Multiple sequence alignment - TraesCS2B01G271400

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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 TraesCS2B01G271400 chr2B 100.000 2540 0 0 1 2540 371166785 371169324 0.000000e+00 4691
1 TraesCS2B01G271400 chr5B 87.436 2157 152 40 1 2123 689486204 689488275 0.000000e+00 2372
2 TraesCS2B01G271400 chr5B 87.719 114 4 6 2242 2347 689488469 689488580 9.540000e-25 124
3 TraesCS2B01G271400 chr2A 94.836 1433 44 7 702 2123 376076746 376075333 0.000000e+00 2209
4 TraesCS2B01G271400 chr2A 96.792 717 21 1 1 715 376077482 376076766 0.000000e+00 1195
5 TraesCS2B01G271400 chr2A 91.885 382 17 8 2130 2504 376075193 376074819 2.900000e-144 521
6 TraesCS2B01G271400 chr5D 87.229 1198 68 25 702 1886 546365626 546366751 0.000000e+00 1286
7 TraesCS2B01G271400 chr5D 92.435 423 29 3 183 603 546358614 546359035 3.620000e-168 601
8 TraesCS2B01G271400 chr5D 90.830 229 20 1 1896 2123 546371656 546371884 3.170000e-79 305
9 TraesCS2B01G271400 chr5D 85.816 141 15 2 2402 2540 546379251 546379388 7.320000e-31 145
10 TraesCS2B01G271400 chr5D 95.455 66 3 0 601 666 546361501 546361566 3.460000e-19 106
11 TraesCS2B01G271400 chr2D 94.782 824 24 6 702 1513 299888069 299887253 0.000000e+00 1266
12 TraesCS2B01G271400 chr2D 95.994 724 17 5 1 715 299888808 299888088 0.000000e+00 1166
13 TraesCS2B01G271400 chr2D 97.117 555 14 1 1571 2123 299886930 299886376 0.000000e+00 935
14 TraesCS2B01G271400 chr2D 90.585 393 13 7 2153 2540 299886222 299885849 1.360000e-137 499
15 TraesCS2B01G271400 chr3A 82.955 616 64 25 730 1325 724300309 724300903 3.750000e-143 518
16 TraesCS2B01G271400 chr3A 84.601 552 41 17 1442 1983 724301038 724301555 2.250000e-140 508
17 TraesCS2B01G271400 chr3A 90.260 154 14 1 1970 2123 724303070 724303222 1.540000e-47 200


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 TraesCS2B01G271400 chr2B 371166785 371169324 2539 False 4691.000000 4691 100.000000 1 2540 1 chr2B.!!$F1 2539
1 TraesCS2B01G271400 chr5B 689486204 689488580 2376 False 1248.000000 2372 87.577500 1 2347 2 chr5B.!!$F1 2346
2 TraesCS2B01G271400 chr2A 376074819 376077482 2663 True 1308.333333 2209 94.504333 1 2504 3 chr2A.!!$R1 2503
3 TraesCS2B01G271400 chr5D 546365626 546366751 1125 False 1286.000000 1286 87.229000 702 1886 1 chr5D.!!$F1 1184
4 TraesCS2B01G271400 chr5D 546358614 546361566 2952 False 353.500000 601 93.945000 183 666 2 chr5D.!!$F4 483
5 TraesCS2B01G271400 chr2D 299885849 299888808 2959 True 966.500000 1266 94.619500 1 2540 4 chr2D.!!$R1 2539
6 TraesCS2B01G271400 chr3A 724300309 724303222 2913 False 408.666667 518 85.938667 730 2123 3 chr3A.!!$F1 1393

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
219 243 0.247974 GTACCTGGACATCGTCGACG 60.248 60.0 31.3 31.3 41.45 5.12 F
1152 3717 0.914417 ATGCGGAGGAAGAAGGGGAA 60.914 55.0 0.0 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 3996 0.110295 CACCACCCAATCAGTGTCCA 59.890 55.000 0.0 0.0 33.20 4.02 R
2198 6783 3.072184 ACTGGGAGTATCTTGCCATGATC 59.928 47.826 0.0 0.0 37.96 2.92 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
106 108 3.118555 TCCGGTCGGTGATTTTGTCATAT 60.119 43.478 9.36 0.00 39.48 1.78
137 139 0.863119 GAGCGCAATCATCAAACCGC 60.863 55.000 11.47 0.00 41.51 5.68
139 141 1.135699 GCGCAATCATCAAACCGCTG 61.136 55.000 0.30 0.00 38.52 5.18
177 192 7.753630 AGATAGGCACAAATTGAAGATAGGAT 58.246 34.615 0.00 0.00 0.00 3.24
219 243 0.247974 GTACCTGGACATCGTCGACG 60.248 60.000 31.30 31.30 41.45 5.12
220 244 1.985447 TACCTGGACATCGTCGACGC 61.985 60.000 32.19 18.11 39.60 5.19
221 245 2.485582 CTGGACATCGTCGACGCT 59.514 61.111 32.19 21.45 39.60 5.07
222 246 1.869574 CTGGACATCGTCGACGCTG 60.870 63.158 32.97 32.97 40.80 5.18
223 247 3.248171 GGACATCGTCGACGCTGC 61.248 66.667 34.10 26.51 38.86 5.25
224 248 3.248171 GACATCGTCGACGCTGCC 61.248 66.667 34.10 24.17 38.86 4.85
599 634 1.682005 CAATGGCGGTGGGGTGAAT 60.682 57.895 0.00 0.00 0.00 2.57
690 3195 1.664965 AGTGTTCGGTCGCTCTTGC 60.665 57.895 0.00 0.00 0.00 4.01
755 3291 3.417601 GGCTTAAACGGGCCGATC 58.582 61.111 35.78 8.68 38.91 3.69
808 3344 3.894257 CGAGAGCACAAAGACTCCA 57.106 52.632 0.00 0.00 33.18 3.86
853 3389 2.164338 GTCCGAGGACAAGTCTTCTCT 58.836 52.381 16.75 0.00 44.02 3.10
854 3390 2.559231 GTCCGAGGACAAGTCTTCTCTT 59.441 50.000 16.75 0.00 44.02 2.85
855 3391 2.820787 TCCGAGGACAAGTCTTCTCTTC 59.179 50.000 10.08 0.00 34.03 2.87
856 3392 2.823154 CCGAGGACAAGTCTTCTCTTCT 59.177 50.000 10.08 0.00 34.03 2.85
857 3393 3.119637 CCGAGGACAAGTCTTCTCTTCTC 60.120 52.174 10.08 1.74 34.03 2.87
1014 3570 1.851021 TTGCAATGGCGTCCGAAGTG 61.851 55.000 0.00 0.00 45.35 3.16
1152 3717 0.914417 ATGCGGAGGAAGAAGGGGAA 60.914 55.000 0.00 0.00 0.00 3.97
1219 3788 2.523168 TGTCGTGGGAGGAGTGCA 60.523 61.111 0.00 0.00 0.00 4.57
1254 3823 2.670148 GGAGGGCTCCGACATGGTT 61.670 63.158 0.00 0.00 40.36 3.67
1365 3934 4.735132 TCCGACCAAGCCGAAGCG 62.735 66.667 0.00 0.00 46.67 4.68
1427 3996 2.446802 GGAATCCGCTCCCTCCCT 60.447 66.667 0.00 0.00 0.00 4.20
1547 4178 7.948034 TGTCTTTGGGTAACTAATAATTGGG 57.052 36.000 0.00 0.00 36.70 4.12
1548 4179 6.893005 TGTCTTTGGGTAACTAATAATTGGGG 59.107 38.462 0.00 0.00 36.70 4.96
1569 4200 4.567747 GGGAGGGTTAGATTTTTCAGCTCA 60.568 45.833 0.00 0.00 0.00 4.26
1807 4708 0.985549 GAGCACGATGACGACAAGAC 59.014 55.000 0.00 0.00 42.66 3.01
1914 4819 4.668138 TTATAACCTTGGTCAAGCCCTT 57.332 40.909 5.26 0.11 37.11 3.95
2012 6453 4.005650 AGCTGGTTACTGTCATTGACATG 58.994 43.478 19.29 15.03 41.94 3.21
2119 6560 6.303839 TCTTTTAACTAGTCACTTGGCCAAT 58.696 36.000 20.85 6.15 0.00 3.16
2123 6564 1.741706 CTAGTCACTTGGCCAATGCAG 59.258 52.381 20.85 9.95 40.13 4.41
2124 6565 0.111061 AGTCACTTGGCCAATGCAGA 59.889 50.000 20.85 11.63 40.13 4.26
2125 6566 1.180029 GTCACTTGGCCAATGCAGAT 58.820 50.000 20.85 0.00 40.13 2.90
2126 6567 1.133790 GTCACTTGGCCAATGCAGATC 59.866 52.381 20.85 2.69 40.13 2.75
2128 6569 1.822990 CACTTGGCCAATGCAGATCTT 59.177 47.619 20.85 0.00 40.13 2.40
2181 6762 7.041848 TCGCTTTATGGATTGACATTGTATCTG 60.042 37.037 0.00 0.00 32.39 2.90
2198 6783 7.848223 TGTATCTGTGGTTTAAGTCATCATG 57.152 36.000 0.00 0.00 0.00 3.07
2215 6802 6.092396 GTCATCATGATCATGGCAAGATACTC 59.908 42.308 30.54 11.10 39.24 2.59
2216 6803 4.903054 TCATGATCATGGCAAGATACTCC 58.097 43.478 30.54 0.00 39.24 3.85
2224 6811 1.834263 GGCAAGATACTCCCAGTGACT 59.166 52.381 0.00 0.00 0.00 3.41
2225 6812 2.159028 GGCAAGATACTCCCAGTGACTC 60.159 54.545 0.00 0.00 0.00 3.36
2226 6813 2.497675 GCAAGATACTCCCAGTGACTCA 59.502 50.000 0.00 0.00 0.00 3.41
2287 6875 6.913170 TGAAATAAGTTCCAGTTGATTGCTC 58.087 36.000 0.00 0.00 35.12 4.26
2295 6883 4.851843 TCCAGTTGATTGCTCTCATTGAT 58.148 39.130 0.00 0.00 0.00 2.57
2366 6962 6.682863 CGATTATTTAAATACTGCCGCTATGC 59.317 38.462 7.43 0.00 0.00 3.14
2372 6968 2.036958 TACTGCCGCTATGCAATGTT 57.963 45.000 0.00 0.00 41.51 2.71
2373 6969 0.452987 ACTGCCGCTATGCAATGTTG 59.547 50.000 0.00 0.00 41.51 3.33
2374 6970 0.734309 CTGCCGCTATGCAATGTTGA 59.266 50.000 0.00 0.00 41.51 3.18
2375 6971 1.335810 CTGCCGCTATGCAATGTTGAT 59.664 47.619 0.00 0.00 41.51 2.57
2376 6972 2.549329 CTGCCGCTATGCAATGTTGATA 59.451 45.455 0.00 0.00 41.51 2.15
2377 6973 2.290367 TGCCGCTATGCAATGTTGATAC 59.710 45.455 0.00 0.00 38.56 2.24
2378 6974 2.549754 GCCGCTATGCAATGTTGATACT 59.450 45.455 0.00 0.00 0.00 2.12
2379 6975 3.364366 GCCGCTATGCAATGTTGATACTC 60.364 47.826 0.00 0.00 0.00 2.59
2380 6976 3.809279 CCGCTATGCAATGTTGATACTCA 59.191 43.478 0.00 0.00 0.00 3.41
2478 7074 7.399478 GGCTATAGGACTAATAATACAGGTGGT 59.601 40.741 1.04 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 139 2.364970 CCTATCTCTGGTCTTCCTGCAG 59.635 54.545 6.78 6.78 33.50 4.41
139 141 1.069978 GCCTATCTCTGGTCTTCCTGC 59.930 57.143 0.00 0.00 33.50 4.85
177 192 3.056962 TCGCAAGCTAAATGCAATCCAAA 60.057 39.130 9.42 0.00 44.01 3.28
224 248 2.587194 CAGCATTCTCCGAGCCCG 60.587 66.667 0.00 0.00 0.00 6.13
225 249 2.899339 GCAGCATTCTCCGAGCCC 60.899 66.667 0.00 0.00 0.00 5.19
226 250 2.124983 TGCAGCATTCTCCGAGCC 60.125 61.111 0.00 0.00 0.00 4.70
227 251 1.449246 ACTGCAGCATTCTCCGAGC 60.449 57.895 15.27 0.00 0.00 5.03
599 634 2.047274 CCGCCTTCCGCTCTTTCA 60.047 61.111 0.00 0.00 35.03 2.69
690 3195 4.596212 AGTAGGGGATAAGGAAATTACCCG 59.404 45.833 0.00 0.00 36.40 5.28
808 3344 0.914902 GAGGGGGTCTTTAGTGGGCT 60.915 60.000 0.00 0.00 0.00 5.19
1096 3655 4.124351 CACCGCTTCTACCGCCGA 62.124 66.667 0.00 0.00 0.00 5.54
1152 3717 1.078426 GTACAGGCAGAACCCGCAT 60.078 57.895 0.00 0.00 40.58 4.73
1219 3788 4.845580 CTTCTCCGCCGCCTGCAT 62.846 66.667 0.00 0.00 41.33 3.96
1254 3823 1.669115 GACTTGGAAGCAGCGCTCA 60.669 57.895 7.13 0.00 38.25 4.26
1427 3996 0.110295 CACCACCCAATCAGTGTCCA 59.890 55.000 0.00 0.00 33.20 4.02
1547 4178 4.589908 TGAGCTGAAAAATCTAACCCTCC 58.410 43.478 0.00 0.00 0.00 4.30
1548 4179 5.882557 TCATGAGCTGAAAAATCTAACCCTC 59.117 40.000 0.00 0.00 0.00 4.30
1807 4708 9.033481 TCAAGAAATTCTAAAGCAAATTGTGTG 57.967 29.630 0.00 0.00 0.00 3.82
1914 4819 3.378911 TTGTTAGACATCGCAGTCACA 57.621 42.857 9.26 3.80 40.98 3.58
2012 6453 6.872920 TGGTAAATGAAGGCAAACCATATTC 58.127 36.000 0.00 0.00 39.06 1.75
2123 6564 6.945218 ACCATATAGAGGCATCAGAAAGATC 58.055 40.000 0.00 0.00 33.72 2.75
2124 6565 6.949117 ACCATATAGAGGCATCAGAAAGAT 57.051 37.500 0.00 0.00 37.48 2.40
2125 6566 6.782494 TGTACCATATAGAGGCATCAGAAAGA 59.218 38.462 0.00 0.00 0.00 2.52
2126 6567 6.870965 GTGTACCATATAGAGGCATCAGAAAG 59.129 42.308 0.00 0.00 0.00 2.62
2128 6569 5.048013 CGTGTACCATATAGAGGCATCAGAA 60.048 44.000 0.00 0.00 0.00 3.02
2139 6720 3.620929 AGCGACACGTGTACCATATAG 57.379 47.619 23.44 6.83 0.00 1.31
2161 6742 6.899089 ACCACAGATACAATGTCAATCCATA 58.101 36.000 0.00 0.00 0.00 2.74
2181 6762 6.732154 CCATGATCATGATGACTTAAACCAC 58.268 40.000 32.71 0.00 41.20 4.16
2198 6783 3.072184 ACTGGGAGTATCTTGCCATGATC 59.928 47.826 0.00 0.00 37.96 2.92
2417 7013 7.808856 CAGTAACTCTGAGGTCAAACTAGTAAC 59.191 40.741 9.85 0.00 46.27 2.50
2478 7074 4.350816 TCCTGAGATGGTCCTTTTCTTTCA 59.649 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.