Multiple sequence alignment - TraesCS5D01G392500

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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 TraesCS5D01G392500 chr5D 100.000 4718 0 0 1 4718 460754523 460759240 0.000000e+00 8713
1 TraesCS5D01G392500 chr5D 91.667 72 6 0 3954 4025 374634683 374634754 3.000000e-17 100
2 TraesCS5D01G392500 chr5A 95.730 3817 103 12 944 4718 580944231 580948029 0.000000e+00 6091
3 TraesCS5D01G392500 chr5A 91.667 924 29 23 3 917 580943361 580944245 0.000000e+00 1236
4 TraesCS5D01G392500 chr5B 95.908 3201 104 9 761 3952 566683851 566687033 0.000000e+00 5160
5 TraesCS5D01G392500 chr5B 94.968 616 17 3 4112 4714 566687030 566687644 0.000000e+00 953
6 TraesCS5D01G392500 chr5B 97.287 516 13 1 3 517 566682852 566683367 0.000000e+00 874
7 TraesCS5D01G392500 chr5B 94.350 177 9 1 592 767 566683715 566683891 2.160000e-68 270
8 TraesCS5D01G392500 chr4D 88.189 254 29 1 3 256 35062173 35061921 7.670000e-78 302
9 TraesCS5D01G392500 chr4D 93.137 102 5 2 3 102 38280661 38280560 1.060000e-31 148
10 TraesCS5D01G392500 chr4D 93.258 89 4 1 3 89 30018481 30018569 3.830000e-26 130
11 TraesCS5D01G392500 chr4B 94.231 104 3 2 2 102 42010671 42010568 6.320000e-34 156
12 TraesCS5D01G392500 chr4B 89.474 95 8 1 3 95 42762366 42762272 8.290000e-23 119
13 TraesCS5D01G392500 chr4B 87.368 95 10 1 3 95 42719458 42719364 1.800000e-19 108
14 TraesCS5D01G392500 chr4A 92.857 98 4 2 7 102 564945560 564945464 6.370000e-29 139


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 TraesCS5D01G392500 chr5D 460754523 460759240 4717 False 8713.00 8713 100.00000 1 4718 1 chr5D.!!$F2 4717
1 TraesCS5D01G392500 chr5A 580943361 580948029 4668 False 3663.50 6091 93.69850 3 4718 2 chr5A.!!$F1 4715
2 TraesCS5D01G392500 chr5B 566682852 566687644 4792 False 1814.25 5160 95.62825 3 4714 4 chr5B.!!$F1 4711

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
893 1181 0.107703 TGGTTGATCCACATCGCTCC 60.108 55.000 0.0 0.0 41.93 4.70 F
979 1267 2.097038 CGACTCCTTCTGCCGCTTG 61.097 63.158 0.0 0.0 0.00 4.01 F
1800 2094 0.320374 CCCTAGGCGACTGTCACAAA 59.680 55.000 0.0 0.0 43.88 2.83 F
2037 2331 1.093159 GGCAGATCAAGAAGGCACAG 58.907 55.000 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 2088 0.464036 ATATCTCCGCGGCTTTGTGA 59.536 50.0 23.51 11.44 0.00 3.58 R
2037 2331 0.678048 GTCCAGATCCCAACACCAGC 60.678 60.0 0.00 0.00 0.00 4.85 R
3294 3588 0.325296 TCTCCGGGTCCAGCTTGTAT 60.325 55.0 0.00 0.00 0.00 2.29 R
4029 4326 0.458370 GGCCACAATGTGATTTCCGC 60.458 55.0 15.91 8.18 35.23 5.54 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
556 561 1.592223 GAGAGAGTGTGAACGGGGG 59.408 63.158 0.00 0.00 0.00 5.40
559 564 1.889530 GAGAGTGTGAACGGGGGAGG 61.890 65.000 0.00 0.00 0.00 4.30
562 567 4.257810 TGTGAACGGGGGAGGGGA 62.258 66.667 0.00 0.00 0.00 4.81
563 568 2.931649 GTGAACGGGGGAGGGGAA 60.932 66.667 0.00 0.00 0.00 3.97
575 583 2.115427 GGAGGGGAAAAGAGAGAGAGG 58.885 57.143 0.00 0.00 0.00 3.69
576 584 2.292587 GGAGGGGAAAAGAGAGAGAGGA 60.293 54.545 0.00 0.00 0.00 3.71
579 587 2.292587 GGGGAAAAGAGAGAGAGGAGGA 60.293 54.545 0.00 0.00 0.00 3.71
583 861 0.933700 AAGAGAGAGAGGAGGAGGGG 59.066 60.000 0.00 0.00 0.00 4.79
607 885 5.420104 GGGGGAGCGTATAAGTTAAGCTATA 59.580 44.000 9.80 0.00 38.39 1.31
661 939 3.838903 AGTTTCTGTCTCGAGGGGTAAAT 59.161 43.478 13.56 0.33 0.00 1.40
856 1141 1.251251 CCACTTTGAAAGAGGCCCAG 58.749 55.000 12.53 0.00 32.51 4.45
893 1181 0.107703 TGGTTGATCCACATCGCTCC 60.108 55.000 0.00 0.00 41.93 4.70
979 1267 2.097038 CGACTCCTTCTGCCGCTTG 61.097 63.158 0.00 0.00 0.00 4.01
1476 1770 2.743928 GCCACCCTGCTCTTCACG 60.744 66.667 0.00 0.00 0.00 4.35
1581 1875 2.284190 GGCAGCATCTACAAGGAGAAC 58.716 52.381 0.00 0.00 0.00 3.01
1788 2082 3.522553 GAACATATATCGCACCCTAGGC 58.477 50.000 2.05 0.00 0.00 3.93
1800 2094 0.320374 CCCTAGGCGACTGTCACAAA 59.680 55.000 0.00 0.00 43.88 2.83
1839 2133 1.696336 CAGATTGTCGGGATCCATCCT 59.304 52.381 15.23 0.00 46.35 3.24
2037 2331 1.093159 GGCAGATCAAGAAGGCACAG 58.907 55.000 0.00 0.00 0.00 3.66
2325 2619 1.774254 TGCTACATGGTAATGGGGGAG 59.226 52.381 0.00 0.00 38.19 4.30
2330 2624 3.197983 ACATGGTAATGGGGGAGAAAGA 58.802 45.455 0.00 0.00 38.19 2.52
2334 2628 4.672899 TGGTAATGGGGGAGAAAGAAAAG 58.327 43.478 0.00 0.00 0.00 2.27
3036 3330 2.222013 GGAACTCCGGTCCTTGGGT 61.222 63.158 0.00 0.00 0.00 4.51
3147 3441 5.393787 CGCATGGAACTCCTACTACAAAGTA 60.394 44.000 0.00 0.00 37.15 2.24
3294 3588 1.416401 GTTCGGGATTATCTGGAGGCA 59.584 52.381 0.00 0.00 0.00 4.75
3561 3855 2.127708 GTGGAAGATCACCCCATACCT 58.872 52.381 0.00 0.00 31.94 3.08
3636 3933 1.304464 TCTCCGAAGAGAGGCTGCA 60.304 57.895 0.50 0.00 44.42 4.41
3772 4069 2.487746 TGGCCCTGTCTATGTGGATA 57.512 50.000 0.00 0.00 0.00 2.59
3887 4184 3.056179 CCAGGTTTTGTCACACTGGTTTT 60.056 43.478 4.32 0.00 42.83 2.43
3902 4199 7.436080 CACACTGGTTTTGGAATGATAATATGC 59.564 37.037 0.00 0.00 0.00 3.14
3983 4280 4.021981 TGGATCATCGTTTCAGAGCGATAT 60.022 41.667 10.42 6.46 45.61 1.63
3984 4281 5.183140 TGGATCATCGTTTCAGAGCGATATA 59.817 40.000 10.42 4.71 45.61 0.86
3985 4282 5.513495 GGATCATCGTTTCAGAGCGATATAC 59.487 44.000 10.42 6.23 45.61 1.47
3986 4283 5.432885 TCATCGTTTCAGAGCGATATACA 57.567 39.130 10.42 0.00 45.61 2.29
3987 4284 5.212934 TCATCGTTTCAGAGCGATATACAC 58.787 41.667 10.42 0.00 45.61 2.90
3988 4285 4.895224 TCGTTTCAGAGCGATATACACT 57.105 40.909 0.00 0.00 33.44 3.55
3989 4286 5.244785 TCGTTTCAGAGCGATATACACTT 57.755 39.130 0.00 0.00 33.44 3.16
3990 4287 5.034797 TCGTTTCAGAGCGATATACACTTG 58.965 41.667 0.00 0.00 33.44 3.16
3991 4288 4.798907 CGTTTCAGAGCGATATACACTTGT 59.201 41.667 0.00 0.00 0.00 3.16
3992 4289 5.969435 CGTTTCAGAGCGATATACACTTGTA 59.031 40.000 0.00 0.00 34.67 2.41
4017 4314 0.253894 TACAGACCTCCATCCGTCGA 59.746 55.000 0.00 0.00 34.10 4.20
4029 4326 2.380084 TCCGTCGATCTTTTTCCAGG 57.620 50.000 0.00 0.00 0.00 4.45
4126 4423 4.360563 CGGAGCCTTACTGTACAACATAG 58.639 47.826 0.00 0.00 0.00 2.23
4146 4443 6.372659 ACATAGAGTACATGAAAAACTGCCTG 59.627 38.462 0.00 0.00 0.00 4.85
4149 4446 5.471456 AGAGTACATGAAAAACTGCCTGAAG 59.529 40.000 0.00 0.00 0.00 3.02
4164 4487 3.502211 GCCTGAAGCAAAAACACTAGCTA 59.498 43.478 0.00 0.00 42.97 3.32
4649 4983 3.111098 GCCTGATGATCAACGAAAATGC 58.889 45.455 0.00 0.00 0.00 3.56
4714 5048 5.242393 ACAAACAAAGATGAGATGGGTGAAG 59.758 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.281577 TCCATCAGGTATGCTGCACAA 59.718 47.619 3.57 0.00 33.92 3.33
1 2 0.911053 TCCATCAGGTATGCTGCACA 59.089 50.000 3.57 0.00 33.92 4.57
59 60 0.451299 CATACTCGTCGAGATCGCCG 60.451 60.000 28.33 0.00 42.38 6.46
556 561 3.031013 CTCCTCTCTCTCTTTTCCCCTC 58.969 54.545 0.00 0.00 0.00 4.30
559 564 3.031013 CTCCTCCTCTCTCTCTTTTCCC 58.969 54.545 0.00 0.00 0.00 3.97
562 567 2.292851 CCCCTCCTCCTCTCTCTCTTTT 60.293 54.545 0.00 0.00 0.00 2.27
563 568 1.290732 CCCCTCCTCCTCTCTCTCTTT 59.709 57.143 0.00 0.00 0.00 2.52
583 861 2.367894 AGCTTAACTTATACGCTCCCCC 59.632 50.000 0.00 0.00 0.00 5.40
589 867 9.623350 AGCTTTAGTATAGCTTAACTTATACGC 57.377 33.333 9.10 0.34 46.42 4.42
607 885 3.600388 CGGTCCAAATCTCAGCTTTAGT 58.400 45.455 0.00 0.00 0.00 2.24
754 1033 3.391382 CTGACCCCGACCTGGACC 61.391 72.222 0.00 0.00 42.00 4.46
755 1034 3.391382 CCTGACCCCGACCTGGAC 61.391 72.222 0.00 0.00 42.00 4.02
758 1037 3.775654 GAGCCTGACCCCGACCTG 61.776 72.222 0.00 0.00 0.00 4.00
919 1207 4.862823 GAGGAGGACGGGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
920 1208 2.392816 TAGAGGAGGACGGGGAGGG 61.393 68.421 0.00 0.00 0.00 4.30
921 1209 1.152715 GTAGAGGAGGACGGGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
922 1210 0.179012 GAGTAGAGGAGGACGGGGAG 60.179 65.000 0.00 0.00 0.00 4.30
923 1211 1.643475 GGAGTAGAGGAGGACGGGGA 61.643 65.000 0.00 0.00 0.00 4.81
924 1212 1.152715 GGAGTAGAGGAGGACGGGG 60.153 68.421 0.00 0.00 0.00 5.73
925 1213 1.526455 CGGAGTAGAGGAGGACGGG 60.526 68.421 0.00 0.00 0.00 5.28
926 1214 2.188161 GCGGAGTAGAGGAGGACGG 61.188 68.421 0.00 0.00 0.00 4.79
927 1215 0.748729 AAGCGGAGTAGAGGAGGACG 60.749 60.000 0.00 0.00 0.00 4.79
928 1216 1.026584 GAAGCGGAGTAGAGGAGGAC 58.973 60.000 0.00 0.00 0.00 3.85
929 1217 0.106619 GGAAGCGGAGTAGAGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
930 1218 1.110518 GGGAAGCGGAGTAGAGGAGG 61.111 65.000 0.00 0.00 0.00 4.30
931 1219 1.448922 CGGGAAGCGGAGTAGAGGAG 61.449 65.000 0.00 0.00 0.00 3.69
1040 1328 2.124236 CGTACGCCTCCTCCTCCT 60.124 66.667 0.52 0.00 0.00 3.69
1476 1770 1.611936 GCCTCCTTGAACCTGTTCTCC 60.612 57.143 11.03 0.00 40.14 3.71
1581 1875 2.956964 GCCTTGTCGATCTCGCCG 60.957 66.667 0.00 0.00 39.60 6.46
1635 1929 2.022129 CCACAGCGACACGTCCTTC 61.022 63.158 0.00 0.00 0.00 3.46
1704 1998 4.397420 TCATTGCCTTGATAACACAGTGT 58.603 39.130 0.00 0.00 0.00 3.55
1785 2079 1.598130 GGCTTTGTGACAGTCGCCT 60.598 57.895 11.68 0.00 34.80 5.52
1788 2082 2.551270 GCGGCTTTGTGACAGTCG 59.449 61.111 0.00 0.00 42.42 4.18
1794 2088 0.464036 ATATCTCCGCGGCTTTGTGA 59.536 50.000 23.51 11.44 0.00 3.58
1800 2094 1.924320 GCTCGTATATCTCCGCGGCT 61.924 60.000 23.51 10.28 0.00 5.52
1839 2133 4.973055 CGGGCGACGGTGTTGGAA 62.973 66.667 0.00 0.00 39.42 3.53
1866 2160 3.443329 CAGAGTCTCTGTACATCTGTGCT 59.557 47.826 20.06 1.18 39.58 4.40
1869 2163 4.013728 GACCAGAGTCTCTGTACATCTGT 58.986 47.826 24.93 15.13 42.80 3.41
2037 2331 0.678048 GTCCAGATCCCAACACCAGC 60.678 60.000 0.00 0.00 0.00 4.85
2325 2619 5.756918 AGGTAAGGGATAGCCTTTTCTTTC 58.243 41.667 0.00 0.00 34.89 2.62
2330 2624 8.577164 TTTATAGAGGTAAGGGATAGCCTTTT 57.423 34.615 0.00 0.00 34.89 2.27
2334 2628 5.722441 AGCTTTATAGAGGTAAGGGATAGCC 59.278 44.000 0.00 0.00 32.22 3.93
2455 2749 2.843113 ACTCTGGATTTTCAGGAGGAGG 59.157 50.000 0.00 0.00 35.58 4.30
3147 3441 5.002516 CCTTTCTCTTCTGCTCTTGATGTT 58.997 41.667 0.00 0.00 0.00 2.71
3294 3588 0.325296 TCTCCGGGTCCAGCTTGTAT 60.325 55.000 0.00 0.00 0.00 2.29
3333 3627 2.875933 GTTGATCAAGGACGAACCAACA 59.124 45.455 8.80 0.00 42.04 3.33
3375 3669 2.418368 TGCACTGGTTCTTGTTCTGT 57.582 45.000 0.00 0.00 0.00 3.41
3561 3855 5.984725 TGTAAATCCTCGAATGGAAGCTTA 58.015 37.500 0.00 0.00 39.85 3.09
3636 3933 6.711194 CCTTGTAGATCAGATGCAGATTGAAT 59.289 38.462 0.00 0.00 0.00 2.57
3748 4045 2.158900 CCACATAGACAGGGCCAAGTAG 60.159 54.545 6.18 0.00 0.00 2.57
3887 4184 7.231317 GGAAGAAACAGGCATATTATCATTCCA 59.769 37.037 0.00 0.00 32.22 3.53
3902 4199 6.927416 TCATGATCAAATTGGAAGAAACAGG 58.073 36.000 0.00 0.00 0.00 4.00
3983 4280 9.038072 TGGAGGTCTGTATATTTTACAAGTGTA 57.962 33.333 0.00 0.00 0.00 2.90
3984 4281 7.913789 TGGAGGTCTGTATATTTTACAAGTGT 58.086 34.615 0.00 0.00 0.00 3.55
3985 4282 8.964476 ATGGAGGTCTGTATATTTTACAAGTG 57.036 34.615 0.00 0.00 0.00 3.16
3986 4283 8.211629 GGATGGAGGTCTGTATATTTTACAAGT 58.788 37.037 0.00 0.00 0.00 3.16
3987 4284 7.385205 CGGATGGAGGTCTGTATATTTTACAAG 59.615 40.741 0.00 0.00 0.00 3.16
3988 4285 7.147620 ACGGATGGAGGTCTGTATATTTTACAA 60.148 37.037 0.00 0.00 35.99 2.41
3989 4286 6.325545 ACGGATGGAGGTCTGTATATTTTACA 59.674 38.462 0.00 0.00 35.99 2.41
3990 4287 6.756221 ACGGATGGAGGTCTGTATATTTTAC 58.244 40.000 0.00 0.00 35.99 2.01
3991 4288 6.294342 CGACGGATGGAGGTCTGTATATTTTA 60.294 42.308 0.00 0.00 37.82 1.52
3992 4289 5.509163 CGACGGATGGAGGTCTGTATATTTT 60.509 44.000 0.00 0.00 37.82 1.82
4008 4305 2.609459 CCTGGAAAAAGATCGACGGATG 59.391 50.000 0.00 0.00 31.51 3.51
4029 4326 0.458370 GGCCACAATGTGATTTCCGC 60.458 55.000 15.91 8.18 35.23 5.54
4126 4423 5.689383 TTCAGGCAGTTTTTCATGTACTC 57.311 39.130 0.00 0.00 0.00 2.59
4146 4443 4.912187 GCTTGTAGCTAGTGTTTTTGCTTC 59.088 41.667 0.00 0.00 38.45 3.86
4164 4487 7.115947 GTCTTTTGTATCGTGTTACTAGCTTGT 59.884 37.037 6.00 6.00 0.00 3.16
4244 4567 5.129485 CACCTGGTGGTAGAGATTTATCAGT 59.871 44.000 19.23 0.00 46.60 3.41
4649 4983 4.108336 CGGTACTCATCATCTTGACACTG 58.892 47.826 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.