Multiple sequence alignment - TraesCS2B01G209500

Loading Multiple Alignment...

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 TraesCS2B01G209500 chr2B 100.000 3825 0 0 1 3825 191741224 191745048 0.000000e+00 7064
1 TraesCS2B01G209500 chr2D 95.780 3839 85 24 17 3825 134789900 134793691 0.000000e+00 6120
2 TraesCS2B01G209500 chr2A 95.276 3662 79 36 177 3825 142707146 142710726 0.000000e+00 5718
3 TraesCS2B01G209500 chr2A 88.525 183 6 8 1 180 142706683 142706853 1.390000e-49 207


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 TraesCS2B01G209500 chr2B 191741224 191745048 3824 False 7064.0 7064 100.0000 1 3825 1 chr2B.!!$F1 3824
1 TraesCS2B01G209500 chr2D 134789900 134793691 3791 False 6120.0 6120 95.7800 17 3825 1 chr2D.!!$F1 3808
2 TraesCS2B01G209500 chr2A 142706683 142710726 4043 False 2962.5 5718 91.9005 1 3825 2 chr2A.!!$F1 3824

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
384 699 0.036858 AAGGACCAGCGAGAGAAAGC 60.037 55.0 0.0 0.0 0.00 3.51 F
1140 1487 0.112412 ATTTGCTTGTTCCGAGGGGT 59.888 50.0 0.0 0.0 33.83 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1766 0.179045 CCTAAGGGCCAACATCCGAG 60.179 60.0 6.18 0.0 0.0 4.63 R
3067 3427 1.026718 CCTAGGCTGCCGTTTTCCTG 61.027 60.0 13.96 0.0 0.0 3.86 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
41 43 5.335127 GCAGTATAACAATTTGACCAGCAG 58.665 41.667 2.79 0.00 0.00 4.24
66 70 6.359804 CACATGATCCTCCCAGAAATAGAAA 58.640 40.000 0.00 0.00 0.00 2.52
101 105 5.723295 TCATGTCAACGATCTCATTCTCAA 58.277 37.500 0.00 0.00 0.00 3.02
150 168 1.810455 TAATCCCCGGGAACTTAGGG 58.190 55.000 26.32 1.48 44.67 3.53
157 175 2.743179 GGGAACTTAGGGGGAGCCG 61.743 68.421 0.00 0.00 0.00 5.52
294 609 3.854669 CCCAATCCTCTCCGCGCT 61.855 66.667 5.56 0.00 0.00 5.92
328 643 0.462047 GGCCTAACCAGTCCACATCG 60.462 60.000 0.00 0.00 38.86 3.84
345 660 2.048127 GGGTCACTGACACTCCGC 60.048 66.667 11.34 0.00 32.50 5.54
380 695 1.984570 CCCAAGGACCAGCGAGAGA 60.985 63.158 0.00 0.00 0.00 3.10
382 697 0.321671 CCAAGGACCAGCGAGAGAAA 59.678 55.000 0.00 0.00 0.00 2.52
384 699 0.036858 AAGGACCAGCGAGAGAAAGC 60.037 55.000 0.00 0.00 0.00 3.51
385 700 1.188219 AGGACCAGCGAGAGAAAGCA 61.188 55.000 0.00 0.00 35.48 3.91
388 703 0.394565 ACCAGCGAGAGAAAGCAACT 59.605 50.000 0.00 0.00 35.48 3.16
475 799 1.401539 GGAAACATTCACCGCAGAAGC 60.402 52.381 0.00 0.00 37.42 3.86
486 810 2.561373 CAGAAGCCGCCGAAAACC 59.439 61.111 0.00 0.00 0.00 3.27
507 831 3.656045 CGGAAAAAGCGCACGGGT 61.656 61.111 11.47 0.00 0.00 5.28
510 834 3.588891 GAAAAAGCGCACGGGTCGG 62.589 63.158 11.47 0.00 0.00 4.79
560 893 0.811616 CGGCGAGAGGGGAAAGATTG 60.812 60.000 0.00 0.00 0.00 2.67
642 979 0.901124 GAGAGGAGAAAGAGGCAGCA 59.099 55.000 0.00 0.00 0.00 4.41
643 980 0.903942 AGAGGAGAAAGAGGCAGCAG 59.096 55.000 0.00 0.00 0.00 4.24
644 981 0.744057 GAGGAGAAAGAGGCAGCAGC 60.744 60.000 0.00 0.00 41.10 5.25
645 982 1.002868 GGAGAAAGAGGCAGCAGCA 60.003 57.895 2.65 0.00 44.61 4.41
646 983 1.025647 GGAGAAAGAGGCAGCAGCAG 61.026 60.000 2.65 0.00 44.61 4.24
647 984 1.646624 GAGAAAGAGGCAGCAGCAGC 61.647 60.000 2.65 0.00 44.61 5.25
730 1073 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
732 1075 4.855230 ACCACCACCACCACCCCT 62.855 66.667 0.00 0.00 0.00 4.79
733 1076 2.530661 CCACCACCACCACCCCTA 60.531 66.667 0.00 0.00 0.00 3.53
735 1078 2.530916 ACCACCACCACCCCTACC 60.531 66.667 0.00 0.00 0.00 3.18
1008 1355 2.841988 AGGAGGAGGATGGCGCTC 60.842 66.667 7.64 0.00 0.00 5.03
1023 1370 0.868406 CGCTCTTCCGCAAGTTCTTT 59.132 50.000 0.00 0.00 0.00 2.52
1140 1487 0.112412 ATTTGCTTGTTCCGAGGGGT 59.888 50.000 0.00 0.00 33.83 4.95
1141 1488 0.536460 TTTGCTTGTTCCGAGGGGTC 60.536 55.000 0.00 0.00 33.83 4.46
1142 1489 2.434359 GCTTGTTCCGAGGGGTCG 60.434 66.667 0.00 0.00 33.83 4.79
1143 1490 2.434359 CTTGTTCCGAGGGGTCGC 60.434 66.667 0.00 0.00 33.83 5.19
1144 1491 3.952628 CTTGTTCCGAGGGGTCGCC 62.953 68.421 0.00 0.00 33.83 5.54
1146 1493 4.452733 GTTCCGAGGGGTCGCCTG 62.453 72.222 14.22 5.85 33.83 4.85
1149 1496 4.452733 CCGAGGGGTCGCCTGTTC 62.453 72.222 14.22 0.00 0.00 3.18
1150 1497 4.452733 CGAGGGGTCGCCTGTTCC 62.453 72.222 14.22 0.00 0.00 3.62
1151 1498 4.452733 GAGGGGTCGCCTGTTCCG 62.453 72.222 14.22 0.00 0.00 4.30
1223 1570 4.463891 ACTGTTGCTTTCAGGGGATTTATG 59.536 41.667 7.87 0.00 37.25 1.90
1319 1669 0.763223 ACTCGGTCCAGTTCTGGGTT 60.763 55.000 17.37 0.00 0.00 4.11
1329 1679 1.559682 AGTTCTGGGTTGTCAGTGTGT 59.440 47.619 0.00 0.00 36.25 3.72
1355 1713 3.999001 CACAAGACTCAGATTTAGCTGCA 59.001 43.478 1.02 0.00 35.86 4.41
1356 1714 4.634883 CACAAGACTCAGATTTAGCTGCAT 59.365 41.667 1.02 0.00 35.86 3.96
1357 1715 5.123502 CACAAGACTCAGATTTAGCTGCATT 59.876 40.000 1.02 0.00 35.86 3.56
1358 1716 5.709164 ACAAGACTCAGATTTAGCTGCATTT 59.291 36.000 1.02 0.00 35.86 2.32
1359 1717 5.814764 AGACTCAGATTTAGCTGCATTTG 57.185 39.130 1.02 0.00 35.86 2.32
1360 1718 5.494724 AGACTCAGATTTAGCTGCATTTGA 58.505 37.500 1.02 0.00 35.86 2.69
1361 1719 5.353678 AGACTCAGATTTAGCTGCATTTGAC 59.646 40.000 1.02 0.00 35.86 3.18
1362 1720 4.397417 ACTCAGATTTAGCTGCATTTGACC 59.603 41.667 1.02 0.00 35.86 4.02
1406 1764 5.652014 TCCATATTCGAATTTTGTCTTGCCT 59.348 36.000 17.19 0.00 0.00 4.75
1408 1766 6.473455 CCATATTCGAATTTTGTCTTGCCTTC 59.527 38.462 17.19 0.00 0.00 3.46
1614 1974 4.023707 ACTTTGCTGTGTCTAGAAACATGC 60.024 41.667 16.22 19.39 34.35 4.06
1616 1976 2.069273 GCTGTGTCTAGAAACATGCGT 58.931 47.619 16.22 0.00 0.00 5.24
1650 2010 4.141846 TGCAGTATGAAGATGAGGTTCCTC 60.142 45.833 11.53 11.53 39.69 3.71
1883 2243 2.879103 TGGTCTCCAATTTCTGGTCC 57.121 50.000 0.00 0.00 46.51 4.46
1964 2324 2.442236 ACCCACAGCAATATGAAGGG 57.558 50.000 0.00 0.00 41.63 3.95
1982 2342 1.073897 GTGCCCACTCCTTCAGCTT 59.926 57.895 0.00 0.00 0.00 3.74
2277 2637 0.329261 TGGTTCAGAATGGCCTCCAG 59.671 55.000 3.32 0.00 36.75 3.86
2425 2785 1.266989 GGTTCTTTTTGAGACGCCCAG 59.733 52.381 0.00 0.00 33.02 4.45
3067 3427 1.678970 GATGGTGGGGTGGCAGTTC 60.679 63.158 0.00 0.00 0.00 3.01
3153 3513 5.824904 ATTCAGGTAGCATGAATGACAAC 57.175 39.130 14.64 0.00 43.87 3.32
3166 3526 3.246112 ACAACGGGCCAGCACCTA 61.246 61.111 4.39 0.00 0.00 3.08
3297 3657 3.118592 AGGTGGTTGCTGCTTCTATAGAC 60.119 47.826 0.67 0.00 0.00 2.59
3789 4149 9.809096 GACAGAAGACTGAATCATAGTAAATCA 57.191 33.333 0.00 0.00 46.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.760530 TGTTATACTGCCATTCTGAGCT 57.239 40.909 0.00 0.00 0.00 4.09
24 26 2.954989 TGTGCTGCTGGTCAAATTGTTA 59.045 40.909 0.00 0.00 0.00 2.41
41 43 2.425143 TTTCTGGGAGGATCATGTGC 57.575 50.000 0.00 0.00 36.25 4.57
93 97 2.549754 GTGTGGTGTGAGGTTGAGAATG 59.450 50.000 0.00 0.00 0.00 2.67
94 98 2.487265 GGTGTGGTGTGAGGTTGAGAAT 60.487 50.000 0.00 0.00 0.00 2.40
101 105 1.226262 GGTTGGTGTGGTGTGAGGT 59.774 57.895 0.00 0.00 0.00 3.85
150 168 1.078143 ATTCTTCACTGCGGCTCCC 60.078 57.895 0.00 0.00 0.00 4.30
157 175 1.696832 GCCCGACGATTCTTCACTGC 61.697 60.000 0.00 0.00 0.00 4.40
328 643 2.048127 GCGGAGTGTCAGTGACCC 60.048 66.667 20.43 13.11 0.00 4.46
353 668 4.748144 GTCCTTGGGGCCAGCTGG 62.748 72.222 29.34 29.34 38.53 4.85
367 682 0.320771 TTGCTTTCTCTCGCTGGTCC 60.321 55.000 0.00 0.00 0.00 4.46
380 695 2.985847 GCCGGCTGGAGTTGCTTT 60.986 61.111 22.15 0.00 37.49 3.51
451 775 1.209127 GCGGTGAATGTTTCCGTGG 59.791 57.895 0.00 0.00 45.11 4.94
475 799 2.050805 CCGTTTGGTTTTCGGCGG 60.051 61.111 7.21 0.00 37.90 6.13
486 810 1.536462 CCGTGCGCTTTTTCCGTTTG 61.536 55.000 9.73 0.00 0.00 2.93
507 831 1.337447 CCCGAGTTTTTACTGCTCCGA 60.337 52.381 0.00 0.00 0.00 4.55
510 834 2.742589 CCTTCCCGAGTTTTTACTGCTC 59.257 50.000 0.00 0.00 0.00 4.26
560 893 0.742635 CCTTTCTTCCTCTCGCTGCC 60.743 60.000 0.00 0.00 0.00 4.85
642 979 2.290122 CTACTACTGCTGCCGCTGCT 62.290 60.000 21.13 6.53 38.51 4.24
643 980 1.880340 CTACTACTGCTGCCGCTGC 60.880 63.158 14.83 14.83 38.51 5.25
644 981 0.248825 CTCTACTACTGCTGCCGCTG 60.249 60.000 5.46 5.46 40.51 5.18
645 982 1.388065 CCTCTACTACTGCTGCCGCT 61.388 60.000 0.70 0.00 36.97 5.52
646 983 1.066587 CCTCTACTACTGCTGCCGC 59.933 63.158 0.00 0.00 0.00 6.53
647 984 1.066303 CTTCCTCTACTACTGCTGCCG 59.934 57.143 0.00 0.00 0.00 5.69
964 1311 4.548513 CCTCTCCCCCTCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
974 1321 0.105709 CCTCCTCTTCCTCCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
975 1322 0.930726 TCCTCCTCTTCCTCCTCTCC 59.069 60.000 0.00 0.00 0.00 3.71
976 1323 1.133482 CCTCCTCCTCTTCCTCCTCTC 60.133 61.905 0.00 0.00 0.00 3.20
977 1324 0.933700 CCTCCTCCTCTTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
978 1325 0.930726 TCCTCCTCCTCTTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
979 1326 0.933700 CTCCTCCTCCTCTTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1008 1355 3.809832 TCTTGAGAAAGAACTTGCGGAAG 59.190 43.478 15.80 15.80 35.07 3.46
1023 1370 0.456221 GATCCGGCGTCTTCTTGAGA 59.544 55.000 6.01 0.00 0.00 3.27
1142 1489 2.781431 AAATCCCCCACGGAACAGGC 62.781 60.000 0.00 0.00 46.47 4.85
1143 1490 0.251608 AAAATCCCCCACGGAACAGG 60.252 55.000 0.00 0.00 46.47 4.00
1144 1491 0.887933 CAAAATCCCCCACGGAACAG 59.112 55.000 0.00 0.00 46.47 3.16
1145 1492 0.540830 CCAAAATCCCCCACGGAACA 60.541 55.000 0.00 0.00 46.47 3.18
1146 1493 1.254975 CCCAAAATCCCCCACGGAAC 61.255 60.000 0.00 0.00 46.47 3.62
1147 1494 1.077625 CCCAAAATCCCCCACGGAA 59.922 57.895 0.00 0.00 46.47 4.30
1149 1496 3.074369 GCCCAAAATCCCCCACGG 61.074 66.667 0.00 0.00 0.00 4.94
1150 1497 1.191489 AAAGCCCAAAATCCCCCACG 61.191 55.000 0.00 0.00 0.00 4.94
1151 1498 1.064003 AAAAGCCCAAAATCCCCCAC 58.936 50.000 0.00 0.00 0.00 4.61
1152 1499 1.063183 CAAAAGCCCAAAATCCCCCA 58.937 50.000 0.00 0.00 0.00 4.96
1153 1500 0.322456 GCAAAAGCCCAAAATCCCCC 60.322 55.000 0.00 0.00 0.00 5.40
1154 1501 0.322456 GGCAAAAGCCCAAAATCCCC 60.322 55.000 0.00 0.00 0.00 4.81
1155 1502 0.673333 CGGCAAAAGCCCAAAATCCC 60.673 55.000 0.19 0.00 0.00 3.85
1156 1503 1.298157 GCGGCAAAAGCCCAAAATCC 61.298 55.000 0.19 0.00 0.00 3.01
1223 1570 6.264067 ACTGAATTCCAGCTCAAATAATAGCC 59.736 38.462 2.27 0.00 46.81 3.93
1329 1679 1.882912 AAATCTGAGTCTTGTGCGCA 58.117 45.000 5.66 5.66 0.00 6.09
1355 1713 8.293699 AGAAATAAAGCCGATTTAGGTCAAAT 57.706 30.769 0.00 0.00 39.63 2.32
1356 1714 7.696992 AGAAATAAAGCCGATTTAGGTCAAA 57.303 32.000 0.00 0.00 36.81 2.69
1357 1715 7.696992 AAGAAATAAAGCCGATTTAGGTCAA 57.303 32.000 0.00 0.00 36.81 3.18
1358 1716 7.148137 GGAAAGAAATAAAGCCGATTTAGGTCA 60.148 37.037 0.00 0.00 36.81 4.02
1359 1717 7.148137 TGGAAAGAAATAAAGCCGATTTAGGTC 60.148 37.037 0.00 0.00 36.81 3.85
1360 1718 6.661805 TGGAAAGAAATAAAGCCGATTTAGGT 59.338 34.615 0.00 0.00 36.81 3.08
1361 1719 7.095695 TGGAAAGAAATAAAGCCGATTTAGG 57.904 36.000 0.00 0.00 36.81 2.69
1406 1764 1.209504 CTAAGGGCCAACATCCGAGAA 59.790 52.381 6.18 0.00 0.00 2.87
1408 1766 0.179045 CCTAAGGGCCAACATCCGAG 60.179 60.000 6.18 0.00 0.00 4.63
1455 1814 9.888878 CTAGATGATTGTTGCATGTTTATAAGG 57.111 33.333 0.00 0.00 0.00 2.69
1614 1974 8.797266 TCTTCATACTGCATATGTACTAAACG 57.203 34.615 4.29 0.00 41.44 3.60
1650 2010 1.020861 TCAAGTGCTGGCATGCTACG 61.021 55.000 18.92 6.89 0.00 3.51
1883 2243 2.711922 CCGACTCCTCTTGTCCCCG 61.712 68.421 0.00 0.00 0.00 5.73
1964 2324 1.073897 AAGCTGAAGGAGTGGGCAC 59.926 57.895 0.00 0.00 0.00 5.01
1982 2342 5.440207 TCAAGAAATGGTGGATCATCTCA 57.560 39.130 0.00 0.00 0.00 3.27
2277 2637 2.417719 CAATATGAGAGGCCGGCTAAC 58.582 52.381 28.56 17.41 0.00 2.34
2425 2785 2.087646 GCTGGAGATGTTTCTTGGTCC 58.912 52.381 0.00 0.00 30.30 4.46
3067 3427 1.026718 CCTAGGCTGCCGTTTTCCTG 61.027 60.000 13.96 0.00 0.00 3.86
3153 3513 4.162690 GGAGTAGGTGCTGGCCCG 62.163 72.222 0.00 0.00 0.00 6.13
3181 3541 2.420687 CCTGCTGTAAACCTCCTGGATC 60.421 54.545 0.00 0.00 37.04 3.36
3297 3657 0.239347 CAAACTTGCGCCCTTCTGAG 59.761 55.000 4.18 0.00 0.00 3.35
3797 4157 6.101650 TCGCATGTATGTTATCTCCAAGAT 57.898 37.500 0.00 0.00 38.70 2.40


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

AutoCloner maintained by Alex Coulton.