Multiple sequence alignment - TraesCS6B01G091600

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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 TraesCS6B01G091600 chr6B 100.000 2273 0 0 1 2273 67339744 67342016 0.000000e+00 4198
1 TraesCS6B01G091600 chr6B 94.251 661 24 9 1306 1960 68794775 68795427 0.000000e+00 998
2 TraesCS6B01G091600 chr6B 95.710 606 19 5 1668 2273 68840926 68840328 0.000000e+00 968
3 TraesCS6B01G091600 chr6B 96.350 274 6 1 2000 2273 68795424 68795693 4.450000e-122 448
4 TraesCS6B01G091600 chr4B 88.021 1319 142 5 1 1304 664171511 664172828 0.000000e+00 1546
5 TraesCS6B01G091600 chr3B 93.678 949 53 3 356 1303 636765258 636766200 0.000000e+00 1413
6 TraesCS6B01G091600 chr3D 85.736 1311 173 12 1 1302 570309811 570311116 0.000000e+00 1373
7 TraesCS6B01G091600 chr3D 85.123 1304 188 4 1 1298 406417572 406418875 0.000000e+00 1328
8 TraesCS6B01G091600 chr5D 85.409 1309 179 10 1 1300 240523352 240522047 0.000000e+00 1349
9 TraesCS6B01G091600 chr2D 84.996 1313 183 12 1 1303 650478416 650477108 0.000000e+00 1321
10 TraesCS6B01G091600 chr7D 84.885 1310 188 8 1 1302 554425494 554426801 0.000000e+00 1314
11 TraesCS6B01G091600 chr1D 84.897 1311 186 8 1 1303 431515444 431516750 0.000000e+00 1314
12 TraesCS6B01G091600 chr5A 84.170 1314 192 14 1 1303 415261553 415260245 0.000000e+00 1260
13 TraesCS6B01G091600 chr2B 76.018 221 37 10 175 385 382728062 382728276 1.440000e-17 100


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 TraesCS6B01G091600 chr6B 67339744 67342016 2272 False 4198 4198 100.0000 1 2273 1 chr6B.!!$F1 2272
1 TraesCS6B01G091600 chr6B 68840328 68840926 598 True 968 968 95.7100 1668 2273 1 chr6B.!!$R1 605
2 TraesCS6B01G091600 chr6B 68794775 68795693 918 False 723 998 95.3005 1306 2273 2 chr6B.!!$F2 967
3 TraesCS6B01G091600 chr4B 664171511 664172828 1317 False 1546 1546 88.0210 1 1304 1 chr4B.!!$F1 1303
4 TraesCS6B01G091600 chr3B 636765258 636766200 942 False 1413 1413 93.6780 356 1303 1 chr3B.!!$F1 947
5 TraesCS6B01G091600 chr3D 570309811 570311116 1305 False 1373 1373 85.7360 1 1302 1 chr3D.!!$F2 1301
6 TraesCS6B01G091600 chr3D 406417572 406418875 1303 False 1328 1328 85.1230 1 1298 1 chr3D.!!$F1 1297
7 TraesCS6B01G091600 chr5D 240522047 240523352 1305 True 1349 1349 85.4090 1 1300 1 chr5D.!!$R1 1299
8 TraesCS6B01G091600 chr2D 650477108 650478416 1308 True 1321 1321 84.9960 1 1303 1 chr2D.!!$R1 1302
9 TraesCS6B01G091600 chr7D 554425494 554426801 1307 False 1314 1314 84.8850 1 1302 1 chr7D.!!$F1 1301
10 TraesCS6B01G091600 chr1D 431515444 431516750 1306 False 1314 1314 84.8970 1 1303 1 chr1D.!!$F1 1302
11 TraesCS6B01G091600 chr5A 415260245 415261553 1308 True 1260 1260 84.1700 1 1303 1 chr5A.!!$R1 1302

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
896 903 0.179015 TTTGCGTTCCTTGGTGCCTA 60.179 50.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2241 0.327924 AGGATGTCCCGCAATCACAA 59.672 50.0 0.0 0.0 40.87 3.33 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
20 21 1.590147 GATTCCGACCACGACCACT 59.410 57.895 0.00 0.00 42.66 4.00
29 30 0.393077 CCACGACCACTCTGAAACCT 59.607 55.000 0.00 0.00 0.00 3.50
34 35 1.891150 GACCACTCTGAAACCTACGGA 59.109 52.381 0.00 0.00 0.00 4.69
56 57 2.654079 CCTCGGCACTGCTCCTCTT 61.654 63.158 0.00 0.00 0.00 2.85
65 66 1.280457 CTGCTCCTCTTACCAGGGTT 58.720 55.000 0.00 0.00 33.81 4.11
80 81 4.141914 ACCAGGGTTTCAGATCTTATCGAC 60.142 45.833 0.00 0.00 0.00 4.20
108 109 1.812571 CGGGGAACTGGAATGAACAAG 59.187 52.381 0.00 0.00 0.00 3.16
111 112 4.403734 GGGGAACTGGAATGAACAAGTTA 58.596 43.478 0.00 0.00 0.00 2.24
192 193 1.674817 CGGGTGGCGAAGATACTTTGT 60.675 52.381 0.00 0.00 0.00 2.83
292 298 4.290942 AGAGGAAGGGACGATTACAGAAT 58.709 43.478 0.00 0.00 0.00 2.40
342 348 2.143925 GCTCTTTGGCGACTACAAGTT 58.856 47.619 0.00 0.00 0.00 2.66
354 360 4.025145 CGACTACAAGTTGTTCCCAAAGTC 60.025 45.833 14.90 17.08 33.24 3.01
412 418 2.731976 CCTGACTTGACTACTTTGCGTC 59.268 50.000 0.00 0.00 0.00 5.19
438 444 1.207488 ACATCAAGCAGGTGGGGCTA 61.207 55.000 0.00 0.00 41.66 3.93
447 453 0.839946 AGGTGGGGCTATGTGATGTC 59.160 55.000 0.00 0.00 0.00 3.06
454 460 2.954318 GGGCTATGTGATGTCTGCAAAT 59.046 45.455 0.00 0.00 0.00 2.32
588 594 4.778842 GTGGACACGTGACATATTGATC 57.221 45.455 25.01 5.46 0.00 2.92
603 609 7.099764 ACATATTGATCGACCCTATGTTCATC 58.900 38.462 2.92 0.00 30.84 2.92
627 633 7.670364 TCGATGAGGAAAGATGCAAGATTATA 58.330 34.615 0.00 0.00 0.00 0.98
672 678 0.946221 CACGGAACTGCTGGACTCAC 60.946 60.000 0.00 0.00 0.00 3.51
723 729 4.702131 GCTTTGAAATGGGTACATGAGACT 59.298 41.667 0.00 0.00 37.40 3.24
760 766 1.066587 CCTTCCTCGCGATGGAGAC 59.933 63.158 19.98 0.00 37.91 3.36
766 772 2.279120 CGCGATGGAGACTGAGGC 60.279 66.667 0.00 0.00 0.00 4.70
810 816 2.750237 GCCGGGTGGGTCACAATC 60.750 66.667 2.18 0.00 38.44 2.67
818 824 1.608590 GTGGGTCACAATCAACACTGG 59.391 52.381 0.00 0.00 34.08 4.00
896 903 0.179015 TTTGCGTTCCTTGGTGCCTA 60.179 50.000 0.00 0.00 0.00 3.93
924 931 1.681780 CCACTGGTTGGCATAACGGAT 60.682 52.381 0.00 0.00 39.07 4.18
984 991 3.879351 CTTTGCGCAACTCCGTGGC 62.879 63.158 24.99 0.00 0.00 5.01
1032 1039 3.196463 CTGCTTGGAGCTAGTTGATCTG 58.804 50.000 1.29 0.00 42.97 2.90
1038 1045 3.055819 TGGAGCTAGTTGATCTGTGGAAC 60.056 47.826 0.00 0.00 37.35 3.62
1065 1072 3.825812 CAACACTCGTTCAGTTGCC 57.174 52.632 0.00 0.00 36.59 4.52
1148 1162 8.375493 ACTCATGTCAGTAGGGAAAGTAATAA 57.625 34.615 0.00 0.00 0.00 1.40
1149 1163 8.258708 ACTCATGTCAGTAGGGAAAGTAATAAC 58.741 37.037 0.00 0.00 0.00 1.89
1193 1207 0.731417 GCTAGCACACTTGATGGCAG 59.269 55.000 10.63 0.00 44.49 4.85
1233 1247 1.202940 AGCCCTGAGTTTCTGGTTTCC 60.203 52.381 2.04 0.00 34.10 3.13
1326 1342 1.497161 ATTGGGACGGAGGGAGTAAG 58.503 55.000 0.00 0.00 0.00 2.34
1461 1477 2.041686 TTATGCCGTTCAACCGCCC 61.042 57.895 0.00 0.00 0.00 6.13
1472 1488 1.028905 CAACCGCCCTTGAACTGAAA 58.971 50.000 0.00 0.00 0.00 2.69
1473 1489 1.407258 CAACCGCCCTTGAACTGAAAA 59.593 47.619 0.00 0.00 0.00 2.29
1474 1490 1.770294 ACCGCCCTTGAACTGAAAAA 58.230 45.000 0.00 0.00 0.00 1.94
1538 1554 6.334989 ACTGCTACGTATTGTACTTTATGCA 58.665 36.000 0.00 0.00 0.00 3.96
1578 1599 7.284034 AGCTTCCATCCTACTGTATTTTCATTG 59.716 37.037 0.00 0.00 0.00 2.82
1586 1607 6.884295 CCTACTGTATTTTCATTGGTGGAGAA 59.116 38.462 0.00 0.00 0.00 2.87
1754 1776 1.537562 CGCGGATACCTTACCCTGTTC 60.538 57.143 0.00 0.00 0.00 3.18
1759 1781 1.188863 TACCTTACCCTGTTCGGAGC 58.811 55.000 0.00 0.00 33.16 4.70
1772 1794 6.073003 CCCTGTTCGGAGCTTGATATATTTTC 60.073 42.308 0.00 0.00 33.16 2.29
1843 1865 5.651139 ACAAAGCTATGATTGATGCTCAAGT 59.349 36.000 2.92 0.00 40.05 3.16
1844 1866 6.152323 ACAAAGCTATGATTGATGCTCAAGTT 59.848 34.615 2.92 0.00 40.05 2.66
1945 1967 4.743151 CGTAATTGGTGCATACGTATGAGT 59.257 41.667 34.11 17.18 38.03 3.41
2092 2114 7.979537 GGGTGTTAAAAAGTTTCTTCACTCATT 59.020 33.333 0.00 0.00 0.00 2.57
2242 2264 1.134521 TGATTGCGGGACATCCTACAC 60.135 52.381 0.00 0.00 35.95 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.393077 AGGTTTCAGAGTGGTCGTGG 59.607 55.000 0.00 0.00 0.00 4.94
50 51 3.269592 TCTGAAACCCTGGTAAGAGGA 57.730 47.619 0.00 0.00 34.69 3.71
53 54 6.183360 CGATAAGATCTGAAACCCTGGTAAGA 60.183 42.308 0.00 0.00 0.00 2.10
56 57 5.068723 GTCGATAAGATCTGAAACCCTGGTA 59.931 44.000 0.00 0.00 0.00 3.25
65 66 5.276726 CGTGTACTCGTCGATAAGATCTGAA 60.277 44.000 9.11 0.00 0.00 3.02
80 81 1.214589 CCAGTTCCCCGTGTACTCG 59.785 63.158 10.28 10.28 0.00 4.18
108 109 5.324697 GTGCAAGAAATTCTGACGGATAAC 58.675 41.667 0.00 0.00 0.00 1.89
111 112 2.749621 GGTGCAAGAAATTCTGACGGAT 59.250 45.455 0.00 0.00 0.00 4.18
192 193 1.270839 CGACTTCTCCAAAGCCCAAGA 60.271 52.381 0.00 0.00 0.00 3.02
261 267 1.487142 GTCCCTTCCTCTAAAGAGCCC 59.513 57.143 1.21 0.00 40.75 5.19
292 298 5.822519 ACAACTGTTTGTTAGCTGATGAAGA 59.177 36.000 0.00 0.00 43.89 2.87
327 333 2.215196 GGAACAACTTGTAGTCGCCAA 58.785 47.619 0.00 0.00 0.00 4.52
354 360 1.280998 ACTCTCCACCAAAATACCCGG 59.719 52.381 0.00 0.00 0.00 5.73
412 418 1.395954 CACCTGCTTGATGTGTCGATG 59.604 52.381 0.00 0.00 0.00 3.84
438 444 3.119743 CCGTTGATTTGCAGACATCACAT 60.120 43.478 5.12 0.00 0.00 3.21
447 453 1.798223 TCTTCGTCCGTTGATTTGCAG 59.202 47.619 0.00 0.00 0.00 4.41
454 460 0.032815 TGCATGTCTTCGTCCGTTGA 59.967 50.000 0.00 0.00 0.00 3.18
588 594 3.569548 CTCATCGATGAACATAGGGTCG 58.430 50.000 27.09 9.24 36.18 4.79
603 609 6.798315 ATAATCTTGCATCTTTCCTCATCG 57.202 37.500 0.00 0.00 0.00 3.84
672 678 1.266786 GGTCGTAACCATCGCGATCG 61.267 60.000 20.85 19.08 45.68 3.69
723 729 3.430453 AGGAAATTCCAAGATCGCCAAA 58.570 40.909 15.21 0.00 39.61 3.28
754 760 1.610673 GTCCAGGCCTCAGTCTCCA 60.611 63.158 0.00 0.00 0.00 3.86
760 766 2.046507 GCACTGTCCAGGCCTCAG 60.047 66.667 16.43 16.43 35.60 3.35
766 772 2.667418 CCTCCAGCACTGTCCAGG 59.333 66.667 0.00 0.00 0.00 4.45
807 813 3.737172 GCGCCGCCAGTGTTGATT 61.737 61.111 0.00 0.00 0.00 2.57
829 835 2.377869 CCCCCTTCATATCCTCAGCATT 59.622 50.000 0.00 0.00 0.00 3.56
896 903 1.829533 CCAACCAGTGGCTTGCACT 60.830 57.895 9.78 0.00 41.72 4.40
924 931 0.391661 GCAACTCTGCGATGAAGGGA 60.392 55.000 0.00 0.00 39.20 4.20
1032 1039 3.345808 TTGCTGCGCGAGTTCCAC 61.346 61.111 12.10 0.00 0.00 4.02
1038 1045 4.126390 CGAGTGTTGCTGCGCGAG 62.126 66.667 12.10 5.65 0.00 5.03
1065 1072 0.597637 ATTCGGTCAAGATAGGCGCG 60.598 55.000 0.00 0.00 0.00 6.86
1193 1207 1.300971 TGCATCAAGCCAACTCTCGC 61.301 55.000 0.00 0.00 44.83 5.03
1303 1319 2.271777 ACTCCCTCCGTCCCAATTAAA 58.728 47.619 0.00 0.00 0.00 1.52
1305 1321 2.852714 TACTCCCTCCGTCCCAATTA 57.147 50.000 0.00 0.00 0.00 1.40
1306 1322 1.838077 CTTACTCCCTCCGTCCCAATT 59.162 52.381 0.00 0.00 0.00 2.32
1307 1323 1.273666 ACTTACTCCCTCCGTCCCAAT 60.274 52.381 0.00 0.00 0.00 3.16
1308 1324 0.115745 ACTTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1309 1325 1.002069 TACTTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1310 1326 2.149973 TTACTTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
1311 1327 7.715266 ATATAATTACTTACTCCCTCCGTCC 57.285 40.000 0.00 0.00 0.00 4.79
1312 1328 9.636879 GAAATATAATTACTTACTCCCTCCGTC 57.363 37.037 0.00 0.00 0.00 4.79
1313 1329 9.151177 TGAAATATAATTACTTACTCCCTCCGT 57.849 33.333 0.00 0.00 0.00 4.69
1478 1494 9.823647 CCATAACTTAGAGTGTGAATATCAACT 57.176 33.333 0.00 0.00 0.00 3.16
1479 1495 9.046296 CCCATAACTTAGAGTGTGAATATCAAC 57.954 37.037 0.00 0.00 0.00 3.18
1496 1512 7.279313 CGTAGCAGTTATTTGTACCCATAACTT 59.721 37.037 17.96 11.16 41.46 2.66
1538 1554 3.616219 TGGAAGCTAATACCGCACAATT 58.384 40.909 0.00 0.00 0.00 2.32
1552 1568 6.313519 TGAAAATACAGTAGGATGGAAGCT 57.686 37.500 0.00 0.00 0.00 3.74
1553 1569 7.420800 CAATGAAAATACAGTAGGATGGAAGC 58.579 38.462 0.00 0.00 0.00 3.86
1578 1599 5.046591 TGGACCGATGATATATTTCTCCACC 60.047 44.000 0.00 0.00 0.00 4.61
1586 1607 4.718774 AGCCTGATGGACCGATGATATATT 59.281 41.667 0.00 0.00 34.57 1.28
1592 1613 0.397675 AGAGCCTGATGGACCGATGA 60.398 55.000 0.00 0.00 34.57 2.92
1754 1776 5.392380 GCCCATGAAAATATATCAAGCTCCG 60.392 44.000 0.00 0.00 0.00 4.63
1759 1781 8.636213 ACAAAGAGCCCATGAAAATATATCAAG 58.364 33.333 0.00 0.00 0.00 3.02
1772 1794 1.250328 TGAAGCACAAAGAGCCCATG 58.750 50.000 0.00 0.00 0.00 3.66
1843 1865 3.831323 TCTCTTGGACAGCCATGAAAAA 58.169 40.909 0.00 0.00 44.79 1.94
1844 1866 3.507162 TCTCTTGGACAGCCATGAAAA 57.493 42.857 0.00 0.00 44.79 2.29
1990 2012 3.411446 CATGCCAAGAAACTGGACAGTA 58.589 45.455 5.25 0.00 41.58 2.74
1991 2013 2.233271 CATGCCAAGAAACTGGACAGT 58.767 47.619 0.00 0.00 44.94 3.55
2066 2088 6.859017 TGAGTGAAGAAACTTTTTAACACCC 58.141 36.000 0.00 0.00 0.00 4.61
2092 2114 4.261238 CCGTTGTAGCACCAACAAACATAA 60.261 41.667 15.87 0.00 43.89 1.90
2219 2241 0.327924 AGGATGTCCCGCAATCACAA 59.672 50.000 0.00 0.00 40.87 3.33
2220 2242 1.134521 GTAGGATGTCCCGCAATCACA 60.135 52.381 0.00 0.00 40.87 3.58
2221 2243 1.134521 TGTAGGATGTCCCGCAATCAC 60.135 52.381 0.00 0.00 40.87 3.06
2224 2246 0.908910 TGTGTAGGATGTCCCGCAAT 59.091 50.000 0.00 0.00 40.87 3.56
2225 2247 0.687920 TTGTGTAGGATGTCCCGCAA 59.312 50.000 0.00 0.00 40.87 4.85
2226 2248 0.908910 ATTGTGTAGGATGTCCCGCA 59.091 50.000 0.00 0.00 40.87 5.69
2228 2250 2.943033 GGAAATTGTGTAGGATGTCCCG 59.057 50.000 0.00 0.00 40.87 5.14
2229 2251 3.947834 CTGGAAATTGTGTAGGATGTCCC 59.052 47.826 0.00 0.00 36.42 4.46
2230 2252 3.378427 GCTGGAAATTGTGTAGGATGTCC 59.622 47.826 0.00 0.00 31.42 4.02
2231 2253 4.009675 TGCTGGAAATTGTGTAGGATGTC 58.990 43.478 0.00 0.00 0.00 3.06
2232 2254 4.032960 TGCTGGAAATTGTGTAGGATGT 57.967 40.909 0.00 0.00 0.00 3.06
2233 2255 5.389859 TTTGCTGGAAATTGTGTAGGATG 57.610 39.130 0.00 0.00 0.00 3.51
2242 2264 5.350365 CCACTCATCATTTTGCTGGAAATTG 59.650 40.000 9.39 9.39 0.00 2.32


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

AutoCloner maintained by Alex Coulton.