Multiple sequence alignment - TraesCS6B01G146600

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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 TraesCS6B01G146600 chr6B 100.000 6170 0 0 1 6170 147576483 147582652 0 11394
1 TraesCS6B01G146600 chr6D 97.958 5190 103 1 1 5187 73062641 73067830 0 8994
2 TraesCS6B01G146600 chr6D 97.228 938 15 2 5242 6170 73067830 73068765 0 1578
3 TraesCS6B01G146600 chr6A 98.015 5138 99 1 1 5135 89586681 89591818 0 8920
4 TraesCS6B01G146600 chr6A 97.979 1039 20 1 5132 6170 89592074 89593111 0 1801


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 TraesCS6B01G146600 chr6B 147576483 147582652 6169 False 11394.0 11394 100.000 1 6170 1 chr6B.!!$F1 6169
1 TraesCS6B01G146600 chr6D 73062641 73068765 6124 False 5286.0 8994 97.593 1 6170 2 chr6D.!!$F1 6169
2 TraesCS6B01G146600 chr6A 89586681 89593111 6430 False 5360.5 8920 97.997 1 6170 2 chr6A.!!$F1 6169

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
777 778 1.133407 CTAGACCAAGCCGAGACAGTC 59.867 57.143 0.0 0.00 0.00 3.51 F
1265 1269 1.811359 GCATGAAGCAGAAAGACAGCT 59.189 47.619 0.0 0.00 43.02 4.24 F
2583 2587 1.618343 GGTATTGCTGTTGCCAAAGGT 59.382 47.619 0.0 0.00 38.71 3.50 F
3201 3205 0.523072 CCCCGCAGTTCAGAATGTTG 59.477 55.000 0.0 0.00 37.40 3.33 F
4072 4076 0.179100 TGAGTTAGAGCATGCTCGCC 60.179 55.000 35.5 27.09 46.90 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2062 0.108207 AGAGGCATCTACCATGCAGC 59.892 55.0 0.00 0.27 46.21 5.25 R
2973 2977 1.053835 TGGCCACACCAGACTCAGAA 61.054 55.0 0.00 0.00 46.36 3.02 R
3841 3845 1.352083 ACTAAGGCCAGACTCTTGCA 58.648 50.0 5.01 0.00 0.00 4.08 R
4608 4612 1.455383 CCACTGTTGCCTGTTGGTCC 61.455 60.0 0.00 0.00 35.27 4.46 R
5575 5847 0.034198 TTCACCGTGAATTCCAGCGA 59.966 50.0 9.99 0.00 30.26 4.93 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
57 58 2.613026 TCGTGGCTTCTCAGAAACAA 57.387 45.000 0.00 0.00 0.00 2.83
66 67 5.917447 GGCTTCTCAGAAACAAGAAATTGAC 59.083 40.000 0.00 0.00 31.45 3.18
137 138 5.159209 CAAGGAGAATGCACAACAAATCTC 58.841 41.667 0.00 0.00 41.32 2.75
152 153 5.724328 ACAAATCTCGAGTGAATTAGCTGA 58.276 37.500 13.13 0.00 0.00 4.26
294 295 2.067766 GAGAAGCTTCTGTCACAGCTG 58.932 52.381 33.07 13.48 46.01 4.24
402 403 4.141274 TGTTCCTTCAAGGAGAACATGGAA 60.141 41.667 6.17 0.00 46.73 3.53
503 504 1.266718 TGCTGTTGAATCGGAAGCAAC 59.733 47.619 15.29 15.29 40.72 4.17
557 558 4.021016 ACATACTGAGAACGAGAGGCTTTT 60.021 41.667 0.00 0.00 0.00 2.27
684 685 5.485209 AAGACCAACTAATCGAGGAAAGT 57.515 39.130 0.00 0.00 0.00 2.66
736 737 9.733556 TTTACCAATCTGTAATTAAAGAGCTGA 57.266 29.630 11.05 0.00 31.19 4.26
777 778 1.133407 CTAGACCAAGCCGAGACAGTC 59.867 57.143 0.00 0.00 0.00 3.51
811 815 2.839632 ATCGCCTGGCCTCATCGA 60.840 61.111 14.12 8.37 34.24 3.59
982 986 5.574443 GCTAAAGGTGAATTGCATGAACTTC 59.426 40.000 0.00 0.00 0.00 3.01
1265 1269 1.811359 GCATGAAGCAGAAAGACAGCT 59.189 47.619 0.00 0.00 43.02 4.24
1422 1426 4.503741 TCAGGCAGAACTTTTGCATAAC 57.496 40.909 6.62 0.00 43.28 1.89
1650 1654 4.875536 TCTGCTCAAAGCGATAATGCTAAA 59.124 37.500 0.00 0.00 46.60 1.85
1736 1740 6.985188 TGCATCTAGAATGGTTAAGAACAC 57.015 37.500 0.00 0.00 0.00 3.32
1953 1957 6.095300 TGAGCAAATGTGAAGAAGTTGAAGAA 59.905 34.615 0.00 0.00 0.00 2.52
2058 2062 3.904136 AAAAGTGAAGCGTTGGATGAG 57.096 42.857 0.00 0.00 0.00 2.90
2257 2261 7.095910 TGAGAAACTTGAAAATGCAGTTGAAA 58.904 30.769 0.00 0.00 0.00 2.69
2583 2587 1.618343 GGTATTGCTGTTGCCAAAGGT 59.382 47.619 0.00 0.00 38.71 3.50
2702 2706 4.216257 TGCATTAGTGAAAGAGTTGGAAGC 59.784 41.667 0.00 0.00 0.00 3.86
2907 2911 7.857734 TGTTGAGAAAATAGAACTGTTGTCA 57.142 32.000 0.00 0.00 0.00 3.58
2973 2977 4.372588 AGAGATCATCTATGGATGGGCAT 58.627 43.478 17.95 5.45 46.70 4.40
3002 3006 1.103398 GGTGTGGCCATGGATAGCAC 61.103 60.000 18.40 16.82 37.17 4.40
3015 3019 4.256110 TGGATAGCACAAGTGATGAACAG 58.744 43.478 4.04 0.00 0.00 3.16
3099 3103 2.680312 TCTATGAACTGGCTGAGCAC 57.320 50.000 6.82 0.00 0.00 4.40
3159 3163 7.458397 ACAGTATTGTACAGAAATGGGAAGAA 58.542 34.615 10.47 0.00 35.25 2.52
3201 3205 0.523072 CCCCGCAGTTCAGAATGTTG 59.477 55.000 0.00 0.00 37.40 3.33
3215 3219 6.778821 TCAGAATGTTGGAACCAGAAGATAA 58.221 36.000 0.00 0.00 37.40 1.75
3367 3371 4.204970 AGCTCAGTGCAGAGGTCA 57.795 55.556 2.06 0.00 42.26 4.02
3482 3486 5.610398 TGAGTTTGTCAGAGATAACTTGCA 58.390 37.500 0.00 0.00 31.41 4.08
3568 3572 7.602753 TCATGATATGGAAATAGAGGTACACG 58.397 38.462 0.00 0.00 0.00 4.49
3576 3580 6.435277 TGGAAATAGAGGTACACGAACTACTT 59.565 38.462 0.00 0.00 0.00 2.24
3608 3612 1.755179 AATGTGCTGCAGGATGGTAC 58.245 50.000 17.12 0.22 35.86 3.34
3660 3664 2.092646 TGTACTGTGCTTGGGTGAACTT 60.093 45.455 0.00 0.00 0.00 2.66
3841 3845 3.944015 GAGTAATCAGTTGGAGCATGCTT 59.056 43.478 23.61 5.39 0.00 3.91
3956 3960 6.855763 AATAAACCAATTGCAGGAAGATGA 57.144 33.333 0.00 0.00 0.00 2.92
4072 4076 0.179100 TGAGTTAGAGCATGCTCGCC 60.179 55.000 35.50 27.09 46.90 5.54
4194 4198 0.183492 AAGAAGGTGGTGCTGAGCAA 59.817 50.000 9.51 0.00 41.47 3.91
4424 4428 9.733556 AAAACTTAAAAATGAAAGGGAACAACT 57.266 25.926 0.00 0.00 0.00 3.16
4467 4471 1.762708 AAACACTATTGATGGGCCGG 58.237 50.000 0.00 0.00 0.00 6.13
4476 4480 0.693622 TGATGGGCCGGTTAACTGAA 59.306 50.000 16.27 0.00 0.00 3.02
4494 4498 5.825507 ACTGAAAATGAGAAGAACTTGCAC 58.174 37.500 0.00 0.00 0.00 4.57
4746 4750 5.338789 GGAGGAATTAGTCAAGGAAGAAGCT 60.339 44.000 0.00 0.00 0.00 3.74
4891 4895 4.281182 TGAAGGAGTTGAACTCTACCAGTC 59.719 45.833 23.06 10.60 44.46 3.51
4932 4936 1.808411 TTGACCTTTCACATCGCCTC 58.192 50.000 0.00 0.00 0.00 4.70
5042 5046 8.736097 AATATGGTGGACATACCTATCACTTA 57.264 34.615 0.00 0.00 44.41 2.24
5104 5108 2.770164 AGGCTACCAATGTGTCAGTC 57.230 50.000 0.00 0.00 0.00 3.51
5205 5468 2.226330 TGCACTTACCGCAGAAATGTT 58.774 42.857 0.00 0.00 33.55 2.71
5419 5682 8.746052 AGGATATTTCCATGTAAAACGAATCA 57.254 30.769 4.92 0.00 45.30 2.57
5575 5847 7.286087 TGCAGAATACTCATATTCCAAATGCTT 59.714 33.333 14.72 0.00 45.49 3.91
5769 6041 3.304928 CCAACTTGCAGAACAGATTCACC 60.305 47.826 0.00 0.00 37.29 4.02
5820 6092 8.370493 TGAGAGAAAACATTCTTGAACTACAG 57.630 34.615 0.00 0.00 0.00 2.74
5960 6232 3.197983 GGTACTGGGAGCTATTCTGTTGT 59.802 47.826 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.746703 AGTTCAAGTTCTCCCTTAACAGTATT 58.253 34.615 0.00 0.00 0.00 1.89
57 58 2.160417 GCTGTTGCTAGCGTCAATTTCT 59.840 45.455 10.77 0.00 33.46 2.52
66 67 1.197492 TCACATTTGCTGTTGCTAGCG 59.803 47.619 10.77 0.00 46.61 4.26
137 138 1.929836 GGCAGTCAGCTAATTCACTCG 59.070 52.381 0.00 0.00 44.79 4.18
152 153 1.822990 CTTCCAGCAATGATTGGCAGT 59.177 47.619 7.35 0.00 34.38 4.40
359 360 1.163554 CAGCTCAGCCTCCAAACTTC 58.836 55.000 0.00 0.00 0.00 3.01
402 403 3.799366 TGTTAATTCAGTCCACGTGTGT 58.201 40.909 15.65 0.00 0.00 3.72
478 479 3.814945 CTTCCGATTCAACAGCAAACTC 58.185 45.455 0.00 0.00 0.00 3.01
503 504 6.183347 ACATTATCCTCCTTCAGTTTCTTGG 58.817 40.000 0.00 0.00 0.00 3.61
684 685 1.864711 GAACTGTTAGTTGCACGCAGA 59.135 47.619 0.00 0.00 38.80 4.26
777 778 1.898079 CGATCATGTTTTTGACACGCG 59.102 47.619 3.53 3.53 42.04 6.01
779 780 2.095768 AGGCGATCATGTTTTTGACACG 60.096 45.455 0.00 0.00 42.04 4.49
811 815 7.765360 TCTTTCAGCATTTTCAACAGTGATTTT 59.235 29.630 0.00 0.00 32.48 1.82
942 946 4.407296 CCTTTAGCAACCTCTAGATGTCCT 59.593 45.833 0.78 4.32 0.00 3.85
982 986 4.438744 GGACATCCGCTCCACTAATTTTTG 60.439 45.833 0.00 0.00 0.00 2.44
1160 1164 4.698780 CCTTTGCAAGATCTGAAGTCATCA 59.301 41.667 0.00 0.00 36.38 3.07
1265 1269 1.032014 GGCCTCAAAAACTGCAGTGA 58.968 50.000 22.49 12.37 0.00 3.41
1558 1562 5.414765 CCACAGAGTCCAAAATACTAAACCC 59.585 44.000 0.00 0.00 0.00 4.11
1560 1564 7.824779 AGATCCACAGAGTCCAAAATACTAAAC 59.175 37.037 0.00 0.00 0.00 2.01
1953 1957 3.952931 AGAACTGCATCTCAAGCTGATT 58.047 40.909 0.00 0.00 35.29 2.57
2058 2062 0.108207 AGAGGCATCTACCATGCAGC 59.892 55.000 0.00 0.27 46.21 5.25
2100 2104 2.291865 TGAGGTAGGATCTGCAGAGTGT 60.292 50.000 22.96 10.85 0.00 3.55
2178 2182 6.894682 TGGCAGTAATGTGGTAGAAATATGA 58.105 36.000 0.00 0.00 0.00 2.15
2421 2425 7.382110 TGAGAACTGGAATTTCAGTCTCTAAG 58.618 38.462 28.07 6.06 46.17 2.18
2583 2587 3.435327 CACGTTGCACTATCAAGGCTTTA 59.565 43.478 0.00 0.00 35.82 1.85
2702 2706 5.303971 CCTCTGTATAGGATTTGAGCTTGG 58.696 45.833 0.00 0.00 39.15 3.61
2907 2911 1.615392 GAAGCACCAACAGCCATCTTT 59.385 47.619 0.00 0.00 0.00 2.52
2973 2977 1.053835 TGGCCACACCAGACTCAGAA 61.054 55.000 0.00 0.00 46.36 3.02
3002 3006 8.658499 TGATATTGAGATCTGTTCATCACTTG 57.342 34.615 0.00 0.00 0.00 3.16
3015 3019 6.537355 TGACCCTGGATTTGATATTGAGATC 58.463 40.000 0.00 0.00 0.00 2.75
3201 3205 6.261158 GCCAAGTTATCTTATCTTCTGGTTCC 59.739 42.308 0.00 0.00 32.07 3.62
3215 3219 3.330701 TCTGTTTCCCAGCCAAGTTATCT 59.669 43.478 0.00 0.00 41.25 1.98
3367 3371 4.338400 GTCCTTTTCGGCCTTTATAGCAAT 59.662 41.667 0.00 0.00 0.00 3.56
3482 3486 7.179338 TCTCCTGTAGTTCAGCTAGATCTTTTT 59.821 37.037 0.00 0.00 42.38 1.94
3568 3572 4.742438 TTCGCACCAAATCAAGTAGTTC 57.258 40.909 0.00 0.00 0.00 3.01
3576 3580 1.612950 AGCACATTTCGCACCAAATCA 59.387 42.857 0.00 0.00 0.00 2.57
3608 3612 5.828747 CACCAGATGGAATTTCAGCATTAG 58.171 41.667 4.50 0.00 38.94 1.73
3660 3664 9.581289 TCATAATGGTCTAAAACTTTCCTCAAA 57.419 29.630 0.00 0.00 0.00 2.69
3719 3723 5.943416 TCTAAATGAATTTCCTTCTCGGCAA 59.057 36.000 0.00 0.00 34.75 4.52
3841 3845 1.352083 ACTAAGGCCAGACTCTTGCA 58.648 50.000 5.01 0.00 0.00 4.08
4041 4045 5.900425 TGCTCTAACTCATCACTCTGATTC 58.100 41.667 0.00 0.00 34.28 2.52
4160 4164 2.159379 CCTTCTTGCAGCCGGTTTATTC 60.159 50.000 1.90 0.00 0.00 1.75
4194 4198 5.050091 CACAAGCGACTGATACTTTTGAGTT 60.050 40.000 0.00 0.00 0.00 3.01
4424 4428 9.948964 TTTTCTCAGATTCAAGTGATTCTATGA 57.051 29.630 5.61 5.01 34.22 2.15
4467 4471 7.915397 TGCAAGTTCTTCTCATTTTCAGTTAAC 59.085 33.333 0.00 0.00 0.00 2.01
4476 4480 5.700832 TGTATCGTGCAAGTTCTTCTCATTT 59.299 36.000 0.00 0.00 0.00 2.32
4494 4498 6.722301 TCTACTCAAGTATTCCGTTGTATCG 58.278 40.000 0.00 0.00 0.00 2.92
4608 4612 1.455383 CCACTGTTGCCTGTTGGTCC 61.455 60.000 0.00 0.00 35.27 4.46
4746 4750 5.620206 TGTTTAGAGGATTCAGAAAGTGCA 58.380 37.500 0.00 0.00 0.00 4.57
4891 4895 2.490115 AGCAGACCTCTCTTAGTTGACG 59.510 50.000 0.00 0.00 0.00 4.35
4932 4936 3.613952 TTTGCTGAATGCGCTGGCG 62.614 57.895 9.73 10.80 46.63 5.69
5042 5046 6.260700 TGCTACTGGTTAACATCCCATTAT 57.739 37.500 8.10 0.00 0.00 1.28
5055 5059 2.787473 TGCTGCTTATGCTACTGGTT 57.213 45.000 0.00 0.00 40.48 3.67
5138 5401 6.147581 CACAACATCAGTCCAATCTTTTCTG 58.852 40.000 0.00 0.00 0.00 3.02
5407 5670 5.856126 TGGTCATCTGTGATTCGTTTTAC 57.144 39.130 0.00 0.00 36.60 2.01
5539 5802 3.255642 TGAGTATTCTGCAAAGGCCAAAC 59.744 43.478 5.01 0.00 40.13 2.93
5575 5847 0.034198 TTCACCGTGAATTCCAGCGA 59.966 50.000 9.99 0.00 30.26 4.93
5769 6041 5.414454 TGATTCCAACTCGTTATTTTGGGAG 59.586 40.000 0.00 0.00 40.31 4.30
5820 6092 6.279513 TCTTCCTTCTCTTTGATCTCTGAC 57.720 41.667 0.00 0.00 0.00 3.51
5893 6165 7.015682 TCCTTCAATCTCAGAAACTGAACTAGT 59.984 37.037 0.00 0.00 40.18 2.57
5960 6232 9.970395 GATCATATGAAAATAAATGGTTCTGCA 57.030 29.630 9.99 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.