Multiple sequence alignment - TraesCS7D01G462000

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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 TraesCS7D01G462000 chr7D 100.000 2357 0 0 1 2357 577855715 577853359 0.000000e+00 4353.0
1 TraesCS7D01G462000 chr7D 85.644 606 67 16 1157 1753 158992803 158993397 9.250000e-174 619.0
2 TraesCS7D01G462000 chr7D 84.488 303 40 3 1754 2055 577918807 577918511 2.290000e-75 292.0
3 TraesCS7D01G462000 chr7D 84.018 219 23 6 1754 1967 578166975 578167186 1.430000e-47 200.0
4 TraesCS7D01G462000 chr7D 94.828 58 3 0 2 59 563518513 563518456 8.970000e-15 91.6
5 TraesCS7D01G462000 chr7D 80.233 86 16 1 1975 2059 577791550 577791635 1.960000e-06 63.9
6 TraesCS7D01G462000 chr2A 91.916 1769 119 10 1 1754 650490730 650492489 0.000000e+00 2453.0
7 TraesCS7D01G462000 chr5B 85.392 1773 222 22 1 1754 17684792 17683038 0.000000e+00 1805.0
8 TraesCS7D01G462000 chr5A 84.977 1764 230 24 12 1754 455337661 455335912 0.000000e+00 1757.0
9 TraesCS7D01G462000 chr7A 84.088 1766 249 20 12 1758 582112544 582110792 0.000000e+00 1676.0
10 TraesCS7D01G462000 chr7A 87.697 634 46 15 1754 2355 670164251 670163618 0.000000e+00 710.0
11 TraesCS7D01G462000 chr7A 73.091 1349 314 34 14 1332 717769110 717767781 3.600000e-118 435.0
12 TraesCS7D01G462000 chr7A 76.329 621 71 36 1754 2351 670345753 670346320 1.800000e-66 263.0
13 TraesCS7D01G462000 chr7B 82.968 1779 251 32 1 1754 87119150 87120901 0.000000e+00 1559.0
14 TraesCS7D01G462000 chr7B 94.475 181 9 1 1754 1933 641365786 641365606 6.420000e-71 278.0
15 TraesCS7D01G462000 chr7B 96.104 154 6 0 1759 1912 641335698 641335545 3.890000e-63 252.0
16 TraesCS7D01G462000 chr7B 75.723 622 84 36 1754 2350 641745149 641745728 1.400000e-62 250.0
17 TraesCS7D01G462000 chr7B 85.294 204 19 4 1754 1951 641451177 641450979 1.430000e-47 200.0
18 TraesCS7D01G462000 chr7B 90.909 132 8 2 1754 1885 642080367 642080494 8.660000e-40 174.0
19 TraesCS7D01G462000 chr1B 82.611 1593 230 28 183 1753 593051645 593053212 0.000000e+00 1363.0
20 TraesCS7D01G462000 chr3A 83.988 1374 205 7 1 1362 712704155 712702785 0.000000e+00 1304.0
21 TraesCS7D01G462000 chr3A 85.406 1206 162 9 9 1201 595278532 595279736 0.000000e+00 1240.0
22 TraesCS7D01G462000 chr1A 83.432 1346 191 21 433 1754 375465445 375466782 0.000000e+00 1221.0
23 TraesCS7D01G462000 chr6B 81.616 1349 229 16 13 1346 450591052 450592396 0.000000e+00 1099.0
24 TraesCS7D01G462000 chr6B 78.874 1297 243 21 12 1292 39894781 39896062 0.000000e+00 848.0
25 TraesCS7D01G462000 chr6B 81.162 568 96 7 1 558 658646400 658645834 1.660000e-121 446.0
26 TraesCS7D01G462000 chr6B 89.362 47 5 0 431 477 492210414 492210460 2.530000e-05 60.2
27 TraesCS7D01G462000 chr6D 83.511 564 79 13 1200 1753 84476721 84476162 4.490000e-142 514.0
28 TraesCS7D01G462000 chr4B 85.163 337 49 1 13 348 241351622 241351958 6.240000e-91 344.0
29 TraesCS7D01G462000 chrUn 84.015 269 32 9 1497 1755 88784423 88784690 5.030000e-62 248.0
30 TraesCS7D01G462000 chr6A 73.984 615 147 6 720 1323 22262258 22262870 1.090000e-58 237.0


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 TraesCS7D01G462000 chr7D 577853359 577855715 2356 True 4353 4353 100.000 1 2357 1 chr7D.!!$R2 2356
1 TraesCS7D01G462000 chr7D 158992803 158993397 594 False 619 619 85.644 1157 1753 1 chr7D.!!$F1 596
2 TraesCS7D01G462000 chr2A 650490730 650492489 1759 False 2453 2453 91.916 1 1754 1 chr2A.!!$F1 1753
3 TraesCS7D01G462000 chr5B 17683038 17684792 1754 True 1805 1805 85.392 1 1754 1 chr5B.!!$R1 1753
4 TraesCS7D01G462000 chr5A 455335912 455337661 1749 True 1757 1757 84.977 12 1754 1 chr5A.!!$R1 1742
5 TraesCS7D01G462000 chr7A 582110792 582112544 1752 True 1676 1676 84.088 12 1758 1 chr7A.!!$R1 1746
6 TraesCS7D01G462000 chr7A 670163618 670164251 633 True 710 710 87.697 1754 2355 1 chr7A.!!$R2 601
7 TraesCS7D01G462000 chr7A 717767781 717769110 1329 True 435 435 73.091 14 1332 1 chr7A.!!$R3 1318
8 TraesCS7D01G462000 chr7A 670345753 670346320 567 False 263 263 76.329 1754 2351 1 chr7A.!!$F1 597
9 TraesCS7D01G462000 chr7B 87119150 87120901 1751 False 1559 1559 82.968 1 1754 1 chr7B.!!$F1 1753
10 TraesCS7D01G462000 chr7B 641745149 641745728 579 False 250 250 75.723 1754 2350 1 chr7B.!!$F2 596
11 TraesCS7D01G462000 chr1B 593051645 593053212 1567 False 1363 1363 82.611 183 1753 1 chr1B.!!$F1 1570
12 TraesCS7D01G462000 chr3A 712702785 712704155 1370 True 1304 1304 83.988 1 1362 1 chr3A.!!$R1 1361
13 TraesCS7D01G462000 chr3A 595278532 595279736 1204 False 1240 1240 85.406 9 1201 1 chr3A.!!$F1 1192
14 TraesCS7D01G462000 chr1A 375465445 375466782 1337 False 1221 1221 83.432 433 1754 1 chr1A.!!$F1 1321
15 TraesCS7D01G462000 chr6B 450591052 450592396 1344 False 1099 1099 81.616 13 1346 1 chr6B.!!$F2 1333
16 TraesCS7D01G462000 chr6B 39894781 39896062 1281 False 848 848 78.874 12 1292 1 chr6B.!!$F1 1280
17 TraesCS7D01G462000 chr6B 658645834 658646400 566 True 446 446 81.162 1 558 1 chr6B.!!$R1 557
18 TraesCS7D01G462000 chr6D 84476162 84476721 559 True 514 514 83.511 1200 1753 1 chr6D.!!$R1 553
19 TraesCS7D01G462000 chr6A 22262258 22262870 612 False 237 237 73.984 720 1323 1 chr6A.!!$F1 603

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
376 385 0.391661 GCTTTGGCGAGAGGTGATCA 60.392 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2326 0.323542 AGGGACACCGTCTCCTACAG 60.324 60.0 3.27 0.0 43.47 2.74 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
205 212 1.885887 CATCGCAAGGGTTTTTCTGGA 59.114 47.619 0.00 0.00 38.47 3.86
268 275 5.872617 TGGTGTAGAATTTGTCGATCGAAAT 59.127 36.000 21.31 14.14 0.00 2.17
282 290 1.211949 TCGAAATAGAAAGGGGGCCTG 59.788 52.381 0.84 0.00 32.13 4.85
376 385 0.391661 GCTTTGGCGAGAGGTGATCA 60.392 55.000 0.00 0.00 0.00 2.92
1031 1056 0.896479 GTGGGGTGCGTTTTGGGTAT 60.896 55.000 0.00 0.00 0.00 2.73
1160 1185 5.640732 GATGTGGAACTGTCGCAATAAAAT 58.359 37.500 0.00 0.00 38.04 1.82
1410 1450 0.693049 TGCAGAACTTCTTCCCTCCC 59.307 55.000 0.00 0.00 0.00 4.30
1443 1486 2.513317 TGGATCATGTGCCCCTTTCATA 59.487 45.455 0.00 0.00 0.00 2.15
1444 1487 3.053019 TGGATCATGTGCCCCTTTCATAA 60.053 43.478 0.00 0.00 0.00 1.90
1457 1500 4.679654 CCCTTTCATAACGCACAAAGTTTC 59.320 41.667 0.00 0.00 33.42 2.78
1462 1505 5.507077 TCATAACGCACAAAGTTTCTGTTC 58.493 37.500 0.00 0.00 33.42 3.18
1465 1508 2.612212 ACGCACAAAGTTTCTGTTCGAT 59.388 40.909 6.72 0.00 35.81 3.59
1495 1543 0.673985 TGGTCGTCTGTGAGGTTCAG 59.326 55.000 0.00 0.00 0.00 3.02
1611 1674 4.437587 GCCCCATGGTGAGCTGCT 62.438 66.667 11.73 0.00 0.00 4.24
1889 1953 1.610038 TCAAACACTGCATTGCTCTGG 59.390 47.619 10.49 0.00 0.00 3.86
1894 1958 2.022195 CACTGCATTGCTCTGGCTATT 58.978 47.619 10.49 0.00 39.59 1.73
1933 2002 5.178252 ACATGACAGAATTCACTCAAACGAG 59.822 40.000 8.44 0.00 36.53 4.18
1944 2013 0.756294 TCAAACGAGGTCCTGCTCAA 59.244 50.000 0.00 0.00 0.00 3.02
1952 2021 2.703007 GAGGTCCTGCTCAATCATACCT 59.297 50.000 0.00 0.00 35.91 3.08
1959 2028 4.946157 CCTGCTCAATCATACCTCAAAAGT 59.054 41.667 0.00 0.00 0.00 2.66
1981 2050 1.195900 GTGCACCGCGTATTTCAAGAA 59.804 47.619 5.22 0.00 0.00 2.52
1985 2054 1.083489 CCGCGTATTTCAAGAAGCCA 58.917 50.000 4.92 0.00 0.00 4.75
2015 2087 6.019801 GTCGATACATATCCACAAGTGTGTTC 60.020 42.308 10.40 1.90 44.21 3.18
2017 2089 4.365514 ACATATCCACAAGTGTGTTCCA 57.634 40.909 10.40 0.00 44.21 3.53
2018 2090 4.724399 ACATATCCACAAGTGTGTTCCAA 58.276 39.130 10.40 0.00 44.21 3.53
2115 2197 2.032634 GCAGACGCCCGATGAAACA 61.033 57.895 0.00 0.00 0.00 2.83
2124 2206 2.689983 GCCCGATGAAACAATGGAGAAT 59.310 45.455 0.00 0.00 0.00 2.40
2125 2207 3.243201 GCCCGATGAAACAATGGAGAATC 60.243 47.826 0.00 0.00 0.00 2.52
2171 2274 2.169352 GCTCCTTTATCCTCTGCACAGA 59.831 50.000 0.00 0.00 35.85 3.41
2216 2319 1.070445 CTTCCAGCCTAGCCAGAGATG 59.930 57.143 0.00 0.00 0.00 2.90
2223 2326 2.609244 GCCTAGCCAGAGATGATCGAAC 60.609 54.545 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 212 2.711542 CTTACGCCCCTCATGTTCTTT 58.288 47.619 0.00 0.00 0.00 2.52
248 255 9.836739 CTTTCTATTTCGATCGACAAATTCTAC 57.163 33.333 19.26 0.00 0.00 2.59
268 275 2.286885 CCCCAGGCCCCCTTTCTA 60.287 66.667 0.00 0.00 0.00 2.10
282 290 6.661805 TCTGTTTATGTAAATCTTTCACCCCC 59.338 38.462 0.00 0.00 0.00 5.40
365 374 1.280421 ACTTTGCCCTGATCACCTCTC 59.720 52.381 0.00 0.00 0.00 3.20
376 385 4.542697 TCCTTTTTGAAGTACTTTGCCCT 58.457 39.130 10.02 0.00 0.00 5.19
1031 1056 5.593909 CACAAATTGTTAGGGCATCTATCCA 59.406 40.000 0.00 0.00 0.00 3.41
1116 1141 1.746615 CCAGCATAACGCAGCCAGT 60.747 57.895 0.00 0.00 46.13 4.00
1410 1450 1.097547 ATGATCCAAAAGAGCGCGGG 61.098 55.000 8.83 0.00 31.78 6.13
1443 1486 2.417239 TCGAACAGAAACTTTGTGCGTT 59.583 40.909 5.75 0.00 45.59 4.84
1444 1487 2.004017 TCGAACAGAAACTTTGTGCGT 58.996 42.857 5.75 0.00 45.59 5.24
1457 1500 6.145048 ACGACCAAACTAGTTTTATCGAACAG 59.855 38.462 35.31 19.43 38.56 3.16
1462 1505 5.632347 ACAGACGACCAAACTAGTTTTATCG 59.368 40.000 30.99 30.99 40.42 2.92
1465 1508 5.904941 TCACAGACGACCAAACTAGTTTTA 58.095 37.500 18.25 0.00 0.00 1.52
1611 1674 2.571757 GTGAGCACCCGTCATCGA 59.428 61.111 0.00 0.00 39.71 3.59
1715 1778 9.541143 CGGGCATTATTAATTTCCATTACTTTT 57.459 29.630 0.00 0.00 0.00 2.27
1889 1953 8.543774 GTCATGTCAGTGTACAAAGATAATAGC 58.456 37.037 0.00 0.00 32.02 2.97
1894 1958 7.227049 TCTGTCATGTCAGTGTACAAAGATA 57.773 36.000 17.67 0.00 36.85 1.98
1933 2002 2.435805 TGAGGTATGATTGAGCAGGACC 59.564 50.000 0.00 0.00 0.00 4.46
1944 2013 3.684788 GTGCACGACTTTTGAGGTATGAT 59.315 43.478 0.00 0.00 0.00 2.45
1981 2050 3.368843 GGATATGTATCGACATGCTGGCT 60.369 47.826 0.00 0.00 46.11 4.75
1985 2054 4.871933 TGTGGATATGTATCGACATGCT 57.128 40.909 12.09 0.00 46.11 3.79
2015 2087 3.305335 GCCCAACAGAACACTGTAATTGG 60.305 47.826 10.69 10.69 43.00 3.16
2017 2089 3.561143 TGCCCAACAGAACACTGTAATT 58.439 40.909 3.33 0.00 43.00 1.40
2018 2090 3.222173 TGCCCAACAGAACACTGTAAT 57.778 42.857 3.33 0.00 43.00 1.89
2143 2240 0.682292 AGGATAAAGGAGCTAGGCGC 59.318 55.000 0.00 0.00 39.57 6.53
2157 2254 1.393603 CTCCGTCTGTGCAGAGGATA 58.606 55.000 19.61 9.12 43.80 2.59
2171 2274 2.039624 ACTGATGAGGCCCTCCGT 59.960 61.111 8.62 0.00 37.47 4.69
2216 2319 2.015587 ACCGTCTCCTACAGTTCGATC 58.984 52.381 0.00 0.00 0.00 3.69
2223 2326 0.323542 AGGGACACCGTCTCCTACAG 60.324 60.000 3.27 0.00 43.47 2.74


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

AutoCloner maintained by Alex Coulton.