Multiple sequence alignment - TraesCS2B01G210500

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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 TraesCS2B01G210500 chr2B 100.000 2540 0 0 1 2540 193395190 193392651 0 4691
1 TraesCS2B01G210500 chr2D 96.971 2542 71 6 1 2540 135605671 135603134 0 4263
2 TraesCS2B01G210500 chr2A 94.111 2547 114 10 1 2540 143727995 143725478 0 3840


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 TraesCS2B01G210500 chr2B 193392651 193395190 2539 True 4691 4691 100.000 1 2540 1 chr2B.!!$R1 2539
1 TraesCS2B01G210500 chr2D 135603134 135605671 2537 True 4263 4263 96.971 1 2540 1 chr2D.!!$R1 2539
2 TraesCS2B01G210500 chr2A 143725478 143727995 2517 True 3840 3840 94.111 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
994 998 1.331214 ATTGTGCCACTCCCAACAAG 58.669 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1882 1.197721 GTTTGGTGATCAAGTGAGGCG 59.802 52.381 0.0 0.0 36.62 5.52 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
255 256 2.697654 CCTGAGCCTCAAGAGACAAAG 58.302 52.381 0.00 0.00 0.00 2.77
352 353 2.667473 TCTAGGCCGTAGCACTTTTC 57.333 50.000 0.00 0.00 42.56 2.29
441 442 4.759693 TCCACGCAAACTTCATTATTGACT 59.240 37.500 0.00 0.00 0.00 3.41
467 468 6.446318 TGAACAAAATCTAGCAGCGAAAAAT 58.554 32.000 0.00 0.00 0.00 1.82
472 473 8.296713 ACAAAATCTAGCAGCGAAAAATAAGAA 58.703 29.630 0.00 0.00 0.00 2.52
543 544 5.188434 TCTGAACTAATCATGGCAAGGAAG 58.812 41.667 0.00 0.00 37.44 3.46
549 550 6.534634 ACTAATCATGGCAAGGAAGTATACC 58.465 40.000 0.00 0.00 0.00 2.73
745 748 4.464951 ACGGGACAGTATACATGAAAGACA 59.535 41.667 5.50 0.00 0.00 3.41
756 759 3.070446 ACATGAAAGACACACCTTACGGA 59.930 43.478 0.00 0.00 0.00 4.69
762 765 3.841643 AGACACACCTTACGGAATAACG 58.158 45.455 0.00 0.00 40.31 3.18
836 839 6.471146 ACTAGGAAAATAGATAGGCATGCAG 58.529 40.000 21.36 4.50 0.00 4.41
877 881 6.666113 TCCACTTTAAACTCCTGGAAACTTTT 59.334 34.615 0.00 0.00 0.00 2.27
884 888 4.542697 ACTCCTGGAAACTTTTGCCTTTA 58.457 39.130 0.00 0.00 0.00 1.85
962 966 6.442564 AGGACTACCATCATAACACAAACCTA 59.557 38.462 0.00 0.00 38.94 3.08
994 998 1.331214 ATTGTGCCACTCCCAACAAG 58.669 50.000 0.00 0.00 0.00 3.16
1041 1047 9.771534 GAAGCAGAAGAACAGATATTAGGTAAT 57.228 33.333 0.00 0.00 0.00 1.89
1083 1089 1.593006 GCCGATGACAATACCTCAACG 59.407 52.381 0.00 0.00 34.65 4.10
1104 1110 1.105759 CATGGCTAAAGCTGGGCCTC 61.106 60.000 20.47 0.00 45.45 4.70
1311 1317 0.321298 TACGCTTTCCTCCAACTGCC 60.321 55.000 0.00 0.00 0.00 4.85
1455 1461 4.202264 GCAGTAGAGGAAGCTGCCTATTTA 60.202 45.833 15.35 3.98 46.93 1.40
1492 1498 4.384056 CTTCAAAGCAAGTCTTCAGGAGA 58.616 43.478 0.00 0.00 32.88 3.71
1872 1878 7.233348 TGCTCTAAGGACTCCAATTCAAATTTT 59.767 33.333 0.00 0.00 0.00 1.82
1876 1882 9.305925 CTAAGGACTCCAATTCAAATTTTATGC 57.694 33.333 0.00 0.00 0.00 3.14
1951 1957 7.809331 CACATTTGCTGCTTTATCAAAGACTTA 59.191 33.333 0.00 0.00 41.02 2.24
2111 2119 9.631452 CATATCTCAAGTCGTACATGTGAATAT 57.369 33.333 9.11 0.00 0.00 1.28
2127 2135 9.494479 CATGTGAATATGTGTATTCTTGTCAAC 57.506 33.333 8.97 0.67 44.24 3.18
2197 2206 8.924511 AATAGTGTGGAAGAATCAGAGAAAAA 57.075 30.769 0.00 0.00 0.00 1.94
2233 2242 5.503662 TTGACATGTCAATGGATGCATAC 57.496 39.130 32.36 0.42 43.90 2.39
2253 2262 6.398517 GCATACGTGGAAAGAACAAAATTTCG 60.399 38.462 0.00 0.00 36.49 3.46
2301 2310 3.282021 TGGCATAGGAATCTTCTTGTGC 58.718 45.455 13.10 13.10 45.91 4.57
2447 2457 2.000447 GAGAACGCTTCCAACGCTTAT 59.000 47.619 0.00 0.00 0.00 1.73
2523 2533 6.097696 TCCGAAATACATCACATGTCCTTCTA 59.902 38.462 0.00 0.00 43.67 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 256 2.929531 TCTCATGCACGTTCTCTCTC 57.070 50.000 0.00 0.00 0.00 3.20
352 353 7.493645 TTGATTGACAATATAGCACTCTCAGTG 59.506 37.037 0.00 0.00 40.16 3.66
441 442 3.925379 TCGCTGCTAGATTTTGTTCAGA 58.075 40.909 0.00 0.00 0.00 3.27
451 452 5.008118 GCCTTCTTATTTTTCGCTGCTAGAT 59.992 40.000 0.00 0.00 0.00 1.98
467 468 3.187637 CGAACGGTGAAATTGCCTTCTTA 59.812 43.478 0.00 0.00 0.00 2.10
472 473 0.872388 GTCGAACGGTGAAATTGCCT 59.128 50.000 0.00 0.00 0.00 4.75
543 544 6.038271 GGAATCCACTGTTCATGTTGGTATAC 59.962 42.308 0.00 0.00 0.00 1.47
549 550 5.491070 TCTAGGAATCCACTGTTCATGTTG 58.509 41.667 0.61 0.00 0.00 3.33
671 674 4.237843 TCTTTCCTGATCAGATATGGGCT 58.762 43.478 24.62 0.00 0.00 5.19
721 724 5.041940 GTCTTTCATGTATACTGTCCCGTC 58.958 45.833 4.17 0.00 0.00 4.79
756 759 2.812011 AGCTCGTTGGCTTTTCGTTATT 59.188 40.909 0.00 0.00 39.86 1.40
762 765 0.238553 GGTCAGCTCGTTGGCTTTTC 59.761 55.000 0.00 0.00 41.00 2.29
836 839 5.736951 AAGTGGATCAGGATATGCTAGTC 57.263 43.478 0.00 0.00 0.00 2.59
877 881 3.704061 GCAATAATTCAGGGGTAAAGGCA 59.296 43.478 0.00 0.00 0.00 4.75
884 888 3.099141 CAAGTGGCAATAATTCAGGGGT 58.901 45.455 0.00 0.00 0.00 4.95
994 998 2.092699 CAGGTCCCCTCTTCATCTTTCC 60.093 54.545 0.00 0.00 0.00 3.13
1041 1047 1.338105 CGACCAGCTTCATCACCTTGA 60.338 52.381 0.00 0.00 0.00 3.02
1083 1089 2.789715 GCCCAGCTTTAGCCATGGC 61.790 63.158 30.12 30.12 43.38 4.40
1104 1110 0.644331 CTTCGCTTCTCAGTGCATCG 59.356 55.000 0.00 0.00 0.00 3.84
1311 1317 3.072184 CCCTCATAGGTTGGATGAAGGAG 59.928 52.174 0.00 0.00 37.16 3.69
1455 1461 2.856000 AAGCTCCCAGGCCACACT 60.856 61.111 5.01 0.00 0.00 3.55
1492 1498 1.067295 TCCTCTGGTTGCTTCATGGT 58.933 50.000 0.00 0.00 0.00 3.55
1555 1561 8.522830 ACTTCACAGAAAATGTTTATACATGGG 58.477 33.333 0.00 0.00 44.14 4.00
1872 1878 1.473257 GGTGATCAAGTGAGGCGCATA 60.473 52.381 10.83 0.00 0.00 3.14
1876 1882 1.197721 GTTTGGTGATCAAGTGAGGCG 59.802 52.381 0.00 0.00 36.62 5.52
1951 1957 8.776470 CAAACTTCCAATGCATAGAAATGTTTT 58.224 29.630 17.86 11.05 35.38 2.43
2111 2119 4.055360 CCTGTCGTTGACAAGAATACACA 58.945 43.478 0.89 0.00 42.26 3.72
2127 2135 3.605634 TGGACCAATTAACATCCTGTCG 58.394 45.455 0.00 0.00 32.06 4.35
2146 2154 4.732647 GCTTGTATTCATGCACACTGATGG 60.733 45.833 5.48 0.00 42.06 3.51
2218 2227 2.560504 TCCACGTATGCATCCATTGAC 58.439 47.619 0.19 0.00 32.85 3.18
2233 2242 5.942325 AACGAAATTTTGTTCTTTCCACG 57.058 34.783 16.64 2.46 28.76 4.94
2301 2310 3.747529 CCCCTTGCTTGTTTTTATGCTTG 59.252 43.478 0.00 0.00 0.00 4.01
2447 2457 6.828273 AGCCAACAATTTCTGCATATACAGTA 59.172 34.615 2.85 0.00 38.84 2.74


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

AutoCloner maintained by Alex Coulton.