Multiple sequence alignment - TraesCS3B01G420800

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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 TraesCS3B01G420800 chr3B 100.000 3526 0 0 1 3526 657789714 657793239 0.000000e+00 6512
1 TraesCS3B01G420800 chr2B 97.533 3526 77 4 1 3526 670327102 670330617 0.000000e+00 6021
2 TraesCS3B01G420800 chr2B 97.467 2329 57 2 1198 3526 655657232 655659558 0.000000e+00 3973
3 TraesCS3B01G420800 chr2B 97.341 2332 58 4 1198 3526 717672836 717670506 0.000000e+00 3960
4 TraesCS3B01G420800 chr2B 97.127 2332 63 4 1198 3526 738149116 738151446 0.000000e+00 3932
5 TraesCS3B01G420800 chr2B 96.378 2209 63 12 1 2204 19851990 19854186 0.000000e+00 3620
6 TraesCS3B01G420800 chr2B 96.392 2162 65 8 1 2159 512426253 512424102 0.000000e+00 3548
7 TraesCS3B01G420800 chr2B 97.057 1325 35 2 2202 3526 655691982 655690662 0.000000e+00 2228
8 TraesCS3B01G420800 chr2B 95.413 218 2 3 1 217 655656151 655656361 1.210000e-89 340
9 TraesCS3B01G420800 chr7B 97.505 3527 78 5 1 3526 599829333 599832850 0.000000e+00 6017
10 TraesCS3B01G420800 chr6B 96.691 2206 62 6 1 2204 319457343 319459539 0.000000e+00 3659
11 TraesCS3B01G420800 chr6B 95.696 2207 80 9 1 2204 353552233 353550039 0.000000e+00 3535
12 TraesCS3B01G420800 chr6B 96.830 1325 42 0 2202 3526 353549950 353548626 0.000000e+00 2215
13 TraesCS3B01G420800 chr4B 96.556 2207 63 8 1 2204 603291268 603289072 0.000000e+00 3642
14 TraesCS3B01G420800 chr4B 97.436 1326 33 1 2202 3526 15518896 15520221 0.000000e+00 2259
15 TraesCS3B01G420800 chr4A 95.833 2208 78 9 1 2204 713792479 713790282 0.000000e+00 3555
16 TraesCS3B01G420800 chr4A 96.755 1325 43 0 2202 3526 713790194 713788870 0.000000e+00 2209
17 TraesCS3B01G420800 chr6A 95.333 2207 87 11 1 2204 555104744 555102551 0.000000e+00 3491
18 TraesCS3B01G420800 chr7A 94.703 2209 95 15 1 2204 41970400 41972591 0.000000e+00 3411


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 TraesCS3B01G420800 chr3B 657789714 657793239 3525 False 6512.0 6512 100.000 1 3526 1 chr3B.!!$F1 3525
1 TraesCS3B01G420800 chr2B 670327102 670330617 3515 False 6021.0 6021 97.533 1 3526 1 chr2B.!!$F2 3525
2 TraesCS3B01G420800 chr2B 717670506 717672836 2330 True 3960.0 3960 97.341 1198 3526 1 chr2B.!!$R3 2328
3 TraesCS3B01G420800 chr2B 738149116 738151446 2330 False 3932.0 3932 97.127 1198 3526 1 chr2B.!!$F3 2328
4 TraesCS3B01G420800 chr2B 19851990 19854186 2196 False 3620.0 3620 96.378 1 2204 1 chr2B.!!$F1 2203
5 TraesCS3B01G420800 chr2B 512424102 512426253 2151 True 3548.0 3548 96.392 1 2159 1 chr2B.!!$R1 2158
6 TraesCS3B01G420800 chr2B 655690662 655691982 1320 True 2228.0 2228 97.057 2202 3526 1 chr2B.!!$R2 1324
7 TraesCS3B01G420800 chr2B 655656151 655659558 3407 False 2156.5 3973 96.440 1 3526 2 chr2B.!!$F4 3525
8 TraesCS3B01G420800 chr7B 599829333 599832850 3517 False 6017.0 6017 97.505 1 3526 1 chr7B.!!$F1 3525
9 TraesCS3B01G420800 chr6B 319457343 319459539 2196 False 3659.0 3659 96.691 1 2204 1 chr6B.!!$F1 2203
10 TraesCS3B01G420800 chr6B 353548626 353552233 3607 True 2875.0 3535 96.263 1 3526 2 chr6B.!!$R1 3525
11 TraesCS3B01G420800 chr4B 603289072 603291268 2196 True 3642.0 3642 96.556 1 2204 1 chr4B.!!$R1 2203
12 TraesCS3B01G420800 chr4B 15518896 15520221 1325 False 2259.0 2259 97.436 2202 3526 1 chr4B.!!$F1 1324
13 TraesCS3B01G420800 chr4A 713788870 713792479 3609 True 2882.0 3555 96.294 1 3526 2 chr4A.!!$R1 3525
14 TraesCS3B01G420800 chr6A 555102551 555104744 2193 True 3491.0 3491 95.333 1 2204 1 chr6A.!!$R1 2203
15 TraesCS3B01G420800 chr7A 41970400 41972591 2191 False 3411.0 3411 94.703 1 2204 1 chr7A.!!$F1 2203

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
772 785 0.179176 GTGTGCTTGCGTTGTTGTGA 60.179 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2579 2700 1.274167 AGATTTCACGTACGCCTTCCA 59.726 47.619 16.72 0.0 0.0 3.53 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
63 64 4.900635 AAAAACAAGAGACAGTTGCGAT 57.099 36.364 0.00 0.00 0.00 4.58
65 66 5.597813 AAAACAAGAGACAGTTGCGATAG 57.402 39.130 0.00 0.00 0.00 2.08
66 67 3.944055 ACAAGAGACAGTTGCGATAGT 57.056 42.857 0.00 0.00 39.35 2.12
67 68 3.579709 ACAAGAGACAGTTGCGATAGTG 58.420 45.455 0.00 0.00 39.35 2.74
68 69 3.255888 ACAAGAGACAGTTGCGATAGTGA 59.744 43.478 0.00 0.00 39.35 3.41
69 70 4.237724 CAAGAGACAGTTGCGATAGTGAA 58.762 43.478 0.00 0.00 39.35 3.18
70 71 4.521130 AGAGACAGTTGCGATAGTGAAA 57.479 40.909 0.00 0.00 39.35 2.69
71 72 4.883083 AGAGACAGTTGCGATAGTGAAAA 58.117 39.130 0.00 0.00 39.35 2.29
72 73 5.297547 AGAGACAGTTGCGATAGTGAAAAA 58.702 37.500 0.00 0.00 39.35 1.94
619 627 8.560374 TGTACAAACACGATTCATCAATACAAA 58.440 29.630 0.00 0.00 0.00 2.83
620 628 9.388346 GTACAAACACGATTCATCAATACAAAA 57.612 29.630 0.00 0.00 0.00 2.44
719 732 4.156556 GCCTGATAGTGCACTTTGAATTGA 59.843 41.667 27.06 4.09 0.00 2.57
772 785 0.179176 GTGTGCTTGCGTTGTTGTGA 60.179 50.000 0.00 0.00 0.00 3.58
818 831 3.519510 TGGTACTAGCTTGCCTCAAGAAT 59.480 43.478 10.44 1.32 43.42 2.40
1093 1108 0.313672 TGCAGAATTTGTGGCGGAAC 59.686 50.000 0.00 0.00 0.00 3.62
1113 1128 4.136341 ACCACGTAATCCCCCTATCATA 57.864 45.455 0.00 0.00 0.00 2.15
1172 1188 1.064906 AGATGGGCAGTCAAGTCATGG 60.065 52.381 0.00 0.00 0.00 3.66
1866 1885 0.991355 TTGAACCACACCCACCTCCT 60.991 55.000 0.00 0.00 0.00 3.69
1895 1914 9.454859 CTATCTTCCAACTTTAAGAACTTGGAT 57.545 33.333 13.79 5.11 37.49 3.41
1965 1986 9.624697 GATTTTGCTTGAAACATGTCACTAATA 57.375 29.630 0.00 0.00 0.00 0.98
2001 2023 5.102953 TGCCTTAGTTGCTTGATAGTGAT 57.897 39.130 0.00 0.00 0.00 3.06
2442 2561 6.032956 TCAAGACGCTCTTAAACAAGGATA 57.967 37.500 0.87 0.00 33.78 2.59
2579 2700 2.124570 GGGTCGATGGTGCAGCAT 60.125 61.111 30.31 30.31 0.00 3.79
2594 2715 1.447140 GCATGGAAGGCGTACGTGA 60.447 57.895 17.90 0.00 29.35 4.35
2979 3103 4.275662 TGTGTTGACTTTAAATTGACGCG 58.724 39.130 3.53 3.53 0.00 6.01
3232 3356 8.567948 CAGAAAATCCAAACACACATACTAGTT 58.432 33.333 0.00 0.00 0.00 2.24
3235 3359 5.204409 TCCAAACACACATACTAGTTCGT 57.796 39.130 0.00 0.00 0.00 3.85
3287 3411 6.373779 CATTTACAGACTGAAATGTGGTCAC 58.626 40.000 20.65 0.00 37.96 3.67
3428 3552 3.017442 GAGGTTTACCCCAATCAAGAGC 58.983 50.000 0.00 0.00 36.42 4.09
3469 3593 1.910671 AGGGGCTATTTTGTCACGGTA 59.089 47.619 0.00 0.00 0.00 4.02
3475 3599 3.063588 GCTATTTTGTCACGGTAGAAGCC 59.936 47.826 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 217 1.735198 TAACGTTTCGCCGCTGAGG 60.735 57.895 5.91 0.00 44.97 3.86
317 319 8.832521 CAGTACCTATGTTTGTGTGTTAGAAAA 58.167 33.333 0.00 0.00 0.00 2.29
396 399 7.920682 AGCATGTTTAGTGTTAGGAAAAACTTG 59.079 33.333 0.00 0.00 34.81 3.16
648 661 8.338259 CAAGTCAAACTATATATGTCAGGCAAC 58.662 37.037 0.00 0.00 0.00 4.17
719 732 6.655078 AGATAGCAATTGAACAAAACCAGT 57.345 33.333 10.34 0.00 0.00 4.00
772 785 3.891366 ACTAAACTCAGGCAAGCAAACAT 59.109 39.130 0.00 0.00 0.00 2.71
1093 1108 3.835978 TGTATGATAGGGGGATTACGTGG 59.164 47.826 0.00 0.00 0.00 4.94
1097 1112 7.317722 ACTCTTTGTATGATAGGGGGATTAC 57.682 40.000 0.00 0.00 0.00 1.89
1113 1128 1.800805 CAGCACCATCGACTCTTTGT 58.199 50.000 0.00 0.00 0.00 2.83
1866 1885 7.569599 AGTTCTTAAAGTTGGAAGATAGGGA 57.430 36.000 2.24 0.00 31.91 4.20
1895 1914 3.780804 AACACACAACCAGTAGGCATA 57.219 42.857 0.00 0.00 39.06 3.14
1965 1986 6.567050 CAACTAAGGCATATGTTTGAAGCAT 58.433 36.000 4.29 0.00 0.00 3.79
2135 2159 5.108517 GCAAGTTCAGATTCAACACCAAAA 58.891 37.500 0.00 0.00 0.00 2.44
2187 2211 9.720769 AAGCAACTACAACAAGTACTATTGTAT 57.279 29.630 23.13 13.05 42.49 2.29
2288 2405 5.476091 TCCTTTTTCCACACAAAAACAGT 57.524 34.783 0.00 0.00 32.88 3.55
2545 2666 5.800296 TCGACCCAGAAAATATTCTCAACA 58.200 37.500 0.00 0.00 44.11 3.33
2579 2700 1.274167 AGATTTCACGTACGCCTTCCA 59.726 47.619 16.72 0.00 0.00 3.53
2970 3094 2.817258 TCAAATTCTTCCCGCGTCAATT 59.183 40.909 4.92 0.00 0.00 2.32
2971 3095 2.420022 CTCAAATTCTTCCCGCGTCAAT 59.580 45.455 4.92 0.00 0.00 2.57
2979 3103 1.272704 ACCCTGCCTCAAATTCTTCCC 60.273 52.381 0.00 0.00 0.00 3.97
3088 3212 3.575805 AGGGAAGAATTGGTGCTTGAAA 58.424 40.909 0.00 0.00 0.00 2.69
3232 3356 3.385433 TGTAGTCTTTTGAACCCTCACGA 59.615 43.478 0.00 0.00 0.00 4.35
3235 3359 3.971305 TCCTGTAGTCTTTTGAACCCTCA 59.029 43.478 0.00 0.00 0.00 3.86
3287 3411 3.745797 GCCTGCTTCTCTATTGGGTAAGG 60.746 52.174 0.00 0.00 0.00 2.69
3475 3599 2.495270 ACATCTGTAGTCTCCAGCACTG 59.505 50.000 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.