.490 57.895 0.00 0.00 45.76 4.85
1318 1325 0.321671 TCCTCCAACTGCTTCCTTCG 59.678 55.000 0.00 0.00 0.00 3.79
1538 1545 3.306917 TGATTTGAGCCTGCATTTGTG 57.693 42.857 0.00 0.00 0.00 3.33
1635 1642 6.890268 GGGAATAAGATTCCAAACTTGTACCT 59.110 38.462 17.75 0.00 40.32 3.08
1650 1657 2.903784 TGTACCTACAGTTGCAGGTGAT 59.096 45.455 13.20 0.00 44.93 3.06
1656 1663 2.146342 ACAGTTGCAGGTGATTTCTCG 58.854 47.619 4.49 0.00 0.00 4.04
1832 1839 2.526304 AACTTTAGTCAGCGCTGTCA 57.474 45.000 34.70 16.24 0.00 3.58
1845 1852 0.305922 GCTGTCATGGTGATTAGCGC 59.694 55.000 0.00 0.00 32.61 5.92
1878 1886 6.438425 AGGACTCCAATTCAAATTTATGTGCT 59.562 34.615 0.00 0.00 0.00 4.40
2179 2190 8.033626 TGCATGAATACAAGCAAAATAATGTGA 58.966 29.630 0.00 0.00 45.47 3.58
2437 2449 1.339151 ACTTCCATGAGAACGCTTCCC 60.339 52.381 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
369 370 8.463930 TTCCAGTTGTTTAGTTTGATTGAGAT 57.536 30.769 0.00 0.00 0.00 2.75
371 372 7.649306 CCTTTCCAGTTGTTTAGTTTGATTGAG 59.351 37.037 0.00 0.00 0.00 3.02
385 386 8.531146 CATTTAATATGAACCCTTTCCAGTTGT 58.469 33.333 0.00 0.00 0.00 3.32
387 388 7.125659 CCCATTTAATATGAACCCTTTCCAGTT 59.874 37.037 0.00 0.00 0.00 3.16
426 427 4.391830 TGTTCAGCGTCAATAATGAAGGTC 59.608 41.667 0.00 0.00 42.56 3.85
428 429 4.944962 TGTTCAGCGTCAATAATGAAGG 57.055 40.909 0.00 0.00 37.30 3.46
524 526 9.868277 TTGTATATTTCCTTGCCATTTTTAGTG 57.132 29.630 0.00 0.00 0.00 2.74
530 532 8.538701 TCATGTTTGTATATTTCCTTGCCATTT 58.461 29.630 0.00 0.00 0.00 2.32
531 533 8.076910 TCATGTTTGTATATTTCCTTGCCATT 57.923 30.769 0.00 0.00 0.00 3.16
566 568 1.340399 TGCTCACCTGCCATCTAGGG 61.340 60.000 0.00 0.00 39.71 3.53
575 577 3.311966 GTTTTCTGATTTGCTCACCTGC 58.688 45.455 0.00 0.00 0.00 4.85
596 598 7.279981 TGAAAAACCTCATAGTATGATTGACCG 59.720 37.037 13.22 1.06 38.85 4.79
669 673 2.995746 TCCTGATCAGATATGGGCCTT 58.004 47.619 24.62 0.00 0.00 4.35
785 789 0.788391 CGTACCAGTTTCCTTGTCGC 59.212 55.000 0.00 0.00 0.00 5.19
995 1000 4.034285 TCAGGTCCCCTCTTCATTTTTC 57.966 45.455 0.00 0.00 0.00 2.29
998 1003 2.291217 GCTTCAGGTCCCCTCTTCATTT 60.291 50.000 0.00 0.00 0.00 2.32
999 1004 1.283321 GCTTCAGGTCCCCTCTTCATT 59.717 52.381 0.00 0.00 0.00 2.57
1041 1048 1.509923 GCCAGCTTCATCACCTTGC 59.490 57.895 0.00 0.00 0.00 4.01
1059 1066 2.594962 GGTATTGTCATCGGCGCGG 61.595 63.158 8.83 8.94 0.00 6.46
1318 1325 0.181350 CTGGCCCTCATAGGTTGGAC 59.819 60.000 0.00 0.00 31.93 4.02
1572 1579 6.623486 TGATGCAAAATATTGACTTCACAGG 58.377 36.000 0.00 0.00 38.94 4.00
1635 1642 3.325870 CGAGAAATCACCTGCAACTGTA 58.674 45.455 0.00 0.00 0.00 2.74
1650 1657 5.890424 AGTTTTGAAACTTGTCCGAGAAA 57.110 34.783 3.37 0.00 46.52 2.52
1656 1663 8.751302 TTGTTTTCTAGTTTTGAAACTTGTCC 57.249 30.769 13.71 4.25 46.52 4.02
1751 1758 7.226720 GTGGATTGTATGTATGGTTCCTACTTG 59.773 40.741 0.00 0.00 0.00 3.16
1832 1839 0.467384 AGAGCAGCGCTAATCACCAT 59.533 50.000 10.99 0.00 39.88 3.55
1845 1852 4.478206 TGAATTGGAGTCCTTAGAGCAG 57.522 45.455 11.33 0.00 0.00 4.24
1878 1886 6.627395 AATAACGTTTGGTGATCAAGTGAA 57.373 33.333 5.91 0.00 36.62 3.18
2123 2134 4.943705 TGAGCCAATTAACATCCTGTCTTC 59.056 41.667 0.00 0.00 0.00 2.87
2143 2154 5.729732 GCTTGTATTCATGCACACTGATGAG 60.730 44.000 5.48 0.00 42.06 2.90
2212 2224 6.723339 TCCACATATGCATCCATTGATATGA 58.277 36.000 0.19 0.00 34.01 2.15
2437 2449 4.803613 TCTGCATATACAGTGTAAGCGTTG 59.196 41.667 7.16 6.89 38.84 4.10


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

AutoCloner maintained by Alex Coulton.