Multiple sequence alignment - TraesCS3B01G305400

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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 TraesCS3B01G305400 chr3B 100.000 1600 0 0 866 2465 490600498 490598899 0.000000e+00 2955
1 TraesCS3B01G305400 chr3B 100.000 459 0 0 1 459 490601363 490600905 0.000000e+00 848
2 TraesCS3B01G305400 chr3B 86.335 161 19 3 1198 1358 532667399 532667242 3.260000e-39 172
3 TraesCS3B01G305400 chr3D 89.744 1248 36 22 866 2091 376170284 376169107 0.000000e+00 1511
4 TraesCS3B01G305400 chr3D 88.075 478 28 18 1 459 376170812 376170345 7.760000e-150 540
5 TraesCS3B01G305400 chr3D 89.147 387 15 5 2100 2465 376166146 376165766 8.030000e-125 457
6 TraesCS3B01G305400 chr3D 85.714 161 20 3 1198 1358 406772721 406772564 1.520000e-37 167
7 TraesCS3B01G305400 chr3A 88.745 1004 47 29 1513 2465 500978526 500977538 0.000000e+00 1168
8 TraesCS3B01G305400 chr3A 94.582 646 8 5 866 1490 500979151 500978512 0.000000e+00 974
9 TraesCS3B01G305400 chr3A 85.258 407 24 14 1 373 500979717 500979313 1.070000e-103 387
10 TraesCS3B01G305400 chr3A 86.335 161 19 3 1198 1358 544969639 544969796 3.260000e-39 172
11 TraesCS3B01G305400 chr7B 90.400 125 12 0 1203 1327 712841464 712841588 5.450000e-37 165
12 TraesCS3B01G305400 chr7B 88.462 130 15 0 1198 1327 712841890 712842019 9.130000e-35 158
13 TraesCS3B01G305400 chr1D 81.720 186 26 7 1173 1358 426652242 426652419 5.490000e-32 148
14 TraesCS3B01G305400 chr1A 81.720 186 26 7 1173 1358 521738967 521739144 5.490000e-32 148


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 TraesCS3B01G305400 chr3B 490598899 490601363 2464 True 1901.5 2955 100.000000 1 2465 2 chr3B.!!$R2 2464
1 TraesCS3B01G305400 chr3D 376165766 376170812 5046 True 836.0 1511 88.988667 1 2465 3 chr3D.!!$R2 2464
2 TraesCS3B01G305400 chr3A 500977538 500979717 2179 True 843.0 1168 89.528333 1 2465 3 chr3A.!!$R1 2464

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
295 340 0.251354 AGTCTGATGATGCCGCACTT 59.749 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2190 0.516877 CGTGCGTTGATGTCATTGGT 59.483 50.0 0.0 0.0 0.0 3.67 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
22 23 3.206090 GCTTTTGCTTTGCAGAGGG 57.794 52.632 6.36 0.00 40.61 4.30
103 106 0.698818 AGGGGATCAACCAAGACACC 59.301 55.000 8.23 0.00 41.20 4.16
245 258 2.061773 CGATCGGAATGCGATAAAGCT 58.938 47.619 10.11 0.00 38.13 3.74
281 294 5.334414 GCTCATTGGTACTTTGAACAGTCTG 60.334 44.000 0.00 0.00 0.00 3.51
294 339 0.461516 CAGTCTGATGATGCCGCACT 60.462 55.000 0.00 0.00 0.00 4.40
295 340 0.251354 AGTCTGATGATGCCGCACTT 59.749 50.000 0.00 0.00 0.00 3.16
296 341 0.654683 GTCTGATGATGCCGCACTTC 59.345 55.000 0.00 0.00 0.00 3.01
297 342 0.462581 TCTGATGATGCCGCACTTCC 60.463 55.000 0.00 0.00 0.00 3.46
298 343 1.442526 CTGATGATGCCGCACTTCCC 61.443 60.000 0.00 0.00 0.00 3.97
299 344 1.451927 GATGATGCCGCACTTCCCA 60.452 57.895 0.00 0.00 0.00 4.37
300 345 1.718757 GATGATGCCGCACTTCCCAC 61.719 60.000 0.00 0.00 0.00 4.61
301 346 3.134127 GATGCCGCACTTCCCACC 61.134 66.667 0.00 0.00 0.00 4.61
302 347 3.918253 GATGCCGCACTTCCCACCA 62.918 63.158 0.00 0.00 0.00 4.17
303 348 3.286694 ATGCCGCACTTCCCACCAT 62.287 57.895 0.00 0.00 0.00 3.55
318 363 3.118665 CCCACCATTTCCACATGGATTTC 60.119 47.826 6.72 0.00 46.18 2.17
319 364 3.118665 CCACCATTTCCACATGGATTTCC 60.119 47.826 6.72 0.00 46.18 3.13
335 380 2.715749 TTCCCTAGTGACCATGCATG 57.284 50.000 20.19 20.19 0.00 4.06
379 424 6.906848 TCCTCCCGTCCAAGATTTATTAAAT 58.093 36.000 1.25 1.25 0.00 1.40
386 431 9.796120 CCGTCCAAGATTTATTAAATTGCTTTA 57.204 29.630 3.27 0.00 0.00 1.85
928 998 0.338120 TAAAAGCAAGGGGGATGGGG 59.662 55.000 0.00 0.00 0.00 4.96
957 1035 2.303175 GCCGCCTCCTCCTCTATATAG 58.697 57.143 3.10 3.10 0.00 1.31
1611 1710 0.895559 CCTGTCCACCTTTTGGCTCC 60.896 60.000 0.00 0.00 46.47 4.70
1612 1711 1.228124 TGTCCACCTTTTGGCTCCG 60.228 57.895 0.00 0.00 46.47 4.63
1738 1837 0.381801 CCACGGCCAGCAATATGAAC 59.618 55.000 2.24 0.00 0.00 3.18
1742 1841 0.663153 GGCCAGCAATATGAACGGAC 59.337 55.000 0.00 0.00 0.00 4.79
1768 1873 5.712446 AGAGGAAAAGAAAAATACTCCTGCC 59.288 40.000 0.00 0.00 33.42 4.85
1832 1951 7.542477 GGCAATGATGATGATGATGATCTTTTC 59.458 37.037 0.00 0.00 0.00 2.29
1853 1973 1.145738 TCTTCTTCCCTTTTGCTGCCT 59.854 47.619 0.00 0.00 0.00 4.75
1893 2013 6.427974 CAGCATTCAGTTATTAGATGCAGTG 58.572 40.000 9.01 0.00 36.16 3.66
1894 2014 5.008415 AGCATTCAGTTATTAGATGCAGTGC 59.992 40.000 8.58 8.58 36.16 4.40
1895 2015 5.220912 GCATTCAGTTATTAGATGCAGTGCA 60.221 40.000 22.22 22.22 44.86 4.57
1896 2016 6.427974 CATTCAGTTATTAGATGCAGTGCAG 58.572 40.000 24.20 5.65 43.65 4.41
1897 2017 3.873361 TCAGTTATTAGATGCAGTGCAGC 59.127 43.478 25.49 25.49 45.98 5.25
1970 2104 3.196901 ACACACACACTCCTACTGTTGAA 59.803 43.478 0.00 0.00 0.00 2.69
2071 2208 4.142708 TGAATACCAATGACATCAACGCAC 60.143 41.667 0.00 0.00 0.00 5.34
2073 2210 0.794229 CCAATGACATCAACGCACGC 60.794 55.000 0.00 0.00 0.00 5.34
2074 2211 0.110283 CAATGACATCAACGCACGCA 60.110 50.000 0.00 0.00 0.00 5.24
2077 2214 2.027073 GACATCAACGCACGCAGGA 61.027 57.895 0.00 0.00 0.00 3.86
2078 2215 2.227968 GACATCAACGCACGCAGGAC 62.228 60.000 0.00 0.00 0.00 3.85
2092 2229 1.414550 GCAGGACCAGAGGAATCTACC 59.585 57.143 0.00 0.00 0.00 3.18
2093 2230 2.752030 CAGGACCAGAGGAATCTACCA 58.248 52.381 0.00 0.00 0.00 3.25
2094 2231 3.312890 CAGGACCAGAGGAATCTACCAT 58.687 50.000 0.00 0.00 0.00 3.55
2107 5196 8.677870 AGGAATCTACCATCTATTAGCAAGAT 57.322 34.615 0.00 0.00 33.94 2.40
2128 5217 3.034635 TGAGGAAAGGAGGCATCTACTC 58.965 50.000 0.00 0.00 31.62 2.59
2316 5414 3.855895 GCATTATCATCACATGGTGCAGC 60.856 47.826 9.47 9.47 32.98 5.25
2373 5482 2.299582 TGGCATTTGAACAGGGTCAATG 59.700 45.455 0.00 3.47 37.36 2.82
2376 5485 3.367703 GCATTTGAACAGGGTCAATGGAG 60.368 47.826 0.00 0.00 37.36 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.636850 TTGCGCGTGACGTTTCGC 62.637 61.111 18.67 18.67 46.11 4.70
65 67 4.785453 CGCAACAGGGGAGGGAGC 62.785 72.222 0.00 0.00 0.00 4.70
200 213 7.794349 CGTGTTGACTTTTAGTGATCTCTTTTC 59.206 37.037 2.05 0.00 0.00 2.29
245 258 1.000385 CCAATGAGCGCAACTTTCCAA 60.000 47.619 11.47 0.00 0.00 3.53
257 270 4.757149 AGACTGTTCAAAGTACCAATGAGC 59.243 41.667 0.00 0.00 0.00 4.26
281 294 1.451927 TGGGAAGTGCGGCATCATC 60.452 57.895 5.72 5.03 0.00 2.92
294 339 1.430853 TCCATGTGGAAATGGTGGGAA 59.569 47.619 0.00 0.00 46.24 3.97
295 340 1.079796 TCCATGTGGAAATGGTGGGA 58.920 50.000 0.00 0.00 46.24 4.37
296 341 3.687847 TCCATGTGGAAATGGTGGG 57.312 52.632 0.00 0.00 46.24 4.61
318 363 3.409201 CCATGCATGGTCACTAGGG 57.591 57.895 33.68 8.51 43.05 3.53
335 380 2.957402 TATGAATGGAGTCATGGGCC 57.043 50.000 0.00 0.00 38.69 5.80
1418 1514 3.474570 CTGCCCCTTCCTCGGAGG 61.475 72.222 18.25 18.25 36.46 4.30
1419 1515 4.168291 GCTGCCCCTTCCTCGGAG 62.168 72.222 0.00 0.00 0.00 4.63
1421 1517 4.479993 CTGCTGCCCCTTCCTCGG 62.480 72.222 0.00 0.00 0.00 4.63
1479 1575 4.760047 CGGAAGGGCTCCACCACG 62.760 72.222 0.00 0.00 45.74 4.94
1480 1576 3.316573 CTCGGAAGGGCTCCACCAC 62.317 68.421 0.00 0.00 45.74 4.16
1481 1577 3.003173 CTCGGAAGGGCTCCACCA 61.003 66.667 0.00 0.00 45.74 4.17
1482 1578 2.291043 TTCTCGGAAGGGCTCCACC 61.291 63.158 0.00 0.00 45.74 4.61
1483 1579 1.079057 GTTCTCGGAAGGGCTCCAC 60.079 63.158 0.00 0.00 45.74 4.02
1484 1580 1.229209 AGTTCTCGGAAGGGCTCCA 60.229 57.895 0.00 0.00 45.74 3.86
1485 1581 1.518302 GAGTTCTCGGAAGGGCTCC 59.482 63.158 0.00 0.00 41.40 4.70
1486 1582 1.139947 CGAGTTCTCGGAAGGGCTC 59.860 63.158 13.52 0.00 0.00 4.70
1487 1583 3.007973 GCGAGTTCTCGGAAGGGCT 62.008 63.158 20.97 0.00 0.00 5.19
1488 1584 2.509561 GCGAGTTCTCGGAAGGGC 60.510 66.667 20.97 2.54 0.00 5.19
1489 1585 2.202623 CGCGAGTTCTCGGAAGGG 60.203 66.667 20.97 0.84 0.00 3.95
1490 1586 2.881352 GCGCGAGTTCTCGGAAGG 60.881 66.667 20.97 0.00 0.00 3.46
1491 1587 3.241059 CGCGCGAGTTCTCGGAAG 61.241 66.667 28.94 0.00 0.00 3.46
1647 1746 6.929049 TGGAACCTACATCGATCAATGATAAC 59.071 38.462 0.00 0.00 0.00 1.89
1652 1751 6.564686 CGAAATGGAACCTACATCGATCAATG 60.565 42.308 0.00 0.00 0.00 2.82
1699 1798 2.509422 GTATCCTTCCGGCCACCC 59.491 66.667 2.24 0.00 0.00 4.61
1738 1837 5.638234 AGTATTTTTCTTTTCCTCTCGTCCG 59.362 40.000 0.00 0.00 0.00 4.79
1742 1841 6.402658 GCAGGAGTATTTTTCTTTTCCTCTCG 60.403 42.308 0.00 0.00 32.93 4.04
1832 1951 1.543358 GGCAGCAAAAGGGAAGAAGAG 59.457 52.381 0.00 0.00 0.00 2.85
1853 1973 1.348696 TGCTGCAGAGGAGAAACATGA 59.651 47.619 20.43 0.00 0.00 3.07
1901 2021 4.115199 AATGGTCCCTCCCTGCGC 62.115 66.667 0.00 0.00 34.77 6.09
1902 2022 2.190578 GAATGGTCCCTCCCTGCG 59.809 66.667 0.00 0.00 34.77 5.18
1958 2088 4.756642 CAGCAACTCAATTCAACAGTAGGA 59.243 41.667 0.00 0.00 0.00 2.94
1965 2099 5.091431 GCATCTACAGCAACTCAATTCAAC 58.909 41.667 0.00 0.00 0.00 3.18
1970 2104 1.667724 GCGCATCTACAGCAACTCAAT 59.332 47.619 0.30 0.00 0.00 2.57
2053 2190 0.516877 CGTGCGTTGATGTCATTGGT 59.483 50.000 0.00 0.00 0.00 3.67
2071 2208 1.067821 GTAGATTCCTCTGGTCCTGCG 59.932 57.143 0.00 0.00 32.66 5.18
2073 2210 2.752030 TGGTAGATTCCTCTGGTCCTG 58.248 52.381 0.00 0.00 32.66 3.86
2074 2211 3.208692 AGATGGTAGATTCCTCTGGTCCT 59.791 47.826 0.00 0.00 32.66 3.85
2077 2214 6.439058 GCTAATAGATGGTAGATTCCTCTGGT 59.561 42.308 0.00 0.00 32.66 4.00
2078 2215 6.438741 TGCTAATAGATGGTAGATTCCTCTGG 59.561 42.308 0.00 0.00 32.66 3.86
2092 2229 7.448420 TCCTTTCCTCATCTTGCTAATAGATG 58.552 38.462 6.53 6.53 46.65 2.90
2093 2230 7.256619 CCTCCTTTCCTCATCTTGCTAATAGAT 60.257 40.741 0.00 0.00 32.66 1.98
2094 2231 6.042552 CCTCCTTTCCTCATCTTGCTAATAGA 59.957 42.308 0.00 0.00 0.00 1.98
2107 5196 3.034635 GAGTAGATGCCTCCTTTCCTCA 58.965 50.000 0.00 0.00 0.00 3.86
2110 5199 2.920724 GGAGTAGATGCCTCCTTTCC 57.079 55.000 0.00 0.00 44.29 3.13
2316 5414 5.006844 TGTGTTGTGTGGTGAGTTTAATACG 59.993 40.000 0.00 0.00 0.00 3.06
2426 5536 2.240493 ATAGTGCGGGCTGTCAATAC 57.760 50.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.