Multiple sequence alignment - TraesCS6D01G315500

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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 TraesCS6D01G315500 chr6D 100.000 2435 0 0 1 2435 423799024 423796590 0.000000e+00 4497
1 TraesCS6D01G315500 chr6D 90.226 133 13 0 1674 1806 423797219 423797087 8.950000e-40 174
2 TraesCS6D01G315500 chr6D 90.226 133 13 0 1806 1938 423797351 423797219 8.950000e-40 174
3 TraesCS6D01G315500 chr6A 91.859 2469 111 39 1 2435 568507971 568505559 0.000000e+00 3363
4 TraesCS6D01G315500 chr6A 90.977 133 12 0 1674 1806 568506187 568506055 1.920000e-41 180
5 TraesCS6D01G315500 chr6A 90.977 133 12 0 1806 1938 568506319 568506187 1.920000e-41 180
6 TraesCS6D01G315500 chr6B 94.928 1676 64 7 772 2435 639157967 639156301 0.000000e+00 2604
7 TraesCS6D01G315500 chr6B 84.935 843 53 26 1 822 639158757 639157968 0.000000e+00 785
8 TraesCS6D01G315500 chr6B 91.729 133 11 0 1674 1806 639156930 639156798 4.130000e-43 185
9 TraesCS6D01G315500 chr6B 90.977 133 12 0 1806 1938 639157062 639156930 1.920000e-41 180
10 TraesCS6D01G315500 chr7A 77.111 450 86 12 1279 1713 4780378 4780825 6.730000e-61 244


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 TraesCS6D01G315500 chr6D 423796590 423799024 2434 True 1615.0 4497 93.48400 1 2435 3 chr6D.!!$R1 2434
1 TraesCS6D01G315500 chr6A 568505559 568507971 2412 True 1241.0 3363 91.27100 1 2435 3 chr6A.!!$R1 2434
2 TraesCS6D01G315500 chr6B 639156301 639158757 2456 True 938.5 2604 90.64225 1 2435 4 chr6B.!!$R1 2434

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
400 447 0.036010 AGATGTCAACGCCTCAAGGG 60.036 55.0 0.0 0.0 35.18 3.95 F
617 668 0.037303 CCTCATGTTGCTCCCACAGT 59.963 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1444 3.007290 TCTCTCCATTCAACTCCACTGTG 59.993 47.826 0.0 0.00 0.0 3.66 R
2293 2407 4.406649 TGACCACATGCTGATAGATCTTCA 59.593 41.667 0.0 4.06 0.0 3.02 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
27 28 8.610896 CCAGCTGAGTTCAAAGAAAATATCTAG 58.389 37.037 17.39 0.00 37.42 2.43
168 187 3.051392 GCCACGCATGCAGGTAACC 62.051 63.158 22.81 6.84 37.17 2.85
203 223 9.739276 TTCCTTGCTAAGATCTTATCAGAAAAA 57.261 29.630 15.47 8.05 30.76 1.94
208 228 8.454106 TGCTAAGATCTTATCAGAAAAACAAGC 58.546 33.333 15.47 12.28 30.76 4.01
215 251 2.733956 TCAGAAAAACAAGCTGGGTGT 58.266 42.857 0.00 0.00 0.00 4.16
227 263 1.000506 GCTGGGTGTTGTTCTCTCGTA 59.999 52.381 0.00 0.00 0.00 3.43
228 264 2.927014 GCTGGGTGTTGTTCTCTCGTAG 60.927 54.545 0.00 0.00 0.00 3.51
230 266 2.035449 TGGGTGTTGTTCTCTCGTAGTG 59.965 50.000 0.00 0.00 0.00 2.74
231 267 2.059541 GGTGTTGTTCTCTCGTAGTGC 58.940 52.381 0.00 0.00 0.00 4.40
232 268 2.288273 GGTGTTGTTCTCTCGTAGTGCT 60.288 50.000 0.00 0.00 0.00 4.40
233 269 3.057736 GGTGTTGTTCTCTCGTAGTGCTA 60.058 47.826 0.00 0.00 0.00 3.49
256 292 1.153066 GCTCTAGCTTTGAGGGCCC 60.153 63.158 16.46 16.46 34.05 5.80
257 293 1.144936 CTCTAGCTTTGAGGGCCCG 59.855 63.158 18.44 1.87 0.00 6.13
296 332 5.117406 AGGAGGATGTTTTGGTAGAATCC 57.883 43.478 0.00 0.00 37.63 3.01
396 443 3.689161 CCAAATAAGATGTCAACGCCTCA 59.311 43.478 0.00 0.00 0.00 3.86
397 444 4.155826 CCAAATAAGATGTCAACGCCTCAA 59.844 41.667 0.00 0.00 0.00 3.02
398 445 5.327091 CAAATAAGATGTCAACGCCTCAAG 58.673 41.667 0.00 0.00 0.00 3.02
399 446 1.813513 AAGATGTCAACGCCTCAAGG 58.186 50.000 0.00 0.00 38.53 3.61
400 447 0.036010 AGATGTCAACGCCTCAAGGG 60.036 55.000 0.00 0.00 35.18 3.95
438 485 0.810031 CGGTGGGGAACGATAGCAAG 60.810 60.000 0.00 0.00 42.67 4.01
463 510 5.276820 CGAAAGAAAAATTGTTGCTTGGTCC 60.277 40.000 0.00 0.00 0.00 4.46
554 605 3.584848 AGGTGTCTAGCTTTGTGAGGATT 59.415 43.478 0.00 0.00 0.00 3.01
572 623 1.127343 TTTGAGGCTTTGTTTGGGGG 58.873 50.000 0.00 0.00 0.00 5.40
575 626 1.524008 GAGGCTTTGTTTGGGGGTCG 61.524 60.000 0.00 0.00 0.00 4.79
579 630 1.687563 CTTTGTTTGGGGGTCGTTCT 58.312 50.000 0.00 0.00 0.00 3.01
613 664 2.154139 ACACCTCATGTTGCTCCCA 58.846 52.632 0.00 0.00 38.98 4.37
614 665 0.250901 ACACCTCATGTTGCTCCCAC 60.251 55.000 0.00 0.00 38.98 4.61
615 666 0.250858 CACCTCATGTTGCTCCCACA 60.251 55.000 0.00 0.00 0.00 4.17
617 668 0.037303 CCTCATGTTGCTCCCACAGT 59.963 55.000 0.00 0.00 0.00 3.55
618 669 1.278985 CCTCATGTTGCTCCCACAGTA 59.721 52.381 0.00 0.00 0.00 2.74
619 670 2.092753 CCTCATGTTGCTCCCACAGTAT 60.093 50.000 0.00 0.00 0.00 2.12
620 671 3.134623 CCTCATGTTGCTCCCACAGTATA 59.865 47.826 0.00 0.00 0.00 1.47
621 672 4.375272 CTCATGTTGCTCCCACAGTATAG 58.625 47.826 0.00 0.00 0.00 1.31
622 673 3.134623 TCATGTTGCTCCCACAGTATAGG 59.865 47.826 0.00 0.00 0.00 2.57
623 674 1.209504 TGTTGCTCCCACAGTATAGGC 59.790 52.381 0.00 0.00 0.00 3.93
624 675 1.486726 GTTGCTCCCACAGTATAGGCT 59.513 52.381 0.00 0.00 0.00 4.58
681 732 1.956477 GCAGCTGGGAGTTTCTTTTCA 59.044 47.619 17.12 0.00 0.00 2.69
701 753 1.228124 TTTTCTCCGGTGGCTGTGG 60.228 57.895 0.00 0.00 0.00 4.17
812 913 4.037565 TCACATCGAGGCGTATTTGAGTAT 59.962 41.667 0.00 0.00 0.00 2.12
813 914 5.239963 TCACATCGAGGCGTATTTGAGTATA 59.760 40.000 0.00 0.00 0.00 1.47
838 939 2.037847 GCCAGCCCCATGGAAACT 59.962 61.111 15.22 4.12 43.57 2.66
922 1030 4.963318 ACTTGAGTGATTCAGGAGTTGA 57.037 40.909 0.00 0.00 36.46 3.18
953 1061 7.825761 AGTAGCCTTATAAACCGTGTATGTTTT 59.174 33.333 0.00 0.00 37.18 2.43
954 1062 6.848451 AGCCTTATAAACCGTGTATGTTTTG 58.152 36.000 0.00 0.00 37.18 2.44
955 1063 6.655848 AGCCTTATAAACCGTGTATGTTTTGA 59.344 34.615 0.00 0.00 37.18 2.69
956 1064 7.338449 AGCCTTATAAACCGTGTATGTTTTGAT 59.662 33.333 0.00 0.00 37.18 2.57
957 1065 7.971722 GCCTTATAAACCGTGTATGTTTTGATT 59.028 33.333 0.00 0.00 37.18 2.57
1030 1138 4.877282 GGATAAGTTCCAGGAAGAGATCG 58.123 47.826 0.54 0.00 44.74 3.69
1203 1311 6.906157 AGGAACATGTGATGACATCTTTTT 57.094 33.333 16.25 3.16 41.12 1.94
1419 1528 7.600231 TGGTACCTTCACCGTAATCATATTA 57.400 36.000 14.36 0.00 41.88 0.98
1671 1780 3.684788 CACCAGAATTCTACGGTGGAAAG 59.315 47.826 26.56 9.72 44.26 2.62
1905 2014 6.590068 AGATTGCTCTGCTTTGAGTATGTAT 58.410 36.000 0.00 0.00 36.51 2.29
2009 2118 3.078097 TCATGTAACCGTGTGGGAAATG 58.922 45.455 0.00 0.00 40.75 2.32
2123 2237 7.661536 AAAACTAGACTATCAGGCAGATGTA 57.338 36.000 2.23 0.00 37.57 2.29
2133 2247 8.654997 ACTATCAGGCAGATGTATTGTTTCTAT 58.345 33.333 2.23 0.00 37.57 1.98
2150 2264 8.672823 TGTTTCTATGAGATCTTGGATTGATG 57.327 34.615 0.00 0.00 0.00 3.07
2153 2267 7.370905 TCTATGAGATCTTGGATTGATGTGT 57.629 36.000 0.00 0.00 0.00 3.72
2166 2280 9.906660 TTGGATTGATGTGTGTAATTTAAGTTC 57.093 29.630 0.00 0.00 0.00 3.01
2202 2316 9.643693 GTTGAACAATCATCCATTTGTAAAGAT 57.356 29.630 0.00 0.00 35.09 2.40
2272 2386 7.383300 ACATGTTCATATACAGTCACGATGATG 59.617 37.037 0.00 0.00 0.00 3.07
2374 2488 6.414987 GTCAAATGTTTTGTCTTCTCCTTTCG 59.585 38.462 0.39 0.00 0.00 3.46
2391 2505 5.639506 TCCTTTCGTTTTCTTGCTATCTCTG 59.360 40.000 0.00 0.00 0.00 3.35
2430 2544 7.707624 ATAGAAGATTTGGTTCAAGCATCAA 57.292 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.103208 CACCTCCACGGAGCTGATAC 59.897 60.000 7.64 0.00 40.69 2.24
168 187 7.721286 AGATCTTAGCAAGGAAAATATCGTG 57.279 36.000 0.00 0.00 0.00 4.35
203 223 1.212935 AGAGAACAACACCCAGCTTGT 59.787 47.619 0.00 0.00 31.76 3.16
208 228 2.296471 ACTACGAGAGAACAACACCCAG 59.704 50.000 0.00 0.00 0.00 4.45
215 251 2.159558 CGCTAGCACTACGAGAGAACAA 60.160 50.000 16.45 0.00 0.00 2.83
241 277 0.181350 AATCGGGCCCTCAAAGCTAG 59.819 55.000 22.43 0.00 0.00 3.42
257 293 3.126831 CTCCTAACCACGATGCAGAATC 58.873 50.000 0.00 0.00 0.00 2.52
274 310 4.790790 AGGATTCTACCAAAACATCCTCCT 59.209 41.667 0.00 0.00 39.76 3.69
275 311 5.117406 AGGATTCTACCAAAACATCCTCC 57.883 43.478 0.00 0.00 39.76 4.30
296 332 0.391661 ACACAGGCAAGCATACGGAG 60.392 55.000 0.00 0.00 0.00 4.63
396 443 1.075226 TAGATCTGCCGAGGCCCTT 60.075 57.895 12.05 0.00 41.09 3.95
397 444 1.532794 CTAGATCTGCCGAGGCCCT 60.533 63.158 12.05 6.22 41.09 5.19
398 445 1.403687 AACTAGATCTGCCGAGGCCC 61.404 60.000 12.05 0.00 41.09 5.80
399 446 0.249657 CAACTAGATCTGCCGAGGCC 60.250 60.000 12.05 0.00 41.09 5.19
400 447 0.878086 GCAACTAGATCTGCCGAGGC 60.878 60.000 5.18 7.26 42.35 4.70
401 448 0.596083 CGCAACTAGATCTGCCGAGG 60.596 60.000 5.18 0.00 35.01 4.63
402 449 0.596083 CCGCAACTAGATCTGCCGAG 60.596 60.000 5.18 0.00 35.01 4.63
406 453 0.811616 CCCACCGCAACTAGATCTGC 60.812 60.000 5.18 0.00 35.14 4.26
438 485 4.033932 ACCAAGCAACAATTTTTCTTTCGC 59.966 37.500 0.00 0.00 0.00 4.70
463 510 2.799412 GAGCAAGCATATCTCGTTCCTG 59.201 50.000 0.00 0.00 0.00 3.86
526 577 5.676552 TCACAAAGCTAGACACCTTACAAA 58.323 37.500 0.00 0.00 0.00 2.83
554 605 0.031616 ACCCCCAAACAAAGCCTCAA 60.032 50.000 0.00 0.00 0.00 3.02
572 623 4.307432 TGACCATCTCTGAAAAGAACGAC 58.693 43.478 0.00 0.00 0.00 4.34
575 626 5.278022 GGTGTTGACCATCTCTGAAAAGAAC 60.278 44.000 0.00 0.00 42.59 3.01
579 630 4.389374 GAGGTGTTGACCATCTCTGAAAA 58.611 43.478 0.00 0.00 46.16 2.29
610 661 3.128938 GCGTATCTAGCCTATACTGTGGG 59.871 52.174 0.00 0.00 0.00 4.61
611 662 4.358494 GCGTATCTAGCCTATACTGTGG 57.642 50.000 0.00 0.00 0.00 4.17
622 673 0.935366 GCACAGTCGGCGTATCTAGC 60.935 60.000 6.85 8.23 0.00 3.42
623 674 0.663688 AGCACAGTCGGCGTATCTAG 59.336 55.000 6.85 2.46 36.08 2.43
624 675 0.380733 CAGCACAGTCGGCGTATCTA 59.619 55.000 6.85 0.00 36.08 1.98
633 684 3.190849 CCGATGGCAGCACAGTCG 61.191 66.667 2.73 0.72 0.00 4.18
661 712 1.956477 TGAAAAGAAACTCCCAGCTGC 59.044 47.619 8.66 0.00 0.00 5.25
662 713 3.217626 ACTGAAAAGAAACTCCCAGCTG 58.782 45.455 6.78 6.78 0.00 4.24
663 714 3.584733 ACTGAAAAGAAACTCCCAGCT 57.415 42.857 0.00 0.00 0.00 4.24
681 732 0.535102 CACAGCCACCGGAGAAAACT 60.535 55.000 9.46 0.00 0.00 2.66
717 769 2.159184 TCTGTTAATCAGAGGCTCAGCG 60.159 50.000 18.26 4.74 46.77 5.18
812 913 0.178834 ATGGGGCTGGCCTGGATATA 60.179 55.000 20.47 0.00 36.10 0.86
813 914 1.466788 ATGGGGCTGGCCTGGATAT 60.467 57.895 20.47 4.70 36.10 1.63
838 939 6.954684 AGAAGAGGTTCCATAACAGAACTCTA 59.045 38.462 3.89 0.00 42.63 2.43
922 1030 6.939622 ACACGGTTTATAAGGCTACTAAACT 58.060 36.000 21.47 8.65 36.22 2.66
953 1061 3.964031 ACCCTGCAAACAAAGGTAAATCA 59.036 39.130 0.00 0.00 32.13 2.57
954 1062 4.600692 ACCCTGCAAACAAAGGTAAATC 57.399 40.909 0.00 0.00 32.13 2.17
955 1063 5.144832 AGTACCCTGCAAACAAAGGTAAAT 58.855 37.500 0.00 0.00 36.82 1.40
956 1064 4.538738 AGTACCCTGCAAACAAAGGTAAA 58.461 39.130 0.00 0.00 36.82 2.01
957 1065 4.173290 AGTACCCTGCAAACAAAGGTAA 57.827 40.909 0.00 0.00 36.82 2.85
1092 1200 2.153034 AGTCTACCTCTCTCCCTTGC 57.847 55.000 0.00 0.00 0.00 4.01
1103 1211 2.909217 AGCTTCCCTCAAAGTCTACCT 58.091 47.619 0.00 0.00 0.00 3.08
1336 1444 3.007290 TCTCTCCATTCAACTCCACTGTG 59.993 47.826 0.00 0.00 0.00 3.66
1419 1528 5.319043 TCAGGTTTTAGGTCCAAGTGAAT 57.681 39.130 0.00 0.00 0.00 2.57
1611 1720 7.838884 TGCAAGAAAATTGATGGATGAATACA 58.161 30.769 0.00 0.00 0.00 2.29
1671 1780 6.758416 TGTATATGTCTGACTTGAATGTGAGC 59.242 38.462 9.51 0.00 0.00 4.26
1731 1840 6.706270 AGCAGTCTTTGGTATATTTCATACGG 59.294 38.462 0.00 0.00 35.30 4.02
1733 1842 8.768955 CAGAGCAGTCTTTGGTATATTTCATAC 58.231 37.037 0.00 0.00 37.72 2.39
2042 2151 8.470805 TGTTCTTACAAAATGTTGTTACACCAT 58.529 29.630 6.57 0.00 46.01 3.55
2123 2237 9.863650 ATCAATCCAAGATCTCATAGAAACAAT 57.136 29.630 0.00 0.00 0.00 2.71
2133 2247 5.169992 ACACACATCAATCCAAGATCTCA 57.830 39.130 0.00 0.00 0.00 3.27
2150 2264 9.546909 CTCATGACATGAACTTAAATTACACAC 57.453 33.333 18.49 0.00 39.11 3.82
2166 2280 6.127842 TGGATGATTGTTCAACTCATGACATG 60.128 38.462 9.28 9.28 37.92 3.21
2168 2282 5.315348 TGGATGATTGTTCAACTCATGACA 58.685 37.500 0.00 0.00 37.92 3.58
2272 2386 8.611757 TCTTCACAACATTGCATGTATGTATAC 58.388 33.333 13.61 0.00 44.07 1.47
2293 2407 4.406649 TGACCACATGCTGATAGATCTTCA 59.593 41.667 0.00 4.06 0.00 3.02
2352 2466 6.451064 ACGAAAGGAGAAGACAAAACATTT 57.549 33.333 0.00 0.00 0.00 2.32
2374 2488 8.349983 TGGTAAAAACAGAGATAGCAAGAAAAC 58.650 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.