Multiple sequence alignment - TraesCS6D01G078100

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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 TraesCS6D01G078100 chr6D 100.000 2288 0 0 1 2288 42934264 42931977 0.000000e+00 4226.0
1 TraesCS6D01G078100 chr6D 95.109 920 20 5 1370 2288 445948474 445947579 0.000000e+00 1426.0
2 TraesCS6D01G078100 chr7D 98.865 1322 15 0 1 1322 607108547 607109868 0.000000e+00 2359.0
3 TraesCS6D01G078100 chr7D 98.337 1323 22 0 1 1323 69431692 69433014 0.000000e+00 2322.0
4 TraesCS6D01G078100 chr7D 97.424 893 20 3 1369 2258 148165969 148166861 0.000000e+00 1519.0
5 TraesCS6D01G078100 chr7D 92.178 946 36 21 1370 2288 566871824 566870890 0.000000e+00 1303.0
6 TraesCS6D01G078100 chr7D 100.000 28 0 0 2254 2281 148179247 148179274 4.000000e-03 52.8
7 TraesCS6D01G078100 chr3B 90.242 1322 107 2 1 1322 807311500 807312799 0.000000e+00 1707.0
8 TraesCS6D01G078100 chr3B 94.181 928 20 3 1370 2288 809178313 809179215 0.000000e+00 1384.0
9 TraesCS6D01G078100 chr3B 86.325 351 29 12 1956 2288 54868369 54868718 4.650000e-97 364.0
10 TraesCS6D01G078100 chr7B 83.721 860 89 28 1469 2288 651877033 651877881 0.000000e+00 765.0
11 TraesCS6D01G078100 chr7B 73.102 461 105 18 53 504 603817164 603817614 1.830000e-31 147.0
12 TraesCS6D01G078100 chr7A 83.543 796 72 26 1539 2288 720728643 720729425 0.000000e+00 689.0
13 TraesCS6D01G078100 chr4D 85.425 494 44 10 1578 2045 6227297 6227788 2.640000e-134 488.0
14 TraesCS6D01G078100 chr4D 84.818 494 47 10 1578 2045 42175904 42175413 2.660000e-129 472.0
15 TraesCS6D01G078100 chr4D 84.818 494 47 10 1578 2045 42191732 42191241 2.660000e-129 472.0
16 TraesCS6D01G078100 chr5D 77.278 867 163 26 467 1322 382448299 382449142 1.590000e-131 479.0
17 TraesCS6D01G078100 chr2D 85.185 351 33 12 1956 2288 570143371 570143720 2.180000e-90 342.0
18 TraesCS6D01G078100 chr2D 89.216 102 10 1 1467 1567 578445700 578445801 2.390000e-25 126.0
19 TraesCS6D01G078100 chr2D 78.750 160 23 9 2059 2211 78797303 78797148 1.870000e-16 97.1
20 TraesCS6D01G078100 chr6B 82.934 334 51 6 992 1322 646011253 646011583 1.720000e-76 296.0
21 TraesCS6D01G078100 chr5B 83.453 278 40 6 1048 1322 614062639 614062913 1.050000e-63 254.0
22 TraesCS6D01G078100 chr6A 89.630 135 11 3 1509 1642 259638714 259638582 3.910000e-38 169.0
23 TraesCS6D01G078100 chr4B 87.736 106 9 2 1368 1469 645643264 645643159 1.110000e-23 121.0
24 TraesCS6D01G078100 chr4B 87.736 106 9 2 1368 1469 645722351 645722246 1.110000e-23 121.0
25 TraesCS6D01G078100 chr4B 87.500 104 9 2 1370 1469 650787566 650787669 1.440000e-22 117.0
26 TraesCS6D01G078100 chr4B 86.792 106 10 2 1368 1469 645814743 645814638 5.170000e-22 115.0
27 TraesCS6D01G078100 chr4A 77.990 209 35 10 309 514 691031508 691031708 1.110000e-23 121.0
28 TraesCS6D01G078100 chr2A 86.538 104 10 3 1370 1469 745816397 745816500 6.680000e-21 111.0
29 TraesCS6D01G078100 chr1D 87.255 102 8 4 1469 1567 359496482 359496581 6.680000e-21 111.0
30 TraesCS6D01G078100 chr5A 85.577 104 11 2 1370 1469 3055434 3055331 3.110000e-19 106.0
31 TraesCS6D01G078100 chr1A 83.333 102 12 4 1469 1567 72543199 72543100 3.130000e-14 89.8


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 TraesCS6D01G078100 chr6D 42931977 42934264 2287 True 4226 4226 100.000 1 2288 1 chr6D.!!$R1 2287
1 TraesCS6D01G078100 chr6D 445947579 445948474 895 True 1426 1426 95.109 1370 2288 1 chr6D.!!$R2 918
2 TraesCS6D01G078100 chr7D 607108547 607109868 1321 False 2359 2359 98.865 1 1322 1 chr7D.!!$F4 1321
3 TraesCS6D01G078100 chr7D 69431692 69433014 1322 False 2322 2322 98.337 1 1323 1 chr7D.!!$F1 1322
4 TraesCS6D01G078100 chr7D 148165969 148166861 892 False 1519 1519 97.424 1369 2258 1 chr7D.!!$F2 889
5 TraesCS6D01G078100 chr7D 566870890 566871824 934 True 1303 1303 92.178 1370 2288 1 chr7D.!!$R1 918
6 TraesCS6D01G078100 chr3B 807311500 807312799 1299 False 1707 1707 90.242 1 1322 1 chr3B.!!$F2 1321
7 TraesCS6D01G078100 chr3B 809178313 809179215 902 False 1384 1384 94.181 1370 2288 1 chr3B.!!$F3 918
8 TraesCS6D01G078100 chr7B 651877033 651877881 848 False 765 765 83.721 1469 2288 1 chr7B.!!$F2 819
9 TraesCS6D01G078100 chr7A 720728643 720729425 782 False 689 689 83.543 1539 2288 1 chr7A.!!$F1 749
10 TraesCS6D01G078100 chr5D 382448299 382449142 843 False 479 479 77.278 467 1322 1 chr5D.!!$F1 855

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
302 303 1.315257 CCTCAAGCATCAAACCCCCG 61.315 60.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1340 0.033109 GCCCCTTCCTTAGGTTGCAT 60.033 55.0 0.0 0.0 43.07 3.96 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
236 237 1.619827 CAGCAAGGGCCAATTTTCAGA 59.380 47.619 6.18 0.00 42.56 3.27
302 303 1.315257 CCTCAAGCATCAAACCCCCG 61.315 60.000 0.00 0.00 0.00 5.73
457 458 1.893808 CTCTGTGTTTGCTGCCGGT 60.894 57.895 1.90 0.00 0.00 5.28
545 546 2.583593 GCTAGAACCAGAGCGGCG 60.584 66.667 0.51 0.51 39.03 6.46
952 953 2.125552 CATCGGCGACTCAGGCAA 60.126 61.111 13.76 0.00 36.37 4.52
1229 1230 1.059913 AGTGGAGAAACCTGGTCTGG 58.940 55.000 0.00 0.00 39.86 3.86
1252 1253 0.551396 TCTCCCTGACGATGGAGCTA 59.449 55.000 0.62 0.00 46.39 3.32
1352 1353 1.838112 CAAGGCATGCAACCTAAGGA 58.162 50.000 21.36 0.00 36.14 3.36
1353 1354 2.170166 CAAGGCATGCAACCTAAGGAA 58.830 47.619 21.36 0.00 36.14 3.36
1354 1355 2.134789 AGGCATGCAACCTAAGGAAG 57.865 50.000 21.36 0.00 35.10 3.46
1363 1364 2.632831 CCTAAGGAAGGGGCCATCA 58.367 57.895 4.39 0.00 42.32 3.07
1364 1365 0.926293 CCTAAGGAAGGGGCCATCAA 59.074 55.000 4.39 0.00 42.32 2.57
1365 1366 1.287739 CCTAAGGAAGGGGCCATCAAA 59.712 52.381 4.39 0.00 42.32 2.69
1366 1367 2.659428 CTAAGGAAGGGGCCATCAAAG 58.341 52.381 4.39 0.00 0.00 2.77
1367 1368 1.084018 AAGGAAGGGGCCATCAAAGA 58.916 50.000 4.39 0.00 0.00 2.52
1374 1375 2.919602 AGGGGCCATCAAAGAAACTAGA 59.080 45.455 4.39 0.00 0.00 2.43
1691 1730 8.974060 AAAGAGAATTCTGGTTTACAACACTA 57.026 30.769 14.00 0.00 32.79 2.74
1931 2008 7.653713 CGATATGGTAGACAAAAGATAGCACTT 59.346 37.037 0.00 0.00 30.47 3.16
1960 2037 1.541310 AAGGACCTTGATCGCCGTCA 61.541 55.000 5.76 0.00 0.00 4.35
1977 2054 0.322816 TCATGCCTTCCTGTTGCCTC 60.323 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 191 6.558775 TCATAATACCAGGCATAGAAGTCCTT 59.441 38.462 0.00 0.00 0.00 3.36
302 303 0.181350 CCACTCCCAATCTGCTACCC 59.819 60.000 0.00 0.00 0.00 3.69
457 458 0.465705 GCCCCATCTTCATCTCGTCA 59.534 55.000 0.00 0.00 0.00 4.35
545 546 3.372676 CTGCTCGTGCACATTCGCC 62.373 63.158 18.64 0.00 45.31 5.54
812 813 5.434408 CTCCATCACAATTGATCTTCAGGA 58.566 41.667 13.59 8.62 40.79 3.86
952 953 3.357079 CGCACAGGCTTCCGCTTT 61.357 61.111 0.00 0.00 38.10 3.51
1252 1253 0.321298 AAGACGCTGGCCAAACGTAT 60.321 50.000 27.85 23.57 40.69 3.06
1333 1334 1.838112 TCCTTAGGTTGCATGCCTTG 58.162 50.000 16.68 8.82 37.54 3.61
1334 1335 2.450476 CTTCCTTAGGTTGCATGCCTT 58.550 47.619 16.68 0.00 37.54 4.35
1335 1336 1.341383 CCTTCCTTAGGTTGCATGCCT 60.341 52.381 16.68 13.82 39.39 4.75
1336 1337 1.106285 CCTTCCTTAGGTTGCATGCC 58.894 55.000 16.68 0.00 39.39 4.40
1337 1338 1.106285 CCCTTCCTTAGGTTGCATGC 58.894 55.000 11.82 11.82 43.07 4.06
1338 1339 1.767759 CCCCTTCCTTAGGTTGCATG 58.232 55.000 0.00 0.00 43.07 4.06
1339 1340 0.033109 GCCCCTTCCTTAGGTTGCAT 60.033 55.000 0.00 0.00 43.07 3.96
1340 1341 1.382629 GCCCCTTCCTTAGGTTGCA 59.617 57.895 0.00 0.00 43.07 4.08
1341 1342 1.379977 GGCCCCTTCCTTAGGTTGC 60.380 63.158 0.00 0.00 43.07 4.17
1342 1343 0.631212 ATGGCCCCTTCCTTAGGTTG 59.369 55.000 0.00 0.00 43.07 3.77
1343 1344 0.927029 GATGGCCCCTTCCTTAGGTT 59.073 55.000 0.00 0.00 43.07 3.50
1344 1345 0.253630 TGATGGCCCCTTCCTTAGGT 60.254 55.000 0.00 0.00 43.07 3.08
1345 1346 0.926293 TTGATGGCCCCTTCCTTAGG 59.074 55.000 0.00 0.00 44.33 2.69
1346 1347 2.242196 TCTTTGATGGCCCCTTCCTTAG 59.758 50.000 0.00 0.00 0.00 2.18
1347 1348 2.283834 TCTTTGATGGCCCCTTCCTTA 58.716 47.619 0.00 0.00 0.00 2.69
1348 1349 1.084018 TCTTTGATGGCCCCTTCCTT 58.916 50.000 0.00 0.00 0.00 3.36
1349 1350 1.084018 TTCTTTGATGGCCCCTTCCT 58.916 50.000 0.00 0.00 0.00 3.36
1350 1351 1.550524 GTTTCTTTGATGGCCCCTTCC 59.449 52.381 0.00 0.00 0.00 3.46
1351 1352 2.529632 AGTTTCTTTGATGGCCCCTTC 58.470 47.619 0.00 0.00 0.00 3.46
1352 1353 2.702270 AGTTTCTTTGATGGCCCCTT 57.298 45.000 0.00 0.00 0.00 3.95
1353 1354 2.919602 TCTAGTTTCTTTGATGGCCCCT 59.080 45.455 0.00 0.00 0.00 4.79
1354 1355 3.366052 TCTAGTTTCTTTGATGGCCCC 57.634 47.619 0.00 0.00 0.00 5.80
1355 1356 5.066593 CCTATCTAGTTTCTTTGATGGCCC 58.933 45.833 0.00 0.00 0.00 5.80
1356 1357 5.930135 TCCTATCTAGTTTCTTTGATGGCC 58.070 41.667 0.00 0.00 0.00 5.36
1357 1358 7.011857 CACTTCCTATCTAGTTTCTTTGATGGC 59.988 40.741 0.00 0.00 0.00 4.40
1358 1359 7.011857 GCACTTCCTATCTAGTTTCTTTGATGG 59.988 40.741 0.00 0.00 0.00 3.51
1359 1360 7.254252 CGCACTTCCTATCTAGTTTCTTTGATG 60.254 40.741 0.00 0.00 0.00 3.07
1360 1361 6.758886 CGCACTTCCTATCTAGTTTCTTTGAT 59.241 38.462 0.00 0.00 0.00 2.57
1361 1362 6.100004 CGCACTTCCTATCTAGTTTCTTTGA 58.900 40.000 0.00 0.00 0.00 2.69
1362 1363 5.292101 CCGCACTTCCTATCTAGTTTCTTTG 59.708 44.000 0.00 0.00 0.00 2.77
1363 1364 5.420409 CCGCACTTCCTATCTAGTTTCTTT 58.580 41.667 0.00 0.00 0.00 2.52
1364 1365 4.680975 GCCGCACTTCCTATCTAGTTTCTT 60.681 45.833 0.00 0.00 0.00 2.52
1365 1366 3.181474 GCCGCACTTCCTATCTAGTTTCT 60.181 47.826 0.00 0.00 0.00 2.52
1366 1367 3.124560 GCCGCACTTCCTATCTAGTTTC 58.875 50.000 0.00 0.00 0.00 2.78
1367 1368 2.766828 AGCCGCACTTCCTATCTAGTTT 59.233 45.455 0.00 0.00 0.00 2.66
1374 1375 1.452108 GGCAAGCCGCACTTCCTAT 60.452 57.895 0.00 0.00 45.17 2.57
1931 2008 2.181125 TCAAGGTCCTTATGTACGCCA 58.819 47.619 3.08 0.00 0.00 5.69
1960 2037 0.407139 AAGAGGCAACAGGAAGGCAT 59.593 50.000 0.00 0.00 41.41 4.40


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

AutoCloner maintained by Alex Coulton.