Multiple sequence alignment - TraesCS6D01G077400

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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 TraesCS6D01G077400 chr6D 100.000 3959 0 0 1 3959 41624618 41620660 0.000000e+00 7312
1 TraesCS6D01G077400 chr6A 93.559 3819 179 20 1 3778 52290373 52286581 0.000000e+00 5627
2 TraesCS6D01G077400 chr6A 91.713 3077 219 19 320 3371 74148499 74151564 0.000000e+00 4237
3 TraesCS6D01G077400 chr6A 88.786 865 76 10 3097 3959 555445125 555445970 0.000000e+00 1040
4 TraesCS6D01G077400 chr6A 89.091 330 27 2 1 322 52185935 52185607 6.160000e-108 401
5 TraesCS6D01G077400 chr6A 90.308 227 22 0 3733 3959 74144808 74145034 8.320000e-77 298
6 TraesCS6D01G077400 chr6A 94.149 188 10 1 3772 3959 52243071 52242885 6.480000e-73 285
7 TraesCS6D01G077400 chr7D 91.978 3665 250 24 320 3959 562196833 562200478 0.000000e+00 5099
8 TraesCS6D01G077400 chr7D 91.457 3664 261 29 320 3959 524304002 524307637 0.000000e+00 4985
9 TraesCS6D01G077400 chr7D 90.830 3664 274 41 320 3959 524249276 524252901 0.000000e+00 4848
10 TraesCS6D01G077400 chr7D 91.161 3428 237 27 1 3371 524311303 524314721 0.000000e+00 4591
11 TraesCS6D01G077400 chr7D 89.720 321 30 3 1 320 524303658 524303976 1.320000e-109 407
12 TraesCS6D01G077400 chr7D 89.571 326 25 4 1 320 562196485 562196807 4.760000e-109 405
13 TraesCS6D01G077400 chr7A 89.758 4003 338 30 3 3953 604249794 604253776 0.000000e+00 5055
14 TraesCS6D01G077400 chr7A 89.676 4010 339 29 4 3959 604260574 604264562 0.000000e+00 5042
15 TraesCS6D01G077400 chr7A 89.543 4007 348 31 3 3959 604255197 604259182 0.000000e+00 5012
16 TraesCS6D01G077400 chr7A 89.513 3986 343 35 3 3959 604221556 604225495 0.000000e+00 4975
17 TraesCS6D01G077400 chr7A 92.491 293 22 0 3667 3959 604285729 604286021 1.700000e-113 420
18 TraesCS6D01G077400 chr7A 89.506 324 29 4 1 320 604289790 604290112 4.760000e-109 405
19 TraesCS6D01G077400 chr7B 91.050 3553 246 35 456 3959 560501462 560504991 0.000000e+00 4734
20 TraesCS6D01G077400 chr6B 90.303 330 23 4 1 322 95553176 95553504 1.320000e-114 424
21 TraesCS6D01G077400 chr6B 88.923 325 28 6 1 322 95511327 95511646 1.030000e-105 394
22 TraesCS6D01G077400 chr1D 87.065 201 19 5 3576 3775 234284421 234284227 1.850000e-53 220


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 TraesCS6D01G077400 chr6D 41620660 41624618 3958 True 7312.000000 7312 100.000000 1 3959 1 chr6D.!!$R1 3958
1 TraesCS6D01G077400 chr6A 52286581 52290373 3792 True 5627.000000 5627 93.559000 1 3778 1 chr6A.!!$R3 3777
2 TraesCS6D01G077400 chr6A 74144808 74151564 6756 False 2267.500000 4237 91.010500 320 3959 2 chr6A.!!$F2 3639
3 TraesCS6D01G077400 chr6A 555445125 555445970 845 False 1040.000000 1040 88.786000 3097 3959 1 chr6A.!!$F1 862
4 TraesCS6D01G077400 chr7D 524249276 524252901 3625 False 4848.000000 4848 90.830000 320 3959 1 chr7D.!!$F1 3639
5 TraesCS6D01G077400 chr7D 524303658 524314721 11063 False 3327.666667 4985 90.779333 1 3959 3 chr7D.!!$F2 3958
6 TraesCS6D01G077400 chr7D 562196485 562200478 3993 False 2752.000000 5099 90.774500 1 3959 2 chr7D.!!$F3 3958
7 TraesCS6D01G077400 chr7A 604249794 604264562 14768 False 5036.333333 5055 89.659000 3 3959 3 chr7A.!!$F2 3956
8 TraesCS6D01G077400 chr7A 604221556 604225495 3939 False 4975.000000 4975 89.513000 3 3959 1 chr7A.!!$F1 3956
9 TraesCS6D01G077400 chr7A 604285729 604290112 4383 False 412.500000 420 90.998500 1 3959 2 chr7A.!!$F3 3958
10 TraesCS6D01G077400 chr7B 560501462 560504991 3529 False 4734.000000 4734 91.050000 456 3959 1 chr7B.!!$F1 3503

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
911 4433 0.111061 ACTCATGGGCAGAACAGCAA 59.889 50.0 0.0 0.0 35.83 3.91 F
1030 4555 0.820891 CTGCTGCTTTGTGTCCCAGT 60.821 55.0 0.0 0.0 0.00 4.00 F
1728 5259 0.892063 GGCTCCTCTTCTCGTTCTGT 59.108 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 5259 0.321387 ACGAGAGGTAGTCGCTGACA 60.321 55.0 10.52 0.0 41.26 3.58 R
1897 5428 0.733150 TCGACGAGCGTGATGAGAAT 59.267 50.0 0.00 0.0 41.80 2.40 R
3625 17994 0.819582 CACTGATTCCATTGGCCCAC 59.180 55.0 0.00 0.0 0.00 4.61 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
116 118 8.919145 ACAAGTTGTAACTTTATTGAAATCCCA 58.081 29.630 6.75 0.00 46.52 4.37
268 277 2.500098 ACAGCGCTAAATTGGAGGTCTA 59.500 45.455 10.99 0.00 0.00 2.59
283 292 5.001232 GGAGGTCTAGATGTAGTAGCTCAG 58.999 50.000 19.91 0.00 35.18 3.35
290 299 5.782893 AGATGTAGTAGCTCAGTGAATCC 57.217 43.478 0.00 0.00 0.00 3.01
304 313 0.890996 GAATCCCGGATGCATGGTCC 60.891 60.000 2.46 0.00 0.00 4.46
378 3788 5.410067 TGGTTAGTTTTCGGATAAGTACGG 58.590 41.667 0.00 0.00 30.72 4.02
385 3795 3.680642 TCGGATAAGTACGGTCGAAAG 57.319 47.619 0.00 0.00 30.72 2.62
390 3800 5.049818 CGGATAAGTACGGTCGAAAGTCTAT 60.050 44.000 0.00 0.00 0.00 1.98
394 3804 9.722056 GATAAGTACGGTCGAAAGTCTATAAAA 57.278 33.333 0.00 0.00 0.00 1.52
627 4141 7.383687 TCTGTTTTGACTACGTTTGGATAGAT 58.616 34.615 0.00 0.00 0.00 1.98
905 4427 1.078918 CTCGCACTCATGGGCAGAA 60.079 57.895 0.00 0.00 38.64 3.02
911 4433 0.111061 ACTCATGGGCAGAACAGCAA 59.889 50.000 0.00 0.00 35.83 3.91
935 4457 2.206576 AGCAAAGTTGGCTTCCCTAG 57.793 50.000 0.00 0.00 38.81 3.02
949 4471 3.985019 TCCCTAGGCAACGATAACAAA 57.015 42.857 2.05 0.00 46.39 2.83
954 4476 4.083003 CCTAGGCAACGATAACAAAGCAAA 60.083 41.667 0.00 0.00 46.39 3.68
1030 4555 0.820891 CTGCTGCTTTGTGTCCCAGT 60.821 55.000 0.00 0.00 0.00 4.00
1152 4677 1.916273 ATGGTCGTGGCCACTGGTA 60.916 57.895 32.28 16.96 41.94 3.25
1171 4696 2.134287 GGTAGCCTGCCCGAGATGA 61.134 63.158 0.00 0.00 0.00 2.92
1583 5114 2.987282 AATGTCAGGCACGTCACGCA 62.987 55.000 0.00 0.00 0.00 5.24
1637 5168 1.804396 TTCGGCCAACGGTACTTCGA 61.804 55.000 2.24 0.00 44.45 3.71
1728 5259 0.892063 GGCTCCTCTTCTCGTTCTGT 59.108 55.000 0.00 0.00 0.00 3.41
1744 5275 1.169577 CTGTGTCAGCGACTACCTCT 58.830 55.000 9.49 0.00 33.15 3.69
1776 5307 1.828660 CCTAGACCTCGACGGCCAT 60.829 63.158 2.24 0.00 35.61 4.40
1913 5444 1.202348 TGACATTCTCATCACGCTCGT 59.798 47.619 0.00 0.00 0.00 4.18
2040 5571 8.131731 GCCTAGATTGAATTTAGTGACCAATTC 58.868 37.037 9.70 9.70 39.09 2.17
2087 5621 4.935808 ACGTCATCCATGAGAAAAGGTAAC 59.064 41.667 0.00 0.00 37.51 2.50
2133 5670 6.533723 TCTTATACTGTATTTCGCAGGTGTTG 59.466 38.462 5.52 0.00 38.22 3.33
2393 5937 0.742281 CTGGCGGAGATGGTGAACAG 60.742 60.000 0.00 0.00 0.00 3.16
2529 6073 1.185315 CATTTCGCCTCCACCCAATT 58.815 50.000 0.00 0.00 0.00 2.32
2619 6163 2.710902 CCACGTCATCCTCAGCCGA 61.711 63.158 0.00 0.00 0.00 5.54
2784 6328 1.394917 GCAGCATCACTAGGAACAACG 59.605 52.381 0.00 0.00 0.00 4.10
2946 6490 1.305381 AGCGCACCTCTACCCTCTT 60.305 57.895 11.47 0.00 0.00 2.85
3005 6554 4.318121 CGATAAGGCGAGTGTGCTATTTTC 60.318 45.833 0.00 0.00 34.52 2.29
3010 6559 3.188460 GGCGAGTGTGCTATTTTCTTGAA 59.812 43.478 0.00 0.00 34.52 2.69
3064 6621 4.673534 TTCTTATTTTCGTCCCGCTTTC 57.326 40.909 0.00 0.00 0.00 2.62
3234 6792 6.969043 ACCACCCATCTACTATTGATTTTGA 58.031 36.000 0.00 0.00 0.00 2.69
3306 12265 1.002624 GATGAAAGTGGGTCGGCCA 60.003 57.895 9.07 0.00 36.17 5.36
3314 17650 0.319297 GTGGGTCGGCCATATACGTC 60.319 60.000 9.07 0.00 36.17 4.34
3498 17866 3.163630 TCAACAAGCAGCCTCAAAAAC 57.836 42.857 0.00 0.00 0.00 2.43
3625 17994 8.417780 AAGACACGATTAAAGATCTCTCATTG 57.582 34.615 0.00 0.00 0.00 2.82
3662 18031 9.178758 GAATCAGTGAAGACCCAACTAAATATT 57.821 33.333 0.00 0.00 0.00 1.28
3807 18176 5.813080 ATTAAATGACTCGTGGGCTAAAC 57.187 39.130 0.00 0.00 0.00 2.01
3849 18218 4.512914 GAGGCAGATGGGTGGGGC 62.513 72.222 0.00 0.00 0.00 5.80
3899 18268 2.095718 GGAACTCGCAATTTCCACACTC 60.096 50.000 2.97 0.00 41.01 3.51
3902 18271 1.798223 CTCGCAATTTCCACACTCGAA 59.202 47.619 0.00 0.00 0.00 3.71
3939 18308 1.000052 TCGCCACACTCACGAAACATA 60.000 47.619 0.00 0.00 31.97 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 9.091784 TCGTGAATTCAAAAATTGTTCATGAAA 57.908 25.926 10.35 0.00 38.06 2.69
57 59 8.640091 TCGTGAATTCAAAAATTGTTCATGAA 57.360 26.923 10.35 3.38 38.06 2.57
72 74 6.130298 ACTTGTGAAATGTTCGTGAATTCA 57.870 33.333 3.38 3.38 0.00 2.57
259 268 4.412528 TGAGCTACTACATCTAGACCTCCA 59.587 45.833 0.00 0.00 0.00 3.86
268 277 4.586841 GGGATTCACTGAGCTACTACATCT 59.413 45.833 0.00 0.00 0.00 2.90
283 292 0.466189 ACCATGCATCCGGGATTCAC 60.466 55.000 11.60 3.25 0.00 3.18
304 313 2.205074 CGGGATTTGAAGAGATGGTCG 58.795 52.381 0.00 0.00 0.00 4.79
439 3850 9.026121 AGATACGAAGGCTGATATTAACAGTAT 57.974 33.333 3.30 0.00 37.64 2.12
454 3865 9.525409 TGTCTTAGTTTATTTAGATACGAAGGC 57.475 33.333 0.00 0.00 31.36 4.35
778 4300 9.748708 AAACATGTTTACATATATTCCACATGC 57.251 29.630 22.10 0.00 42.42 4.06
825 4347 8.244802 TGGCTTAGATTTATCTAGATACGAAGC 58.755 37.037 23.77 23.77 40.23 3.86
869 4391 4.163458 TGCGAGACCCCTCTTTATATGTTT 59.837 41.667 0.00 0.00 37.28 2.83
905 4427 3.737972 GCCAACTTTGCTTTACTTGCTGT 60.738 43.478 0.00 0.00 0.00 4.40
935 4457 3.638484 AGTTTGCTTTGTTATCGTTGCC 58.362 40.909 0.00 0.00 0.00 4.52
949 4471 0.955919 GGCTTGCGAGGTAGTTTGCT 60.956 55.000 2.37 0.00 0.00 3.91
954 4476 1.293498 CACAGGCTTGCGAGGTAGT 59.707 57.895 2.37 0.00 0.00 2.73
989 4511 1.279496 AGCCAGCATTGTGGAGACTA 58.721 50.000 8.80 0.00 40.44 2.59
1152 4677 2.136878 CATCTCGGGCAGGCTACCT 61.137 63.158 3.26 0.00 0.00 3.08
1254 4779 0.968393 TGATCGGGATGACGTGGACA 60.968 55.000 0.00 0.00 34.94 4.02
1264 4789 1.141657 CTTGGGACATGTGATCGGGAT 59.858 52.381 1.15 0.00 39.30 3.85
1368 4893 1.373748 GAGCACGGCGTCCTTGTAA 60.374 57.895 10.85 0.00 0.00 2.41
1393 4918 2.501223 TTCATCCACTGGTCGCCGAC 62.501 60.000 9.15 9.15 0.00 4.79
1583 5114 0.515564 GACGTTGCCGCAGTAATGTT 59.484 50.000 0.00 0.00 37.87 2.71
1728 5259 0.321387 ACGAGAGGTAGTCGCTGACA 60.321 55.000 10.52 0.00 41.26 3.58
1744 5275 2.089980 GTCTAGGCCAAGTAGACACGA 58.910 52.381 20.42 0.00 44.02 4.35
1776 5307 6.951198 TGTTGGCCTCCTTAATAATTTTCTCA 59.049 34.615 3.32 0.00 0.00 3.27
1897 5428 0.733150 TCGACGAGCGTGATGAGAAT 59.267 50.000 0.00 0.00 41.80 2.40
1913 5444 2.434185 GCTTGCCGTCACCATCGA 60.434 61.111 0.00 0.00 0.00 3.59
2003 5534 3.686016 TCAATCTAGGCCCTTGAACAAC 58.314 45.455 0.00 0.00 0.00 3.32
2005 5536 4.591321 ATTCAATCTAGGCCCTTGAACA 57.409 40.909 17.56 3.34 40.54 3.18
2040 5571 2.032620 ACCTTGTAGGACTATGAGGCG 58.967 52.381 0.00 0.00 37.67 5.52
2087 5621 9.979578 ATAAGATCTATTTAAGAGTGTGAGCTG 57.020 33.333 0.00 0.00 37.74 4.24
2529 6073 2.281484 GGCACGTTGAAGGGAGCA 60.281 61.111 6.84 0.00 0.00 4.26
2784 6328 2.200067 CCGAAGAGCATGACACTCATC 58.800 52.381 0.00 0.00 34.28 2.92
2848 6392 2.974698 GCGGAGATTGATGGCCGG 60.975 66.667 0.00 0.00 43.73 6.13
2946 6490 3.181515 CGTTATTTGCTCAACGGTGCATA 60.182 43.478 0.00 0.00 42.49 3.14
3064 6621 4.928661 ATCAATCGAAGTGGAACGAAAG 57.071 40.909 0.00 0.00 45.86 2.62
3562 17931 6.126854 TGGCCCATAATCTCATATCTCAGATG 60.127 42.308 0.00 0.00 29.40 2.90
3572 17941 4.282703 GCTTTCATTGGCCCATAATCTCAT 59.717 41.667 0.00 0.00 0.00 2.90
3625 17994 0.819582 CACTGATTCCATTGGCCCAC 59.180 55.000 0.00 0.00 0.00 4.61
3639 18008 8.160765 TCAAATATTTAGTTGGGTCTTCACTGA 58.839 33.333 0.00 0.00 32.63 3.41
3662 18031 8.821686 TTTCTTTCATTGGCCTATAATCTCAA 57.178 30.769 3.32 0.00 0.00 3.02
3791 18160 0.981183 ATGGTTTAGCCCACGAGTCA 59.019 50.000 0.00 0.00 37.31 3.41
3807 18176 7.012894 TCTCGCCTTTGGTGTAAATTATAATGG 59.987 37.037 0.00 0.00 34.40 3.16
3849 18218 3.019564 CCTTAAATGCCTCCTTGGTCTG 58.980 50.000 0.00 0.00 38.35 3.51
3899 18268 2.535984 GACGAGCTGGTCATATGTTTCG 59.464 50.000 22.40 2.86 36.91 3.46
3902 18271 1.802880 GCGACGAGCTGGTCATATGTT 60.803 52.381 25.81 0.00 44.04 2.71


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

AutoCloner maintained by Alex Coulton.