Multiple sequence alignment - TraesCS2B01G254200

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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 TraesCS2B01G254200 chr2B 100.000 2549 0 0 1 2549 282314934 282317482 0 4708
1 TraesCS2B01G254200 chr2B 95.869 1985 78 3 566 2549 602077186 602075205 0 3208
2 TraesCS2B01G254200 chr2B 95.523 1988 82 5 564 2549 596962065 596964047 0 3171
3 TraesCS2B01G254200 chr2B 95.514 1984 78 4 566 2549 543889471 543887499 0 3160
4 TraesCS2B01G254200 chr2B 95.093 1997 88 4 554 2549 36241837 36243824 0 3136
5 TraesCS2B01G254200 chr5B 95.635 1993 82 5 557 2549 269389463 269391450 0 3193
6 TraesCS2B01G254200 chr5B 95.810 1981 77 4 567 2547 446193254 446191280 0 3193
7 TraesCS2B01G254200 chr7B 95.626 1989 79 7 562 2549 621924188 621926169 0 3184
8 TraesCS2B01G254200 chr3B 95.665 1984 76 8 566 2549 703251168 703253141 0 3179
9 TraesCS2B01G254200 chr1B 95.514 1984 83 5 566 2549 663786494 663788471 0 3166
10 TraesCS2B01G254200 chr4D 94.545 550 23 4 17 566 127264526 127265068 0 843
11 TraesCS2B01G254200 chr7D 94.364 550 26 3 17 566 531794805 531794261 0 839
12 TraesCS2B01G254200 chr7D 94.022 552 27 3 17 566 23119507 23120054 0 832
13 TraesCS2B01G254200 chr7D 94.011 551 26 5 17 566 360949009 360949553 0 828
14 TraesCS2B01G254200 chr7D 93.841 552 28 5 17 566 372393168 372393715 0 826
15 TraesCS2B01G254200 chrUn 94.192 551 27 4 17 566 112584440 112583894 0 835
16 TraesCS2B01G254200 chr3D 94.192 551 23 5 17 566 529514906 529515448 0 832
17 TraesCS2B01G254200 chr3D 93.852 553 27 5 17 566 562189039 562188491 0 826
18 TraesCS2B01G254200 chr5D 93.056 576 24 9 1 566 121938935 121939504 0 828


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 TraesCS2B01G254200 chr2B 282314934 282317482 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F2 2548
1 TraesCS2B01G254200 chr2B 602075205 602077186 1981 True 3208 3208 95.869 566 2549 1 chr2B.!!$R2 1983
2 TraesCS2B01G254200 chr2B 596962065 596964047 1982 False 3171 3171 95.523 564 2549 1 chr2B.!!$F3 1985
3 TraesCS2B01G254200 chr2B 543887499 543889471 1972 True 3160 3160 95.514 566 2549 1 chr2B.!!$R1 1983
4 TraesCS2B01G254200 chr2B 36241837 36243824 1987 False 3136 3136 95.093 554 2549 1 chr2B.!!$F1 1995
5 TraesCS2B01G254200 chr5B 269389463 269391450 1987 False 3193 3193 95.635 557 2549 1 chr5B.!!$F1 1992
6 TraesCS2B01G254200 chr5B 446191280 446193254 1974 True 3193 3193 95.810 567 2547 1 chr5B.!!$R1 1980
7 TraesCS2B01G254200 chr7B 621924188 621926169 1981 False 3184 3184 95.626 562 2549 1 chr7B.!!$F1 1987
8 TraesCS2B01G254200 chr3B 703251168 703253141 1973 False 3179 3179 95.665 566 2549 1 chr3B.!!$F1 1983
9 TraesCS2B01G254200 chr1B 663786494 663788471 1977 False 3166 3166 95.514 566 2549 1 chr1B.!!$F1 1983
10 TraesCS2B01G254200 chr4D 127264526 127265068 542 False 843 843 94.545 17 566 1 chr4D.!!$F1 549
11 TraesCS2B01G254200 chr7D 531794261 531794805 544 True 839 839 94.364 17 566 1 chr7D.!!$R1 549
12 TraesCS2B01G254200 chr7D 23119507 23120054 547 False 832 832 94.022 17 566 1 chr7D.!!$F1 549
13 TraesCS2B01G254200 chr7D 360949009 360949553 544 False 828 828 94.011 17 566 1 chr7D.!!$F2 549
14 TraesCS2B01G254200 chr7D 372393168 372393715 547 False 826 826 93.841 17 566 1 chr7D.!!$F3 549
15 TraesCS2B01G254200 chrUn 112583894 112584440 546 True 835 835 94.192 17 566 1 chrUn.!!$R1 549
16 TraesCS2B01G254200 chr3D 529514906 529515448 542 False 832 832 94.192 17 566 1 chr3D.!!$F1 549
17 TraesCS2B01G254200 chr3D 562188491 562189039 548 True 826 826 93.852 17 566 1 chr3D.!!$R1 549
18 TraesCS2B01G254200 chr5D 121938935 121939504 569 False 828 828 93.056 1 566 1 chr5D.!!$F1 565

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
44 50 0.114364 TCCTCACACTACTCCAGCCA 59.886 55.0 0.00 0.0 0.00 4.75 F
729 747 0.393077 CAGCCCTTATAGGTGGGACG 59.607 60.0 10.57 0.0 46.15 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1071 0.453793 AGACGAAGACAGGCATCTCG 59.546 55.0 0.0 0.0 0.00 4.04 R
2023 2045 1.120530 ATCTGCCCTAGTGGTTACCG 58.879 55.0 0.0 0.0 36.04 4.02 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
44 50 0.114364 TCCTCACACTACTCCAGCCA 59.886 55.000 0.00 0.00 0.00 4.75
51 57 0.542938 ACTACTCCAGCCAGAGCACA 60.543 55.000 0.58 0.00 43.56 4.57
97 103 1.148310 CAGCACCACCTCACTTAACG 58.852 55.000 0.00 0.00 0.00 3.18
444 461 6.404293 CCCTGGTTAAATTCGGATGTAACTTG 60.404 42.308 15.08 8.88 36.56 3.16
508 526 4.457603 AGTTCGTATGCAAAAGTTATGCCA 59.542 37.500 0.00 0.00 43.16 4.92
509 527 4.614555 TCGTATGCAAAAGTTATGCCAG 57.385 40.909 0.00 0.00 43.16 4.85
524 542 7.731054 AGTTATGCCAGTTTTACAAATTCCAA 58.269 30.769 0.00 0.00 0.00 3.53
538 556 7.486802 ACAAATTCCAAAGAGATTTTGCAAG 57.513 32.000 0.00 0.00 39.22 4.01
541 559 9.211485 CAAATTCCAAAGAGATTTTGCAAGTAT 57.789 29.630 0.00 0.00 33.11 2.12
719 737 3.418684 ACGTTTTGACTCAGCCCTTAT 57.581 42.857 0.00 0.00 0.00 1.73
729 747 0.393077 CAGCCCTTATAGGTGGGACG 59.607 60.000 10.57 0.00 46.15 4.79
736 754 2.288642 TATAGGTGGGACGAGGCGGT 62.289 60.000 0.00 0.00 0.00 5.68
756 774 4.097892 CGGTAGAGGCAGCCAATTTTATTT 59.902 41.667 15.80 0.00 0.00 1.40
773 791 2.081725 TTTAGACCATTGCACGCGTA 57.918 45.000 13.44 0.00 0.00 4.42
926 944 1.381928 CGACGGTGGGAAGCTAGCTA 61.382 60.000 19.70 0.00 0.00 3.32
953 971 2.444256 GCGGGGATGGGAAGCTAGT 61.444 63.158 0.00 0.00 0.00 2.57
1115 1133 2.187958 TGATCGGAGGGTTTCTCACAT 58.812 47.619 0.00 0.00 44.19 3.21
1152 1170 1.334689 CGTCTGTTCTACGTGTGCAGA 60.335 52.381 0.00 4.09 35.66 4.26
1311 1329 3.682696 TGAACTGCAAGAAGAGCATGAT 58.317 40.909 0.00 0.00 41.82 2.45
1563 1581 6.661304 AAGGCATGAATTATGGAGGAATTC 57.339 37.500 0.00 0.00 41.63 2.17
1578 1596 8.348285 TGGAGGAATTCGTAATCTTGAAATTT 57.652 30.769 0.00 0.00 0.00 1.82
1713 1732 7.330208 ACTTTTGATCAATGAAATGCAGCTAAC 59.670 33.333 9.40 0.00 0.00 2.34
1723 1742 7.320443 TGAAATGCAGCTAACGAATTATTCT 57.680 32.000 3.34 0.00 0.00 2.40
1956 1978 4.914177 AAATGAAGGGTGGAAAATGCAT 57.086 36.364 0.00 0.00 0.00 3.96
2037 2059 2.497770 CGCCGGTAACCACTAGGG 59.502 66.667 1.90 0.00 44.81 3.53
2104 2126 7.498900 ACATAGTGAGACTGTGAAATTTGTCAA 59.501 33.333 7.40 0.00 39.34 3.18
2211 2233 0.179092 GCGTTGGTAACCGCTAGGAT 60.179 55.000 0.00 0.00 46.08 3.24
2390 2415 1.801771 GTATGTTTGCACTGCCACGTA 59.198 47.619 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 50 2.224066 ACTGCGAAGTTAAGTGTGCTCT 60.224 45.455 0.00 0.00 0.00 4.09
51 57 5.401531 TGGATAGAACTGCGAAGTTAAGT 57.598 39.130 9.31 0.00 31.35 2.24
412 429 6.371595 TCCGAATTTAACCAGGGTAACTAA 57.628 37.500 0.00 0.00 0.00 2.24
413 430 6.070078 ACATCCGAATTTAACCAGGGTAACTA 60.070 38.462 0.00 0.00 0.00 2.24
414 431 4.914177 TCCGAATTTAACCAGGGTAACT 57.086 40.909 0.00 0.00 0.00 2.24
418 435 3.732048 ACATCCGAATTTAACCAGGGT 57.268 42.857 0.00 0.00 0.00 4.34
484 502 5.048364 TGGCATAACTTTTGCATACGAACTT 60.048 36.000 6.55 0.00 41.95 2.66
509 527 9.650371 GCAAAATCTCTTTGGAATTTGTAAAAC 57.350 29.630 0.00 0.00 32.03 2.43
524 542 8.547967 TTTCGACTATACTTGCAAAATCTCTT 57.452 30.769 0.00 0.00 0.00 2.85
711 729 0.263765 TCGTCCCACCTATAAGGGCT 59.736 55.000 0.00 0.00 45.07 5.19
719 737 2.898920 CTACCGCCTCGTCCCACCTA 62.899 65.000 0.00 0.00 0.00 3.08
729 747 4.228567 GGCTGCCTCTACCGCCTC 62.229 72.222 12.43 0.00 39.42 4.70
736 754 6.546034 GGTCTAAATAAAATTGGCTGCCTCTA 59.454 38.462 21.03 5.70 0.00 2.43
756 774 0.804544 GCTACGCGTGCAATGGTCTA 60.805 55.000 24.59 0.00 0.00 2.59
909 927 0.753262 CATAGCTAGCTTCCCACCGT 59.247 55.000 24.88 0.00 0.00 4.83
939 957 1.559682 TCCACAACTAGCTTCCCATCC 59.440 52.381 0.00 0.00 0.00 3.51
941 959 1.561542 CCTCCACAACTAGCTTCCCAT 59.438 52.381 0.00 0.00 0.00 4.00
1053 1071 0.453793 AGACGAAGACAGGCATCTCG 59.546 55.000 0.00 0.00 0.00 4.04
1115 1133 1.203052 GACGATTGTGGTTCCTCGGTA 59.797 52.381 0.00 0.00 35.52 4.02
1152 1170 2.706190 CCCGATTCTTACCCCATTCTCT 59.294 50.000 0.00 0.00 0.00 3.10
1196 1214 1.281867 ACCGATTGCTCAAAGATCCCA 59.718 47.619 0.00 0.00 0.00 4.37
1222 1240 1.069703 CACCTGCATGAACACAGAACG 60.070 52.381 0.00 0.00 35.90 3.95
1311 1329 1.213275 CAGCATGCGCAACCATTCA 59.787 52.632 17.11 0.00 42.27 2.57
1723 1742 8.927675 TTTCTAACCTTAATTGTTTGGCTCTA 57.072 30.769 0.00 0.00 0.00 2.43
1973 1995 2.264794 CTTGGGTTCGAGTCCCCG 59.735 66.667 20.23 10.81 44.44 5.73
2023 2045 1.120530 ATCTGCCCTAGTGGTTACCG 58.879 55.000 0.00 0.00 36.04 4.02
2037 2059 1.881973 TGTCAAACTCTTGCCATCTGC 59.118 47.619 0.00 0.00 41.77 4.26
2145 2167 1.343465 GTCTTGGGTTCGAGTCCTCAA 59.657 52.381 8.28 9.27 0.00 3.02
2148 2170 1.533469 CGGTCTTGGGTTCGAGTCCT 61.533 60.000 8.28 0.00 32.56 3.85
2211 2233 4.263462 ACCATGTCAAACTCTTGCCATCTA 60.263 41.667 0.00 0.00 28.75 1.98
2234 2256 9.090103 CTCACTATGTATACATTCCTTCCCTAA 57.910 37.037 22.90 0.94 37.76 2.69
2390 2415 3.577805 AGTGCCACTCTAACCAAAACT 57.422 42.857 0.00 0.00 0.00 2.66
2502 2531 3.787001 GGGGGTGAGAAGCCCTCG 61.787 72.222 12.46 0.00 44.92 4.63


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

AutoCloner maintained by Alex Coulton.