Multiple sequence alignment - TraesCS6D01G391400

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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 TraesCS6D01G391400 chr6D 100.000 2249 0 0 1 2249 466380934 466383182 0.000000e+00 4154
1 TraesCS6D01G391400 chr4A 94.952 2179 88 11 72 2235 616710566 616712737 0.000000e+00 3395
2 TraesCS6D01G391400 chr4A 93.678 348 17 5 1897 2241 553452809 553452464 1.190000e-142 516
3 TraesCS6D01G391400 chr4A 98.667 75 1 0 1 75 616710234 616710308 1.400000e-27 134
4 TraesCS6D01G391400 chr3D 93.739 2220 80 11 72 2235 209670893 209673109 0.000000e+00 3275
5 TraesCS6D01G391400 chr3D 98.667 75 1 0 1 75 209670563 209670637 1.400000e-27 134
6 TraesCS6D01G391400 chr6A 93.360 2229 77 20 72 2235 282150472 282148250 0.000000e+00 3230
7 TraesCS6D01G391400 chr6A 98.667 75 1 0 1 75 282150802 282150728 1.400000e-27 134
8 TraesCS6D01G391400 chr1A 96.378 1546 45 6 298 1839 489295120 489293582 0.000000e+00 2534
9 TraesCS6D01G391400 chr1A 84.728 2246 238 59 72 2238 536290976 536293195 0.000000e+00 2150
10 TraesCS6D01G391400 chr1A 92.483 439 13 9 1817 2235 489293560 489293122 5.310000e-171 610
11 TraesCS6D01G391400 chr1A 97.321 224 6 0 72 295 489316900 489316677 4.530000e-102 381
12 TraesCS6D01G391400 chr1A 98.667 75 1 0 1 75 489317230 489317156 1.400000e-27 134
13 TraesCS6D01G391400 chr2B 95.381 1429 53 4 72 1489 667804511 667805937 0.000000e+00 2261
14 TraesCS6D01G391400 chr2B 95.249 421 19 1 1817 2236 667814544 667814964 0.000000e+00 665
15 TraesCS6D01G391400 chr2B 92.523 428 10 3 1816 2221 64025947 64025520 5.350000e-166 593
16 TraesCS6D01G391400 chr2B 94.648 355 18 1 1485 1838 667814167 667814521 1.170000e-152 549
17 TraesCS6D01G391400 chr2A 85.708 2211 234 53 72 2235 25353700 25351525 0.000000e+00 2257
18 TraesCS6D01G391400 chr5B 92.714 1400 52 10 884 2235 592924540 592923143 0.000000e+00 1975
19 TraesCS6D01G391400 chr6B 92.190 1178 85 2 72 1242 60080083 60078906 0.000000e+00 1659
20 TraesCS6D01G391400 chr6B 95.758 330 9 3 1908 2236 432494976 432494651 5.500000e-146 527
21 TraesCS6D01G391400 chr2D 92.027 1179 85 5 72 1242 610421314 610420137 0.000000e+00 1648
22 TraesCS6D01G391400 chr5D 91.596 1178 91 3 72 1242 432779458 432778282 0.000000e+00 1620
23 TraesCS6D01G391400 chr7D 91.256 1178 96 4 72 1242 570674545 570673368 0.000000e+00 1598
24 TraesCS6D01G391400 chr7D 87.427 342 37 5 1284 1622 570673390 570673052 2.710000e-104 388
25 TraesCS6D01G391400 chr1D 92.868 631 22 7 1628 2235 22597029 22596399 0.000000e+00 894
26 TraesCS6D01G391400 chr7B 88.520 662 29 10 1619 2233 680705666 680705005 0.000000e+00 758
27 TraesCS6D01G391400 chr3B 89.134 635 30 12 1626 2221 754068043 754067409 0.000000e+00 754
28 TraesCS6D01G391400 chr3A 87.729 546 42 15 1711 2234 13915009 13915551 4.110000e-172 614


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 TraesCS6D01G391400 chr6D 466380934 466383182 2248 False 4154.0 4154 100.0000 1 2249 1 chr6D.!!$F1 2248
1 TraesCS6D01G391400 chr4A 616710234 616712737 2503 False 1764.5 3395 96.8095 1 2235 2 chr4A.!!$F1 2234
2 TraesCS6D01G391400 chr3D 209670563 209673109 2546 False 1704.5 3275 96.2030 1 2235 2 chr3D.!!$F1 2234
3 TraesCS6D01G391400 chr6A 282148250 282150802 2552 True 1682.0 3230 96.0135 1 2235 2 chr6A.!!$R1 2234
4 TraesCS6D01G391400 chr1A 536290976 536293195 2219 False 2150.0 2150 84.7280 72 2238 1 chr1A.!!$F1 2166
5 TraesCS6D01G391400 chr1A 489293122 489295120 1998 True 1572.0 2534 94.4305 298 2235 2 chr1A.!!$R1 1937
6 TraesCS6D01G391400 chr1A 489316677 489317230 553 True 257.5 381 97.9940 1 295 2 chr1A.!!$R2 294
7 TraesCS6D01G391400 chr2B 667804511 667805937 1426 False 2261.0 2261 95.3810 72 1489 1 chr2B.!!$F1 1417
8 TraesCS6D01G391400 chr2B 667814167 667814964 797 False 607.0 665 94.9485 1485 2236 2 chr2B.!!$F2 751
9 TraesCS6D01G391400 chr2A 25351525 25353700 2175 True 2257.0 2257 85.7080 72 2235 1 chr2A.!!$R1 2163
10 TraesCS6D01G391400 chr5B 592923143 592924540 1397 True 1975.0 1975 92.7140 884 2235 1 chr5B.!!$R1 1351
11 TraesCS6D01G391400 chr6B 60078906 60080083 1177 True 1659.0 1659 92.1900 72 1242 1 chr6B.!!$R1 1170
12 TraesCS6D01G391400 chr2D 610420137 610421314 1177 True 1648.0 1648 92.0270 72 1242 1 chr2D.!!$R1 1170
13 TraesCS6D01G391400 chr5D 432778282 432779458 1176 True 1620.0 1620 91.5960 72 1242 1 chr5D.!!$R1 1170
14 TraesCS6D01G391400 chr7D 570673052 570674545 1493 True 993.0 1598 89.3415 72 1622 2 chr7D.!!$R1 1550
15 TraesCS6D01G391400 chr1D 22596399 22597029 630 True 894.0 894 92.8680 1628 2235 1 chr1D.!!$R1 607
16 TraesCS6D01G391400 chr7B 680705005 680705666 661 True 758.0 758 88.5200 1619 2233 1 chr7B.!!$R1 614
17 TraesCS6D01G391400 chr3B 754067409 754068043 634 True 754.0 754 89.1340 1626 2221 1 chr3B.!!$R1 595
18 TraesCS6D01G391400 chr3A 13915009 13915551 542 False 614.0 614 87.7290 1711 2234 1 chr3A.!!$F1 523

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
100 362 0.966179 GGTTTTTGGCAGGGTGTAGG 59.034 55.000 0.00 0.0 0.0 3.18 F
179 463 1.408127 CCGCAATTGGTGTAGATGGGA 60.408 52.381 7.72 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1195 1489 0.320374 TCCGCGTCACTTTCCATCTT 59.680 50.000 4.92 0.0 0.00 2.40 R
1330 1638 3.256383 CAGGACATTTGGCAAGAATGTGA 59.744 43.478 19.33 0.0 45.11 3.58 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
100 362 0.966179 GGTTTTTGGCAGGGTGTAGG 59.034 55.000 0.00 0.00 0.00 3.18
155 439 3.096092 GGGAAATACACTGGCCAATTGA 58.904 45.455 18.81 0.44 0.00 2.57
156 440 3.513515 GGGAAATACACTGGCCAATTGAA 59.486 43.478 18.81 0.00 0.00 2.69
179 463 1.408127 CCGCAATTGGTGTAGATGGGA 60.408 52.381 7.72 0.00 0.00 4.37
279 565 6.012745 AGTTGAAATTGGCTATTGGAGAACT 58.987 36.000 0.00 0.00 0.00 3.01
296 582 2.887151 ACTACAAGGGCTTGCAATCT 57.113 45.000 0.00 0.00 44.03 2.40
429 722 4.193826 ACTAGATAATATGTGGCCTGCG 57.806 45.455 3.32 0.00 0.00 5.18
450 743 4.051922 CGGCTTGGACATATGAAGTAGAC 58.948 47.826 10.38 2.85 0.00 2.59
591 884 5.468746 TGAGTATGTTAGCAATAATTCGGCC 59.531 40.000 0.00 0.00 0.00 6.13
616 909 7.930865 CCAAGGTTTTCAACAATTGGATTAAGA 59.069 33.333 10.83 0.00 45.40 2.10
860 1154 3.279434 ACTTGGAGAAAAACGAGTGCTT 58.721 40.909 0.00 0.00 0.00 3.91
866 1160 4.968181 GGAGAAAAACGAGTGCTTTTGTAC 59.032 41.667 0.00 0.00 35.17 2.90
1057 1351 8.898728 AGGTAAATCCTGGATTTGATATGATCT 58.101 33.333 34.18 20.88 46.19 2.75
1195 1489 2.677902 CGAAAGACATGCAAGGAGCCTA 60.678 50.000 0.00 0.00 44.83 3.93
1244 1538 1.108132 ACTCCTCCTCCGCGGTATTC 61.108 60.000 27.15 0.00 0.00 1.75
1247 1541 1.202964 TCCTCCTCCGCGGTATTCATA 60.203 52.381 27.15 1.93 0.00 2.15
1337 1645 9.809096 TTCATGATACTACTTCTTCTCACATTC 57.191 33.333 0.00 0.00 0.00 2.67
1653 1998 8.424274 AACCATGATCTTTTGTTTGAAGAAAC 57.576 30.769 0.00 0.00 41.72 2.78
1813 2184 9.395707 GAGATTATGCTGAATTGATGATGTTTC 57.604 33.333 0.00 0.00 0.00 2.78
1837 2294 3.061322 TGTCAAAATGCTGCTGAAATGC 58.939 40.909 0.00 0.00 0.00 3.56
1933 2390 4.022155 TGAAATGCTGTCAAAATGCTGCTA 60.022 37.500 0.00 0.00 0.00 3.49
1952 2430 6.642540 GCTGCTAAAAAGTTGCTATCTTGTTT 59.357 34.615 0.00 0.00 0.00 2.83
2063 2543 4.343526 TGTTGTTGAAATGTATGCTTGGGT 59.656 37.500 0.00 0.00 0.00 4.51
2141 2623 4.811557 CACTAGTGGTATTTTGGCTAGAGC 59.188 45.833 15.49 0.00 41.14 4.09
2187 2671 3.740832 GCAAGTTGGTTTTTCATAGTGGC 59.259 43.478 4.75 0.00 0.00 5.01
2238 2722 3.186001 GCATTCTGGCTATTGTCTCATCG 59.814 47.826 0.00 0.00 0.00 3.84
2239 2723 4.375272 CATTCTGGCTATTGTCTCATCGT 58.625 43.478 0.00 0.00 0.00 3.73
2240 2724 5.532557 CATTCTGGCTATTGTCTCATCGTA 58.467 41.667 0.00 0.00 0.00 3.43
2241 2725 5.791336 TTCTGGCTATTGTCTCATCGTAT 57.209 39.130 0.00 0.00 0.00 3.06
2242 2726 6.894339 TTCTGGCTATTGTCTCATCGTATA 57.106 37.500 0.00 0.00 0.00 1.47
2243 2727 6.894339 TCTGGCTATTGTCTCATCGTATAA 57.106 37.500 0.00 0.00 0.00 0.98
2244 2728 7.468141 TCTGGCTATTGTCTCATCGTATAAT 57.532 36.000 0.00 0.00 0.00 1.28
2245 2729 7.539436 TCTGGCTATTGTCTCATCGTATAATC 58.461 38.462 0.00 0.00 0.00 1.75
2246 2730 7.176690 TCTGGCTATTGTCTCATCGTATAATCA 59.823 37.037 0.00 0.00 0.00 2.57
2247 2731 7.090808 TGGCTATTGTCTCATCGTATAATCAC 58.909 38.462 0.00 0.00 0.00 3.06
2248 2732 7.039714 TGGCTATTGTCTCATCGTATAATCACT 60.040 37.037 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 362 1.070601 GCATCAACCCCCAAATATGGC 59.929 52.381 0.00 0.00 46.09 4.40
155 439 1.904287 TCTACACCAATTGCGGCTTT 58.096 45.000 0.00 0.00 0.00 3.51
156 440 1.745087 CATCTACACCAATTGCGGCTT 59.255 47.619 0.00 0.00 0.00 4.35
179 463 4.196971 GCTACCGGAAACATCCAACTATT 58.803 43.478 9.46 0.00 0.00 1.73
296 582 1.152376 TCCAACCCCTTGCATGCAA 60.152 52.632 30.12 30.12 0.00 4.08
375 668 7.814587 CCTTTGAACTTTTTCTTGAAGTTGAGT 59.185 33.333 6.94 0.00 44.81 3.41
429 722 5.023533 TGTCTACTTCATATGTCCAAGCC 57.976 43.478 1.90 0.00 0.00 4.35
450 743 4.337274 TCTGCCATTAGTGAATCATGCTTG 59.663 41.667 0.00 0.00 0.00 4.01
616 909 3.450578 CAAGTGCAAGTTGCTTCACATT 58.549 40.909 27.17 11.12 45.31 2.71
860 1154 5.278907 CCACAAATCTGCCATCTTGTACAAA 60.279 40.000 10.03 1.56 31.00 2.83
866 1160 5.163513 GTTTACCACAAATCTGCCATCTTG 58.836 41.667 0.00 0.00 0.00 3.02
1057 1351 3.971305 TCACTCTTGGTAAGTTTGGGAGA 59.029 43.478 0.00 0.00 0.00 3.71
1195 1489 0.320374 TCCGCGTCACTTTCCATCTT 59.680 50.000 4.92 0.00 0.00 2.40
1244 1538 8.545229 ACAAGTGAAAGAGATGAGACTTTATG 57.455 34.615 0.00 0.00 36.63 1.90
1328 1636 3.507233 GGACATTTGGCAAGAATGTGAGA 59.493 43.478 19.33 0.00 45.11 3.27
1329 1637 3.508793 AGGACATTTGGCAAGAATGTGAG 59.491 43.478 19.33 0.37 45.11 3.51
1330 1638 3.256383 CAGGACATTTGGCAAGAATGTGA 59.744 43.478 19.33 0.00 45.11 3.58
1337 1645 4.395959 AATATGCAGGACATTTGGCAAG 57.604 40.909 0.00 0.00 40.38 4.01
1391 1735 4.436332 CTTGCTTCAGCCTTTGACTTTTT 58.564 39.130 0.00 0.00 41.18 1.94
1503 1847 6.719370 AGGAGGTGTACAAGAAATTGCAATAA 59.281 34.615 13.39 0.00 0.00 1.40
1575 1919 3.964031 TCCCAACCAAATGCACTAAACTT 59.036 39.130 0.00 0.00 0.00 2.66
1813 2184 3.306917 TTCAGCAGCATTTTGACATGG 57.693 42.857 0.00 0.00 0.00 3.66
1933 2390 8.829612 CATCCAAAAACAAGATAGCAACTTTTT 58.170 29.630 0.00 0.00 0.00 1.94
1952 2430 8.970020 ACATAATCTTACTTTGCATCATCCAAA 58.030 29.630 0.00 0.00 0.00 3.28
2063 2543 6.958192 ACTTCTATACCCTTACCTCTTCACAA 59.042 38.462 0.00 0.00 0.00 3.33
2141 2623 7.120579 TGCCAATATACCACTACTTTCAGTTTG 59.879 37.037 0.00 0.00 0.00 2.93
2187 2671 3.716601 AGAAACCGAACTTGCCAAAATG 58.283 40.909 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.