Multiple sequence alignment - TraesCS3B01G170200

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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 TraesCS3B01G170200 chr3B 100.000 4054 0 0 1 4054 170821776 170817723 0.000000e+00 7487
1 TraesCS3B01G170200 chr3B 96.677 4063 116 9 1 4054 772608509 772612561 0.000000e+00 6737
2 TraesCS3B01G170200 chr3B 95.990 4065 145 7 1 4054 770030514 770034571 0.000000e+00 6588
3 TraesCS3B01G170200 chr5B 96.873 4061 113 7 1 4054 426072399 426076452 0.000000e+00 6783
4 TraesCS3B01G170200 chr5B 95.086 4090 158 22 1 4050 450541646 450545732 0.000000e+00 6399
5 TraesCS3B01G170200 chr5B 92.308 325 18 1 1 325 157575878 157576195 4.780000e-124 455
6 TraesCS3B01G170200 chr7B 96.600 4059 126 4 1 4054 379737877 379741928 0.000000e+00 6721
7 TraesCS3B01G170200 chr7B 96.551 4059 128 5 1 4054 747732794 747728743 0.000000e+00 6709
8 TraesCS3B01G170200 chr7B 96.254 4058 131 12 1 4054 81909529 81913569 0.000000e+00 6632
9 TraesCS3B01G170200 chr4B 95.556 4073 159 16 1 4054 327348203 327352272 0.000000e+00 6499
10 TraesCS3B01G170200 chr4B 95.296 4060 135 14 1 4054 427293832 427289823 0.000000e+00 6388
11 TraesCS3B01G170200 chr6B 94.652 4095 176 19 1 4054 524370174 524366082 0.000000e+00 6309
12 TraesCS3B01G170200 chr2B 95.520 3214 120 12 1 3209 797488958 797492152 0.000000e+00 5116
13 TraesCS3B01G170200 chrUn 91.279 172 8 3 1 172 200662891 200663055 1.130000e-55 228


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 TraesCS3B01G170200 chr3B 170817723 170821776 4053 True 7487 7487 100.000 1 4054 1 chr3B.!!$R1 4053
1 TraesCS3B01G170200 chr3B 772608509 772612561 4052 False 6737 6737 96.677 1 4054 1 chr3B.!!$F2 4053
2 TraesCS3B01G170200 chr3B 770030514 770034571 4057 False 6588 6588 95.990 1 4054 1 chr3B.!!$F1 4053
3 TraesCS3B01G170200 chr5B 426072399 426076452 4053 False 6783 6783 96.873 1 4054 1 chr5B.!!$F2 4053
4 TraesCS3B01G170200 chr5B 450541646 450545732 4086 False 6399 6399 95.086 1 4050 1 chr5B.!!$F3 4049
5 TraesCS3B01G170200 chr7B 379737877 379741928 4051 False 6721 6721 96.600 1 4054 1 chr7B.!!$F2 4053
6 TraesCS3B01G170200 chr7B 747728743 747732794 4051 True 6709 6709 96.551 1 4054 1 chr7B.!!$R1 4053
7 TraesCS3B01G170200 chr7B 81909529 81913569 4040 False 6632 6632 96.254 1 4054 1 chr7B.!!$F1 4053
8 TraesCS3B01G170200 chr4B 327348203 327352272 4069 False 6499 6499 95.556 1 4054 1 chr4B.!!$F1 4053
9 TraesCS3B01G170200 chr4B 427289823 427293832 4009 True 6388 6388 95.296 1 4054 1 chr4B.!!$R1 4053
10 TraesCS3B01G170200 chr6B 524366082 524370174 4092 True 6309 6309 94.652 1 4054 1 chr6B.!!$R1 4053
11 TraesCS3B01G170200 chr2B 797488958 797492152 3194 False 5116 5116 95.520 1 3209 1 chr2B.!!$F1 3208

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
94 126 1.474478 ACGTGAACAAATGTGTGGCAA 59.526 42.857 0.00 0.00 38.27 4.52 F
1327 1401 0.678048 ACGATCAAAAGGGAGCTGCC 60.678 55.000 18.04 18.04 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1611 0.248498 CGAACAGCGCTTCCTCGATA 60.248 55.000 21.82 0.0 0.0 2.92 R
3092 3182 1.134848 TCGGCATGTTCATCGTCATCA 60.135 47.619 0.00 0.0 0.0 3.07 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
58 60 3.678056 AACTGTAGAATGAGGCGAACA 57.322 42.857 0.00 0.00 0.00 3.18
94 126 1.474478 ACGTGAACAAATGTGTGGCAA 59.526 42.857 0.00 0.00 38.27 4.52
95 127 1.851666 CGTGAACAAATGTGTGGCAAC 59.148 47.619 0.00 0.00 38.27 4.17
96 128 2.479389 CGTGAACAAATGTGTGGCAACT 60.479 45.455 0.00 0.00 38.27 3.16
97 129 3.242903 CGTGAACAAATGTGTGGCAACTA 60.243 43.478 0.00 0.00 38.27 2.24
98 130 4.677584 GTGAACAAATGTGTGGCAACTAA 58.322 39.130 0.00 0.00 38.27 2.24
99 131 5.105752 GTGAACAAATGTGTGGCAACTAAA 58.894 37.500 0.00 0.00 38.27 1.85
100 132 5.005299 GTGAACAAATGTGTGGCAACTAAAC 59.995 40.000 0.00 0.00 38.27 2.01
252 287 5.102953 ACTATGATAGTTGCCACACACAT 57.897 39.130 0.00 0.00 34.86 3.21
826 888 6.820656 TGTTTTCAAGTGCATTTACCAATGTT 59.179 30.769 0.00 0.00 41.84 2.71
897 967 2.285026 CGCGTGTGTGTTCATGCTATAC 60.285 50.000 0.00 0.00 44.99 1.47
1123 1193 2.124570 CAACCGCCCCATCTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
1278 1352 0.768221 AACAGAGCCTCCCAGGAACA 60.768 55.000 0.00 0.00 37.67 3.18
1327 1401 0.678048 ACGATCAAAAGGGAGCTGCC 60.678 55.000 18.04 18.04 0.00 4.85
1438 1512 1.811941 GCCTCCAGGGAATTCGTGATC 60.812 57.143 7.78 0.00 37.23 2.92
1537 1611 3.893200 TCCCGTACGAGGTCAATAATGAT 59.107 43.478 18.76 0.00 38.01 2.45
1819 1893 3.253188 GCTAATGACTGCCAGTGTTTTCA 59.747 43.478 0.00 0.00 0.00 2.69
1898 1976 2.319472 GTGCAGGCGAATCTGAAAAAC 58.681 47.619 0.00 0.00 36.93 2.43
2265 2350 6.291648 TGGATCATACATTATCCTGCTCTC 57.708 41.667 0.00 0.00 41.94 3.20
2683 2770 2.433318 GGACGTGCACTCAGCTCC 60.433 66.667 16.19 6.92 45.94 4.70
2946 3036 3.256631 GCAGTTCACTTCATTTGTCCCAT 59.743 43.478 0.00 0.00 0.00 4.00
3110 3200 2.031314 CACTGATGACGATGAACATGCC 59.969 50.000 0.00 0.00 0.00 4.40
3408 3510 3.430098 GCAATGGGTTTGTTGTCTGACAA 60.430 43.478 18.69 18.69 37.65 3.18
3533 3635 1.455383 CGCTTGAACAAAGGTGCCCT 61.455 55.000 0.00 0.00 36.30 5.19
3604 3707 1.537889 AACACCGGGGATCCTGTCA 60.538 57.895 12.96 0.00 0.00 3.58
3606 3709 0.031515 ACACCGGGGATCCTGTCATA 60.032 55.000 12.96 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 2.079158 CACGTTCAGTCATTCTGCCAT 58.921 47.619 0.00 0.00 43.32 4.40
94 126 6.243216 TGTTCAGGGAGTTTAGTGTTTAGT 57.757 37.500 0.00 0.00 0.00 2.24
95 127 7.562454 TTTGTTCAGGGAGTTTAGTGTTTAG 57.438 36.000 0.00 0.00 0.00 1.85
96 128 7.558444 ACATTTGTTCAGGGAGTTTAGTGTTTA 59.442 33.333 0.00 0.00 0.00 2.01
97 129 6.379988 ACATTTGTTCAGGGAGTTTAGTGTTT 59.620 34.615 0.00 0.00 0.00 2.83
98 130 5.891551 ACATTTGTTCAGGGAGTTTAGTGTT 59.108 36.000 0.00 0.00 0.00 3.32
99 131 5.299279 CACATTTGTTCAGGGAGTTTAGTGT 59.701 40.000 0.00 0.00 0.00 3.55
100 132 5.530915 TCACATTTGTTCAGGGAGTTTAGTG 59.469 40.000 0.00 0.00 0.00 2.74
252 287 0.961019 GTTTGGCACATGGAAGAGCA 59.039 50.000 0.00 0.00 39.30 4.26
826 888 5.302360 AGAACATAAACGTGGCAAGTAAGA 58.698 37.500 6.48 0.00 0.00 2.10
897 967 7.935338 AAATGTCAACTAGTGAATGCAAAAG 57.065 32.000 0.00 0.00 38.23 2.27
1123 1193 3.124466 GCCAACCAATAACAAAAATCGGC 59.876 43.478 0.00 0.00 0.00 5.54
1258 1332 1.276622 GTTCCTGGGAGGCTCTGTTA 58.723 55.000 15.23 0.00 34.61 2.41
1278 1352 8.415553 TGAATTTTTCAATCAACACAGTCAGAT 58.584 29.630 0.00 0.00 36.59 2.90
1327 1401 0.602106 CCTGCATACCCATCTCAGCG 60.602 60.000 0.00 0.00 0.00 5.18
1537 1611 0.248498 CGAACAGCGCTTCCTCGATA 60.248 55.000 21.82 0.00 0.00 2.92
1898 1976 2.872245 ACACCAGTTCATGTTCTTCACG 59.128 45.455 0.00 0.00 0.00 4.35
2158 2240 2.669364 GCAGTTGCCATGCTAATATGC 58.331 47.619 0.00 0.00 40.59 3.14
2265 2350 4.721132 TGGGTACTTTGTAGTTGGGAAAG 58.279 43.478 0.00 0.00 35.78 2.62
2596 2682 2.094854 GCATGCTTGGCCATTAGCTATC 60.095 50.000 25.89 13.13 43.05 2.08
2603 2689 3.152341 GTCTATAGCATGCTTGGCCATT 58.848 45.455 28.02 0.44 0.00 3.16
2643 2729 6.099557 TCCATCCACTTTCCAAATTTTTGAGT 59.900 34.615 4.63 0.00 40.55 3.41
2815 2905 4.080356 ACTGCCCAATTAGATGCTCAACTA 60.080 41.667 0.00 0.00 0.00 2.24
2946 3036 2.668001 CGGTTGGTCGATGTGTACGTTA 60.668 50.000 0.00 0.00 0.00 3.18
3051 3141 4.151883 TCCATGTCATCATCGTCATCCTA 58.848 43.478 0.00 0.00 31.15 2.94
3092 3182 1.134848 TCGGCATGTTCATCGTCATCA 60.135 47.619 0.00 0.00 0.00 3.07
3430 3532 2.926586 GCTCACTGCACGTAACAGATGA 60.927 50.000 21.00 17.73 42.31 2.92
3500 3602 2.607892 AAGCGAGCAGAAACACGGC 61.608 57.895 0.00 0.00 39.85 5.68
3533 3635 2.033448 GGGTGTCACCGGCAATGA 59.967 61.111 15.93 0.00 39.83 2.57
3604 3707 2.158696 GCTTCCTCAGGTCTGGCAATAT 60.159 50.000 0.00 0.00 0.00 1.28
3606 3709 0.034670 GCTTCCTCAGGTCTGGCAAT 60.035 55.000 0.00 0.00 0.00 3.56
3984 4087 4.396166 GTGTCATAGTTAGCAGTTGCCATT 59.604 41.667 0.00 0.00 43.38 3.16


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

AutoCloner maintained by Alex Coulton.