Multiple sequence alignment - TraesCS6A01G202300

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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 TraesCS6A01G202300 chr6A 100.000 3110 0 0 1 3110 338112131 338115240 0.000000e+00 5744.0
1 TraesCS6A01G202300 chr6A 92.072 555 35 8 3 555 182010475 182011022 0.000000e+00 773.0
2 TraesCS6A01G202300 chr6A 89.109 606 54 9 3 601 328369348 328369948 0.000000e+00 743.0
3 TraesCS6A01G202300 chr4A 98.331 2517 37 4 597 3110 507908520 507911034 0.000000e+00 4410.0
4 TraesCS6A01G202300 chr4A 90.148 609 47 9 3 601 384985002 384984397 0.000000e+00 780.0
5 TraesCS6A01G202300 chr4A 88.889 621 55 11 3 614 384993015 384992400 0.000000e+00 752.0
6 TraesCS6A01G202300 chr4A 85.333 75 11 0 527 601 326872063 326871989 9.250000e-11 78.7
7 TraesCS6A01G202300 chr5A 97.395 1958 33 3 1154 3110 601209016 601207076 0.000000e+00 3317.0
8 TraesCS6A01G202300 chr5A 97.087 1957 36 2 1154 3110 3992175 3994110 0.000000e+00 3278.0
9 TraesCS6A01G202300 chr5A 95.009 561 22 5 601 1156 601209619 601209060 0.000000e+00 876.0
10 TraesCS6A01G202300 chr5A 95.710 303 9 4 601 900 3983158 3983459 4.660000e-133 484.0
11 TraesCS6A01G202300 chr5A 97.318 261 7 0 896 1156 3991871 3992131 7.910000e-121 444.0
12 TraesCS6A01G202300 chr2A 97.343 1957 34 1 1154 3110 710249203 710251141 0.000000e+00 3310.0
13 TraesCS6A01G202300 chr2A 96.250 560 17 4 600 1156 710248601 710249159 0.000000e+00 915.0
14 TraesCS6A01G202300 chr2A 90.017 601 55 4 3 601 310749729 310749132 0.000000e+00 773.0
15 TraesCS6A01G202300 chr2A 89.684 601 57 4 3 601 310758093 310757496 0.000000e+00 761.0
16 TraesCS6A01G202300 chr2A 89.465 598 54 7 3 595 222974847 222975440 0.000000e+00 747.0
17 TraesCS6A01G202300 chr2A 89.055 603 57 7 3 601 384100349 384100946 0.000000e+00 739.0
18 TraesCS6A01G202300 chr7A 97.191 1958 31 3 1154 3110 664221147 664219213 0.000000e+00 3290.0
19 TraesCS6A01G202300 chr7A 94.662 562 16 5 598 1156 664221741 664221191 0.000000e+00 859.0
20 TraesCS6A01G202300 chr3B 96.797 1967 52 2 1154 3110 82367469 82365504 0.000000e+00 3273.0
21 TraesCS6A01G202300 chr3B 93.153 555 28 6 606 1156 82368061 82367513 0.000000e+00 806.0
22 TraesCS6A01G202300 chr3B 88.927 578 40 9 599 1156 76135570 76134997 0.000000e+00 691.0
23 TraesCS6A01G202300 chr4B 96.985 1957 38 2 1154 3110 531077985 531079920 0.000000e+00 3267.0
24 TraesCS6A01G202300 chr4B 95.552 562 21 4 598 1156 531077381 531077941 0.000000e+00 896.0
25 TraesCS6A01G202300 chr6B 95.927 1964 70 7 1154 3110 92572457 92574417 0.000000e+00 3175.0
26 TraesCS6A01G202300 chr6B 95.197 1957 73 4 1154 3110 612966408 612968343 0.000000e+00 3073.0
27 TraesCS6A01G202300 chr6B 92.403 566 33 10 597 1156 612965803 612966364 0.000000e+00 798.0
28 TraesCS6A01G202300 chr6B 94.094 254 15 0 903 1156 92572160 92572413 1.350000e-103 387.0
29 TraesCS6A01G202300 chr1A 90.972 576 40 11 3 573 317163430 317162862 0.000000e+00 765.0
30 TraesCS6A01G202300 chr7B 89.194 583 38 12 595 1156 665248958 665248380 0.000000e+00 704.0


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 TraesCS6A01G202300 chr6A 338112131 338115240 3109 False 5744.0 5744 100.0000 1 3110 1 chr6A.!!$F3 3109
1 TraesCS6A01G202300 chr6A 182010475 182011022 547 False 773.0 773 92.0720 3 555 1 chr6A.!!$F1 552
2 TraesCS6A01G202300 chr6A 328369348 328369948 600 False 743.0 743 89.1090 3 601 1 chr6A.!!$F2 598
3 TraesCS6A01G202300 chr4A 507908520 507911034 2514 False 4410.0 4410 98.3310 597 3110 1 chr4A.!!$F1 2513
4 TraesCS6A01G202300 chr4A 384984397 384985002 605 True 780.0 780 90.1480 3 601 1 chr4A.!!$R2 598
5 TraesCS6A01G202300 chr4A 384992400 384993015 615 True 752.0 752 88.8890 3 614 1 chr4A.!!$R3 611
6 TraesCS6A01G202300 chr5A 601207076 601209619 2543 True 2096.5 3317 96.2020 601 3110 2 chr5A.!!$R1 2509
7 TraesCS6A01G202300 chr5A 3991871 3994110 2239 False 1861.0 3278 97.2025 896 3110 2 chr5A.!!$F2 2214
8 TraesCS6A01G202300 chr2A 710248601 710251141 2540 False 2112.5 3310 96.7965 600 3110 2 chr2A.!!$F3 2510
9 TraesCS6A01G202300 chr2A 310749132 310749729 597 True 773.0 773 90.0170 3 601 1 chr2A.!!$R1 598
10 TraesCS6A01G202300 chr2A 310757496 310758093 597 True 761.0 761 89.6840 3 601 1 chr2A.!!$R2 598
11 TraesCS6A01G202300 chr2A 222974847 222975440 593 False 747.0 747 89.4650 3 595 1 chr2A.!!$F1 592
12 TraesCS6A01G202300 chr2A 384100349 384100946 597 False 739.0 739 89.0550 3 601 1 chr2A.!!$F2 598
13 TraesCS6A01G202300 chr7A 664219213 664221741 2528 True 2074.5 3290 95.9265 598 3110 2 chr7A.!!$R1 2512
14 TraesCS6A01G202300 chr3B 82365504 82368061 2557 True 2039.5 3273 94.9750 606 3110 2 chr3B.!!$R2 2504
15 TraesCS6A01G202300 chr3B 76134997 76135570 573 True 691.0 691 88.9270 599 1156 1 chr3B.!!$R1 557
16 TraesCS6A01G202300 chr4B 531077381 531079920 2539 False 2081.5 3267 96.2685 598 3110 2 chr4B.!!$F1 2512
17 TraesCS6A01G202300 chr6B 612965803 612968343 2540 False 1935.5 3073 93.8000 597 3110 2 chr6B.!!$F2 2513
18 TraesCS6A01G202300 chr6B 92572160 92574417 2257 False 1781.0 3175 95.0105 903 3110 2 chr6B.!!$F1 2207
19 TraesCS6A01G202300 chr1A 317162862 317163430 568 True 765.0 765 90.9720 3 573 1 chr1A.!!$R1 570
20 TraesCS6A01G202300 chr7B 665248380 665248958 578 True 704.0 704 89.1940 595 1156 1 chr7B.!!$R1 561

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
466 480 0.908910 TGAGGTGCACCGGTATGATT 59.091 50.000 29.68 10.18 42.08 2.57 F
1113 1169 1.065273 ATTAATCGACGGCTCGCGT 59.935 52.632 5.77 0.00 39.96 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2234 0.467384 GAGCTGCCTCCTATTGAGCA 59.533 55.0 0.00 0.0 39.98 4.26 R
2732 2868 1.595466 GCAAGAGCATCCTGATGAGG 58.405 55.0 11.23 0.0 41.20 3.86 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
64 67 3.600388 AGAATGACGATGAGAAACACCC 58.400 45.455 0.00 0.00 0.00 4.61
224 236 8.759782 AGAATAACTCCGGAAAGATTAGAAGAA 58.240 33.333 5.23 0.00 0.00 2.52
466 480 0.908910 TGAGGTGCACCGGTATGATT 59.091 50.000 29.68 10.18 42.08 2.57
544 560 5.181748 CACCGGAGAAGAAAGAGAATGAAT 58.818 41.667 9.46 0.00 0.00 2.57
547 563 7.334421 CACCGGAGAAGAAAGAGAATGAATAAA 59.666 37.037 9.46 0.00 0.00 1.40
570 586 1.275291 TGAACTTGAGGCTCCGTTAGG 59.725 52.381 12.86 0.00 39.46 2.69
582 598 2.022195 TCCGTTAGGATCTTCGTGAGG 58.978 52.381 0.00 0.00 42.75 3.86
584 600 2.426024 CCGTTAGGATCTTCGTGAGGAA 59.574 50.000 0.00 0.00 41.02 3.36
595 611 4.466370 TCTTCGTGAGGAACACCAGATAAT 59.534 41.667 0.00 0.00 45.73 1.28
663 679 4.409218 GAGCGCACGGTACCACGA 62.409 66.667 19.76 0.00 37.61 4.35
930 986 1.346062 CTCGTCATCCTGGATCCCAT 58.654 55.000 9.90 0.00 30.82 4.00
1095 1151 3.005539 GGAGAGGGAGGTGCAGCA 61.006 66.667 19.63 0.00 0.00 4.41
1100 1156 1.849039 AGAGGGAGGTGCAGCATTAAT 59.151 47.619 19.63 0.00 0.00 1.40
1113 1169 1.065273 ATTAATCGACGGCTCGCGT 59.935 52.632 5.77 0.00 39.96 6.01
1178 1280 2.927856 TTCCCAAGCCAGCTCGGA 60.928 61.111 0.00 1.21 36.56 4.55
1182 1284 4.379243 CAAGCCAGCTCGGACCGT 62.379 66.667 14.79 0.00 36.56 4.83
1185 1287 4.681978 GCCAGCTCGGACCGTTGT 62.682 66.667 14.79 0.00 36.56 3.32
1390 1492 5.105554 TGAGCTTCACCAAATACTCTCTCTC 60.106 44.000 0.00 0.00 0.00 3.20
1432 1564 5.946486 TCTCTCTACCTATCTCTTCATGCA 58.054 41.667 0.00 0.00 0.00 3.96
1714 1847 4.846779 TGGCATTGTTTGTCTCTTTACC 57.153 40.909 0.00 0.00 0.00 2.85
2080 2214 1.203523 CTCAACTCCTACTTGCGCTCT 59.796 52.381 9.73 0.00 0.00 4.09
2100 2234 3.331889 TCTGCCTCTTCCTCCTTTTCATT 59.668 43.478 0.00 0.00 0.00 2.57
2519 2653 2.362717 TGTGGTGTACGTCACTCATCAA 59.637 45.455 16.02 0.00 45.50 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.661968 AGAAGAGTTTCTTTTAAATCTTGCCC 58.338 34.615 4.10 0.0 41.08 5.36
64 67 3.627577 CCGGAGTATCTCAACAATTTGGG 59.372 47.826 0.00 0.0 34.04 4.12
184 195 9.162764 CCGGAGTTATTCTCAAATTCTTTTCTA 57.837 33.333 0.00 0.0 44.40 2.10
185 196 7.883311 TCCGGAGTTATTCTCAAATTCTTTTCT 59.117 33.333 0.00 0.0 44.40 2.52
359 373 4.021229 TCCACTCTGCTTTCGTAATCCTA 58.979 43.478 0.00 0.0 0.00 2.94
466 480 5.920903 TCCTTTCCTCGTTTCAGAAGTTTA 58.079 37.500 0.00 0.0 0.00 2.01
544 560 3.260884 ACGGAGCCTCAAGTTCATCTTTA 59.739 43.478 0.00 0.0 33.63 1.85
547 563 1.270907 ACGGAGCCTCAAGTTCATCT 58.729 50.000 0.00 0.0 0.00 2.90
577 593 7.275920 AGATGTTATTATCTGGTGTTCCTCAC 58.724 38.462 0.00 0.0 36.12 3.51
1178 1280 1.271656 CGAGGAAGAGGTAACAACGGT 59.728 52.381 0.00 0.0 41.41 4.83
1182 1284 0.245539 CGGCGAGGAAGAGGTAACAA 59.754 55.000 0.00 0.0 41.41 2.83
1185 1287 2.718073 GGCGGCGAGGAAGAGGTAA 61.718 63.158 12.98 0.0 0.00 2.85
1390 1492 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.0 0.00 3.20
1432 1564 1.011595 TTACAGAGAGGGAGGAGGCT 58.988 55.000 0.00 0.0 0.00 4.58
1714 1847 9.214953 GATTTAAACATGAGAAATAGCAGAACG 57.785 33.333 0.00 0.0 0.00 3.95
2080 2214 3.424703 CAATGAAAAGGAGGAAGAGGCA 58.575 45.455 0.00 0.0 0.00 4.75
2100 2234 0.467384 GAGCTGCCTCCTATTGAGCA 59.533 55.000 0.00 0.0 39.98 4.26
2173 2307 1.643868 GAATCGCCATCGTGCACCAA 61.644 55.000 12.15 0.0 36.96 3.67
2196 2330 3.213206 AGTTGCAGATTCCTGTTGTCA 57.787 42.857 0.00 0.0 42.35 3.58
2468 2602 2.493278 GCCAAAGCCTCAAGAAAGCATA 59.507 45.455 0.00 0.0 0.00 3.14
2519 2653 4.947388 TCAGCAACTGGTAAAAACTCAACT 59.053 37.500 0.00 0.0 31.51 3.16
2708 2844 4.850386 ACTACCCAGTTCCATAAACTCCTT 59.150 41.667 0.00 0.0 45.28 3.36
2732 2868 1.595466 GCAAGAGCATCCTGATGAGG 58.405 55.000 11.23 0.0 41.20 3.86
2762 2898 2.221169 TCCATTAGCCACATCGATTGC 58.779 47.619 0.00 0.0 0.00 3.56


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

AutoCloner maintained by Alex Coulton.