Multiple sequence alignment - TraesCS6B01G291600

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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 TraesCS6B01G291600 chr6B 100.000 2803 0 0 1 2803 524962052 524964854 0.000000e+00 5177
1 TraesCS6B01G291600 chr6D 93.153 2001 77 27 9 1972 353652100 353650123 0.000000e+00 2881
2 TraesCS6B01G291600 chr6D 93.535 495 9 6 1976 2462 353650066 353649587 0.000000e+00 715
3 TraesCS6B01G291600 chr6D 92.135 356 12 7 2461 2803 353649553 353649201 3.250000e-134 488
4 TraesCS6B01G291600 chr6A 90.993 1299 49 21 720 1969 488604778 488606057 0.000000e+00 1688
5 TraesCS6B01G291600 chr6A 86.278 634 41 25 1976 2579 488606116 488606733 0.000000e+00 647
6 TraesCS6B01G291600 chr6A 84.388 711 48 27 8 695 488603858 488604528 8.470000e-180 640


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 TraesCS6B01G291600 chr6B 524962052 524964854 2802 False 5177.000000 5177 100.000000 1 2803 1 chr6B.!!$F1 2802
1 TraesCS6B01G291600 chr6D 353649201 353652100 2899 True 1361.333333 2881 92.941000 9 2803 3 chr6D.!!$R1 2794
2 TraesCS6B01G291600 chr6A 488603858 488606733 2875 False 991.666667 1688 87.219667 8 2579 3 chr6A.!!$F1 2571

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
71 72 0.180406 AGGTTGCACAAGACCGACTT 59.82 50.0 0.0 0.0 40.89 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2436 0.944311 CCGTCGTGCTTAACTGCTGT 60.944 55.0 0.0 0.0 0.0 4.4 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
71 72 0.180406 AGGTTGCACAAGACCGACTT 59.820 50.000 0.00 0.00 40.89 3.01
73 74 1.295792 GTTGCACAAGACCGACTTCA 58.704 50.000 0.00 0.00 36.61 3.02
76 77 1.138069 TGCACAAGACCGACTTCAAGA 59.862 47.619 0.00 0.00 36.61 3.02
88 95 3.260740 GACTTCAAGAGATGCAGGTGAG 58.739 50.000 0.00 0.00 0.00 3.51
172 202 5.959618 ATTAACACCTTGAAGCTGGTAAC 57.040 39.130 0.42 0.00 34.79 2.50
408 442 1.328439 GATACCTACGATTCGCGCTG 58.672 55.000 5.56 0.00 46.04 5.18
420 454 3.567797 GCGCTGCGAACCAGATCC 61.568 66.667 28.07 0.00 44.64 3.36
427 461 1.586564 CGAACCAGATCCGCGAGAC 60.587 63.158 8.23 0.00 0.00 3.36
666 715 1.304547 ACAGTAGGTGCTCCTCGCT 60.305 57.895 11.38 8.22 43.94 4.93
677 726 0.458197 CTCCTCGCTGTTGCTCAGAG 60.458 60.000 12.29 9.48 46.27 3.35
691 740 1.946768 CTCAGAGTCGGACTGGAGATC 59.053 57.143 22.61 7.43 36.22 2.75
696 745 1.004862 AGTCGGACTGGAGATCTGTCA 59.995 52.381 10.41 0.00 43.46 3.58
749 1023 2.880890 GGAAGCTGTTTCTTTGCTCAGA 59.119 45.455 4.26 0.00 35.85 3.27
754 1028 4.453819 AGCTGTTTCTTTGCTCAGATGTAC 59.546 41.667 0.00 0.00 30.41 2.90
769 1045 1.926886 GTACGCGCTCTACACGTCG 60.927 63.158 5.73 0.00 40.99 5.12
925 1202 1.749638 TGCCCGAAAAACCACACGT 60.750 52.632 0.00 0.00 0.00 4.49
1002 1283 1.614385 CGACGCTGTGAGTTCGTATT 58.386 50.000 0.00 0.00 36.50 1.89
1060 1345 1.133976 AGGCAGAGAGAGAGAGAGAGC 60.134 57.143 0.00 0.00 0.00 4.09
1062 1347 1.586422 CAGAGAGAGAGAGAGAGCGG 58.414 60.000 0.00 0.00 0.00 5.52
1064 1349 1.152963 AGAGAGAGAGAGAGCGGGC 60.153 63.158 0.00 0.00 0.00 6.13
1619 1937 3.564027 GCCCGATGAAGGCGTTCG 61.564 66.667 13.98 3.49 41.41 3.95
1669 1987 2.367202 GCGGGGGTGAGATTCCTCA 61.367 63.158 0.00 0.00 46.48 3.86
1844 2168 1.134946 GCAATGCGCTCAATTACCCTT 59.865 47.619 9.73 0.00 37.77 3.95
1888 2212 2.093711 GCTTTTGTTGTCCCTTGGTGTT 60.094 45.455 0.00 0.00 0.00 3.32
1927 2251 2.097036 CTCCACCGTGTAGTACCATCA 58.903 52.381 0.00 0.00 0.00 3.07
1968 2294 2.289002 CCCATTTGATCTGCGCTACTTC 59.711 50.000 9.73 0.84 0.00 3.01
1972 2298 2.299993 TGATCTGCGCTACTTCCTTG 57.700 50.000 9.73 0.00 0.00 3.61
1973 2299 1.824852 TGATCTGCGCTACTTCCTTGA 59.175 47.619 9.73 0.00 0.00 3.02
1974 2300 2.233676 TGATCTGCGCTACTTCCTTGAA 59.766 45.455 9.73 0.00 0.00 2.69
2045 2428 0.394938 AACACGATGGTACCAGCACA 59.605 50.000 28.50 0.53 31.91 4.57
2053 2436 1.070914 TGGTACCAGCACAACATCGAA 59.929 47.619 11.60 0.00 0.00 3.71
2586 3018 3.941483 GGAATCTTTCGGAGAAGATTGCA 59.059 43.478 24.46 0.00 43.80 4.08
2589 3021 4.008074 TCTTTCGGAGAAGATTGCACTT 57.992 40.909 0.00 0.00 45.90 3.16
2590 3022 3.997021 TCTTTCGGAGAAGATTGCACTTC 59.003 43.478 8.63 8.63 45.90 3.01
2600 3032 5.444663 AAGATTGCACTTCTTCCAGAAAC 57.555 39.130 5.46 0.00 33.19 2.78
2614 3046 2.480419 CCAGAAACGAAAATGTCTCGCT 59.520 45.455 0.00 0.00 39.97 4.93
2622 3054 1.429463 AAATGTCTCGCTTCGTCACC 58.571 50.000 0.00 0.00 0.00 4.02
2703 3148 8.762481 TGCTGTAGAGATAAAATGTAGTAGGA 57.238 34.615 0.00 0.00 0.00 2.94
2733 3178 3.450096 AGTCAATATCTGAGCTGCTCACA 59.550 43.478 27.35 18.83 35.39 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.167845 GTCTTGTGCAACCTTTCAGAAAAA 58.832 37.500 0.00 0.00 34.36 1.94
47 48 1.002468 CGGTCTTGTGCAACCTTTCAG 60.002 52.381 3.88 0.00 34.36 3.02
48 49 1.021202 CGGTCTTGTGCAACCTTTCA 58.979 50.000 3.88 0.00 34.36 2.69
49 50 1.002792 GTCGGTCTTGTGCAACCTTTC 60.003 52.381 3.88 0.00 34.36 2.62
51 52 0.180406 AGTCGGTCTTGTGCAACCTT 59.820 50.000 3.88 0.00 34.36 3.50
52 53 0.180406 AAGTCGGTCTTGTGCAACCT 59.820 50.000 3.88 0.00 34.77 3.50
53 54 0.586802 GAAGTCGGTCTTGTGCAACC 59.413 55.000 0.00 0.00 36.40 3.77
54 55 1.295792 TGAAGTCGGTCTTGTGCAAC 58.704 50.000 0.00 0.00 36.40 4.17
71 72 1.277273 CACCTCACCTGCATCTCTTGA 59.723 52.381 0.00 0.00 0.00 3.02
73 74 0.035630 GCACCTCACCTGCATCTCTT 60.036 55.000 0.00 0.00 34.56 2.85
76 77 1.002868 GTGCACCTCACCTGCATCT 60.003 57.895 5.22 0.00 46.08 2.90
88 95 2.688958 AGATTAGTACGAGGAGTGCACC 59.311 50.000 14.63 4.90 37.96 5.01
160 180 4.415881 TTGAGTTCTGTTACCAGCTTCA 57.584 40.909 0.00 0.00 38.66 3.02
332 363 0.894184 GACTGACTGACTGACCCGGA 60.894 60.000 0.73 0.00 0.00 5.14
336 367 2.094957 GCTACTGACTGACTGACTGACC 60.095 54.545 0.00 0.00 0.00 4.02
337 368 2.413502 CGCTACTGACTGACTGACTGAC 60.414 54.545 0.00 0.00 0.00 3.51
338 369 1.807142 CGCTACTGACTGACTGACTGA 59.193 52.381 0.00 0.00 0.00 3.41
339 370 1.730772 GCGCTACTGACTGACTGACTG 60.731 57.143 0.00 0.00 0.00 3.51
408 442 2.956964 CTCGCGGATCTGGTTCGC 60.957 66.667 6.13 2.82 45.15 4.70
666 715 0.315251 CAGTCCGACTCTGAGCAACA 59.685 55.000 4.19 0.00 35.20 3.33
677 726 1.464734 TGACAGATCTCCAGTCCGAC 58.535 55.000 8.71 0.00 0.00 4.79
691 740 0.455633 GCGCAAATCTGGCTTGACAG 60.456 55.000 0.30 0.00 39.84 3.51
696 745 1.533625 TTGTAGCGCAAATCTGGCTT 58.466 45.000 11.47 0.00 38.19 4.35
749 1023 4.684265 CGTGTAGAGCGCGTACAT 57.316 55.556 23.04 0.00 45.13 2.29
1255 1561 4.554036 GAGGATGGGGAGGCGCAC 62.554 72.222 10.83 1.82 0.00 5.34
1606 1924 2.435938 TGCCCGAACGCCTTCATC 60.436 61.111 0.00 0.00 0.00 2.92
1844 2168 3.059386 GGAAATGACGCCGCCCAA 61.059 61.111 0.00 0.00 0.00 4.12
1927 2251 6.432403 TGGGAGCTTAAAATGTCCAATTTT 57.568 33.333 0.00 2.04 35.62 1.82
2045 2428 3.058914 GTGCTTAACTGCTGTTCGATGTT 60.059 43.478 12.67 0.00 37.59 2.71
2053 2436 0.944311 CCGTCGTGCTTAACTGCTGT 60.944 55.000 0.00 0.00 0.00 4.40
2454 2851 2.280797 GCGGTGAACCAGCTCACA 60.281 61.111 6.21 0.00 46.31 3.58
2589 3021 4.447724 CGAGACATTTTCGTTTCTGGAAGA 59.552 41.667 0.00 0.00 35.60 2.87
2590 3022 4.702392 CGAGACATTTTCGTTTCTGGAAG 58.298 43.478 0.00 0.00 33.57 3.46
2591 3023 3.059188 GCGAGACATTTTCGTTTCTGGAA 60.059 43.478 0.00 0.00 40.08 3.53
2600 3032 1.719246 TGACGAAGCGAGACATTTTCG 59.281 47.619 4.18 4.18 45.62 3.46
2614 3046 4.281435 TCAAATACTGGTAGTGGTGACGAA 59.719 41.667 0.00 0.00 0.00 3.85
2622 3054 5.120830 GTGAACAGCTCAAATACTGGTAGTG 59.879 44.000 0.00 0.00 38.25 2.74
2703 3148 6.705381 GCAGCTCAGATATTGACTCACTTAAT 59.295 38.462 0.00 0.00 0.00 1.40
2762 3207 5.133221 ACCTACTGATTGCTCAACAGTTTT 58.867 37.500 16.70 5.77 43.27 2.43
2763 3208 4.718961 ACCTACTGATTGCTCAACAGTTT 58.281 39.130 16.70 6.00 43.27 2.66
2775 3220 2.826128 TCTCACTCGCAACCTACTGATT 59.174 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.