Multiple sequence alignment - TraesCS7A01G501900

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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 TraesCS7A01G501900 chr7A 100.000 2991 0 0 1 2991 691411632 691414622 0.000000e+00 5524
1 TraesCS7A01G501900 chr7A 84.854 1578 160 42 802 2343 84381161 84379627 0.000000e+00 1517
2 TraesCS7A01G501900 chr7A 90.104 384 20 6 495 864 55576330 55576709 1.610000e-132 483
3 TraesCS7A01G501900 chr7A 90.995 211 17 2 1 209 55575723 55575933 1.760000e-72 283
4 TraesCS7A01G501900 chr7A 91.608 143 9 3 210 349 55576190 55576332 8.460000e-46 195
5 TraesCS7A01G501900 chr7A 83.333 126 11 6 622 737 55573582 55573707 1.130000e-19 108
6 TraesCS7A01G501900 chr4D 93.615 2819 108 18 209 2991 485796513 485793731 0.000000e+00 4143
7 TraesCS7A01G501900 chr4D 92.537 201 13 2 1 201 485796999 485796801 1.360000e-73 287
8 TraesCS7A01G501900 chr4B 93.475 2820 107 24 210 2991 619990641 619987861 0.000000e+00 4117
9 TraesCS7A01G501900 chr4B 90.386 2049 133 28 982 2991 545480464 545478441 0.000000e+00 2634
10 TraesCS7A01G501900 chr4B 95.678 1504 41 4 1490 2991 12902495 12901014 0.000000e+00 2396
11 TraesCS7A01G501900 chr4B 83.721 817 64 28 587 1368 12903332 12902550 0.000000e+00 708
12 TraesCS7A01G501900 chr4B 91.364 220 16 3 1 219 619991130 619990913 6.270000e-77 298
13 TraesCS7A01G501900 chr4B 90.184 163 15 1 57 219 12904095 12903934 8.400000e-51 211
14 TraesCS7A01G501900 chr2B 90.920 2456 127 41 604 2991 725229437 725227010 0.000000e+00 3212
15 TraesCS7A01G501900 chr2B 87.928 1168 84 30 1201 2343 728345258 728344123 0.000000e+00 1323
16 TraesCS7A01G501900 chr7B 87.276 2397 160 73 639 2991 678611130 678613425 0.000000e+00 2603
17 TraesCS7A01G501900 chr7B 89.091 220 22 1 2 219 678610165 678610384 3.800000e-69 272
18 TraesCS7A01G501900 chr5D 96.543 1533 46 3 1463 2991 445826288 445824759 0.000000e+00 2531
19 TraesCS7A01G501900 chr5D 96.338 1502 46 2 1490 2991 445965231 445963739 0.000000e+00 2460
20 TraesCS7A01G501900 chr5D 91.218 501 34 8 210 704 445827440 445826944 0.000000e+00 673
21 TraesCS7A01G501900 chr5D 84.848 660 48 27 724 1368 445826957 445826335 4.240000e-173 617
22 TraesCS7A01G501900 chr5D 93.564 202 12 1 1 201 445827950 445827749 1.740000e-77 300
23 TraesCS7A01G501900 chr7D 96.347 1533 49 3 1463 2991 599164187 599165716 0.000000e+00 2514
24 TraesCS7A01G501900 chr7D 95.206 1502 44 3 1490 2991 598893811 598895284 0.000000e+00 2350
25 TraesCS7A01G501900 chr7D 87.234 1504 117 36 982 2437 41036573 41038049 0.000000e+00 1644
26 TraesCS7A01G501900 chr7D 86.276 1603 115 45 802 2343 82633783 82632225 0.000000e+00 1644
27 TraesCS7A01G501900 chr7D 87.691 1178 87 33 210 1368 599163002 599164140 0.000000e+00 1319
28 TraesCS7A01G501900 chr7D 89.412 680 39 15 210 864 41035890 41036561 0.000000e+00 826
29 TraesCS7A01G501900 chr7D 93.151 219 15 0 1 219 41035405 41035623 3.720000e-84 322
30 TraesCS7A01G501900 chr7D 92.237 219 17 0 1 219 579924746 579924528 8.050000e-81 311
31 TraesCS7A01G501900 chr7D 93.269 208 13 1 1 208 599162520 599162726 3.750000e-79 305
32 TraesCS7A01G501900 chr2A 86.644 1460 117 36 913 2343 733209281 733207871 0.000000e+00 1544
33 TraesCS7A01G501900 chr2D 91.823 746 52 4 2249 2989 598952232 598951491 0.000000e+00 1031


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 TraesCS7A01G501900 chr7A 691411632 691414622 2990 False 5524.000000 5524 100.000000 1 2991 1 chr7A.!!$F1 2990
1 TraesCS7A01G501900 chr7A 84379627 84381161 1534 True 1517.000000 1517 84.854000 802 2343 1 chr7A.!!$R1 1541
2 TraesCS7A01G501900 chr7A 55573582 55576709 3127 False 267.250000 483 89.010000 1 864 4 chr7A.!!$F2 863
3 TraesCS7A01G501900 chr4D 485793731 485796999 3268 True 2215.000000 4143 93.076000 1 2991 2 chr4D.!!$R1 2990
4 TraesCS7A01G501900 chr4B 545478441 545480464 2023 True 2634.000000 2634 90.386000 982 2991 1 chr4B.!!$R1 2009
5 TraesCS7A01G501900 chr4B 619987861 619991130 3269 True 2207.500000 4117 92.419500 1 2991 2 chr4B.!!$R3 2990
6 TraesCS7A01G501900 chr4B 12901014 12904095 3081 True 1105.000000 2396 89.861000 57 2991 3 chr4B.!!$R2 2934
7 TraesCS7A01G501900 chr2B 725227010 725229437 2427 True 3212.000000 3212 90.920000 604 2991 1 chr2B.!!$R1 2387
8 TraesCS7A01G501900 chr2B 728344123 728345258 1135 True 1323.000000 1323 87.928000 1201 2343 1 chr2B.!!$R2 1142
9 TraesCS7A01G501900 chr7B 678610165 678613425 3260 False 1437.500000 2603 88.183500 2 2991 2 chr7B.!!$F1 2989
10 TraesCS7A01G501900 chr5D 445963739 445965231 1492 True 2460.000000 2460 96.338000 1490 2991 1 chr5D.!!$R1 1501
11 TraesCS7A01G501900 chr5D 445824759 445827950 3191 True 1030.250000 2531 91.543250 1 2991 4 chr5D.!!$R2 2990
12 TraesCS7A01G501900 chr7D 598893811 598895284 1473 False 2350.000000 2350 95.206000 1490 2991 1 chr7D.!!$F1 1501
13 TraesCS7A01G501900 chr7D 82632225 82633783 1558 True 1644.000000 1644 86.276000 802 2343 1 chr7D.!!$R1 1541
14 TraesCS7A01G501900 chr7D 599162520 599165716 3196 False 1379.333333 2514 92.435667 1 2991 3 chr7D.!!$F3 2990
15 TraesCS7A01G501900 chr7D 41035405 41038049 2644 False 930.666667 1644 89.932333 1 2437 3 chr7D.!!$F2 2436
16 TraesCS7A01G501900 chr2A 733207871 733209281 1410 True 1544.000000 1544 86.644000 913 2343 1 chr2A.!!$R1 1430
17 TraesCS7A01G501900 chr2D 598951491 598952232 741 True 1031.000000 1031 91.823000 2249 2989 1 chr2D.!!$R1 740

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
197 2345 0.398522 TCGGGGCATCACATAGGAGT 60.399 55.000 0.0 0.0 0.0 3.85 F
202 2350 1.599542 GGCATCACATAGGAGTTTCGC 59.400 52.381 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 4299 0.610232 ACTTCACTGCATCCAAGGCC 60.610 55.000 0.00 0.0 0.00 5.19 R
2000 4799 4.437239 GCTTCTGCAGCTAACATCTTCTA 58.563 43.478 9.47 0.0 46.27 2.10 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
34 2176 4.884164 CACTTGCTAATAAAAGGGAGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
115 2257 8.134895 TGTTTCTCCAATTTGTTTGTCTGTATC 58.865 33.333 0.00 0.00 33.15 2.24
118 2260 6.998074 TCTCCAATTTGTTTGTCTGTATCACT 59.002 34.615 0.00 0.00 33.15 3.41
188 2336 1.472552 CGTCAAATAGTCGGGGCATCA 60.473 52.381 0.00 0.00 0.00 3.07
197 2345 0.398522 TCGGGGCATCACATAGGAGT 60.399 55.000 0.00 0.00 0.00 3.85
202 2350 1.599542 GGCATCACATAGGAGTTTCGC 59.400 52.381 0.00 0.00 0.00 4.70
223 2675 3.433709 CGACAGCAAACACAATGTTCAA 58.566 40.909 0.00 0.00 40.14 2.69
337 2845 7.606858 TCAGCATTTCAAATTTTTGTTCACA 57.393 28.000 3.18 0.00 39.18 3.58
357 2865 6.151691 TCACAGTTTTAGAAATTCTGCATGC 58.848 36.000 11.82 11.82 0.00 4.06
360 2868 7.170320 CACAGTTTTAGAAATTCTGCATGCTTT 59.830 33.333 20.33 10.85 0.00 3.51
382 2890 9.571810 GCTTTTCAAAATTTGTTTGGAATTTCT 57.428 25.926 5.56 0.00 36.09 2.52
710 3297 1.961277 CGTCTCCCACACCAAGCAC 60.961 63.158 0.00 0.00 0.00 4.40
768 3439 2.041819 GTCTCCCCTCATCCCCGT 60.042 66.667 0.00 0.00 0.00 5.28
769 3440 2.134933 GTCTCCCCTCATCCCCGTC 61.135 68.421 0.00 0.00 0.00 4.79
1322 4057 7.550551 TGTCATTTGTTTCTGATCTGAGTATCC 59.449 37.037 2.33 0.00 0.00 2.59
1374 4119 3.733960 CCTGCGACGACCTCGACA 61.734 66.667 0.00 0.00 46.14 4.35
1543 4299 9.616634 TGGTAGTAACGATTAATAAGATTAGCG 57.383 33.333 0.00 0.00 0.00 4.26
1568 4332 1.561076 TGGATGCAGTGAAGTGGCTAT 59.439 47.619 0.00 0.00 0.00 2.97
1613 4377 4.401925 TGCTGCTATAGATCTACTCTGCA 58.598 43.478 19.12 19.12 35.28 4.41
1708 4484 1.511850 TCTGTTGCTCGATTGTGTGG 58.488 50.000 0.00 0.00 0.00 4.17
2000 4799 5.300411 TCTGGTGCTATGATGATTGTGAT 57.700 39.130 0.00 0.00 0.00 3.06
2272 5198 9.317936 CTCAGCTGTGATAATGAAATTGTACTA 57.682 33.333 14.67 0.00 36.99 1.82
2383 5322 6.449698 ACTGAGCAAAACAGGAAATATGTTG 58.550 36.000 0.00 0.00 39.91 3.33
2598 5537 6.763303 AATGCTTGACCGTTTTTGTAAATC 57.237 33.333 0.00 0.00 0.00 2.17
2783 5723 5.240623 TCCACTACCAAAGCAACAACTTATG 59.759 40.000 0.00 0.00 0.00 1.90
2922 5884 1.808945 CACAGTTCTGATGTTCTGGGC 59.191 52.381 6.83 0.00 32.92 5.36
2971 5933 5.715070 ACTCTCGGATTTCTTAGTGAACTG 58.285 41.667 0.00 0.00 33.88 3.16
2982 5944 5.902681 TCTTAGTGAACTGTAATCCCATCG 58.097 41.667 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 2203 6.814146 CCTTCTTTCACATCTCTACTACAACC 59.186 42.308 0.00 0.00 0.00 3.77
62 2204 7.379750 ACCTTCTTTCACATCTCTACTACAAC 58.620 38.462 0.00 0.00 0.00 3.32
76 2218 5.576447 TGGAGAAACAAACCTTCTTTCAC 57.424 39.130 0.00 0.00 33.24 3.18
126 2272 2.348888 CCTAGGAGGCGGACAACGT 61.349 63.158 1.05 0.00 46.52 3.99
130 2278 1.120530 GAATTCCTAGGAGGCGGACA 58.879 55.000 12.26 0.00 34.61 4.02
188 2336 1.736032 GCTGTCGCGAAACTCCTATGT 60.736 52.381 12.06 0.00 0.00 2.29
197 2345 0.448197 TTGTGTTTGCTGTCGCGAAA 59.552 45.000 12.06 3.77 41.05 3.46
202 2350 3.063670 TGAACATTGTGTTTGCTGTCG 57.936 42.857 0.00 0.00 41.28 4.35
256 2709 7.227992 TGAACATGTTTTGAATTTTCGAACC 57.772 32.000 13.36 0.00 30.55 3.62
337 2845 7.927629 TGAAAAGCATGCAGAATTTCTAAAACT 59.072 29.630 21.98 0.00 32.60 2.66
351 2859 6.034591 CCAAACAAATTTTGAAAAGCATGCA 58.965 32.000 21.98 0.00 0.00 3.96
514 3028 9.715123 GATTCCAAAATTTGTGAACGAAATTTT 57.285 25.926 4.92 9.99 46.52 1.82
710 3297 2.436292 ACGGAGGAGACGGACGAG 60.436 66.667 0.00 0.00 35.23 4.18
757 3383 0.684479 TGTGAGAGACGGGGATGAGG 60.684 60.000 0.00 0.00 0.00 3.86
759 3385 1.403814 GATGTGAGAGACGGGGATGA 58.596 55.000 0.00 0.00 0.00 2.92
768 3439 0.965866 AAGCGACGGGATGTGAGAGA 60.966 55.000 0.00 0.00 0.00 3.10
769 3440 0.526524 GAAGCGACGGGATGTGAGAG 60.527 60.000 0.00 0.00 0.00 3.20
895 3586 2.363795 TGACCCCCTACTCCGCTG 60.364 66.667 0.00 0.00 0.00 5.18
1079 3791 4.680237 CGTCCTGCCTGGTGCGAA 62.680 66.667 0.00 0.00 45.60 4.70
1543 4299 0.610232 ACTTCACTGCATCCAAGGCC 60.610 55.000 0.00 0.00 0.00 5.19
1568 4332 6.372659 GCAACAGTCTGGATTCTGAAATTCTA 59.627 38.462 4.53 0.00 35.84 2.10
1613 4377 4.712122 CATTTAGTTACCAAATGGCGGT 57.288 40.909 8.07 0.00 38.93 5.68
1708 4484 6.494491 AGTTTACCCAGTAAATTAACCAACCC 59.506 38.462 3.46 0.00 39.64 4.11
2000 4799 4.437239 GCTTCTGCAGCTAACATCTTCTA 58.563 43.478 9.47 0.00 46.27 2.10
2272 5198 5.596836 TCAAATGTTTTCCTGTTCTGCTT 57.403 34.783 0.00 0.00 0.00 3.91
2392 5331 7.095017 GCAGAGTTAAGGCATAATCTATTCCAC 60.095 40.741 0.00 0.00 0.00 4.02
2464 5403 6.429692 TCCAGATGACAAAAATTGTGTCGTAT 59.570 34.615 10.73 5.47 46.89 3.06
2783 5723 7.828717 GGAGTAGTATATCTGGTAGGTAGGAAC 59.171 44.444 0.00 0.00 0.00 3.62
2922 5884 4.272489 TGCCTCTAGAAATGAACATTGGG 58.728 43.478 0.69 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.