Multiple sequence alignment - TraesCS4B01G156600

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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 TraesCS4B01G156600 chr4B 100.000 3643 0 0 1 3643 291844303 291840661 0.000000e+00 6728
1 TraesCS4B01G156600 chr3B 97.723 3645 79 4 1 3643 435966374 435962732 0.000000e+00 6268
2 TraesCS4B01G156600 chr3B 97.669 3646 78 7 1 3643 422227709 422231350 0.000000e+00 6255
3 TraesCS4B01G156600 chr3B 97.172 2970 57 4 1 2968 803578857 803581801 0.000000e+00 4994
4 TraesCS4B01G156600 chr3B 96.711 152 5 0 3207 3358 393332447 393332296 1.680000e-63 254
5 TraesCS4B01G156600 chr2B 97.330 3670 67 6 1 3643 689377296 689380961 0.000000e+00 6205
6 TraesCS4B01G156600 chr2B 95.699 3069 121 6 253 3318 155036386 155039446 0.000000e+00 4926
7 TraesCS4B01G156600 chr2B 96.410 195 7 0 3449 3643 711453992 711454186 4.540000e-84 322
8 TraesCS4B01G156600 chr2B 96.552 145 5 0 3332 3476 45598048 45597904 1.310000e-59 241
9 TraesCS4B01G156600 chr7B 97.422 3646 70 6 1 3643 200355363 200358987 0.000000e+00 6191
10 TraesCS4B01G156600 chr7B 97.898 3282 65 4 1 3280 130340569 130337290 0.000000e+00 5675
11 TraesCS4B01G156600 chr7B 94.904 3120 131 10 170 3275 27333077 27329972 0.000000e+00 4855
12 TraesCS4B01G156600 chr7B 94.101 3170 140 32 127 3278 577217826 577214686 0.000000e+00 4774
13 TraesCS4B01G156600 chr7B 96.410 195 7 0 3449 3643 130330936 130330742 4.540000e-84 322
14 TraesCS4B01G156600 chr7B 95.897 195 8 0 3449 3643 235460968 235461162 2.110000e-82 316
15 TraesCS4B01G156600 chr7B 98.026 152 3 0 3207 3358 130337321 130337170 7.760000e-67 265
16 TraesCS4B01G156600 chr7B 95.862 145 6 0 3332 3476 130336029 130335885 6.080000e-58 235
17 TraesCS4B01G156600 chr6B 95.313 3307 117 17 1 3278 661058519 661055222 0.000000e+00 5214
18 TraesCS4B01G156600 chr6B 96.569 408 14 0 2951 3358 114141223 114141630 0.000000e+00 676
19 TraesCS4B01G156600 chr1B 96.834 379 12 0 2902 3280 550436440 550436818 5.130000e-178 634
20 TraesCS4B01G156600 chr1B 95.897 195 8 0 3449 3643 550443002 550443196 2.110000e-82 316
21 TraesCS4B01G156600 chr1B 96.552 145 5 0 3332 3476 357900151 357900295 1.310000e-59 241
22 TraesCS4B01G156600 chr7A 96.465 198 7 0 1 198 509521620 509521423 9.750000e-86 327
23 TraesCS4B01G156600 chr7A 94.313 211 9 3 1 209 7449381 7449590 1.630000e-83 320
24 TraesCS4B01G156600 chr5A 96.465 198 7 0 1 198 334531069 334530872 9.750000e-86 327
25 TraesCS4B01G156600 chr5B 95.939 197 8 0 3447 3643 246979589 246979393 1.630000e-83 320
26 TraesCS4B01G156600 chr5B 97.241 145 3 1 3332 3476 246979739 246979596 1.010000e-60 244
27 TraesCS4B01G156600 chrUn 95.862 145 6 0 3332 3476 17580529 17580385 6.080000e-58 235


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 TraesCS4B01G156600 chr4B 291840661 291844303 3642 True 6728.000000 6728 100.000 1 3643 1 chr4B.!!$R1 3642
1 TraesCS4B01G156600 chr3B 435962732 435966374 3642 True 6268.000000 6268 97.723 1 3643 1 chr3B.!!$R2 3642
2 TraesCS4B01G156600 chr3B 422227709 422231350 3641 False 6255.000000 6255 97.669 1 3643 1 chr3B.!!$F1 3642
3 TraesCS4B01G156600 chr3B 803578857 803581801 2944 False 4994.000000 4994 97.172 1 2968 1 chr3B.!!$F2 2967
4 TraesCS4B01G156600 chr2B 689377296 689380961 3665 False 6205.000000 6205 97.330 1 3643 1 chr2B.!!$F2 3642
5 TraesCS4B01G156600 chr2B 155036386 155039446 3060 False 4926.000000 4926 95.699 253 3318 1 chr2B.!!$F1 3065
6 TraesCS4B01G156600 chr7B 200355363 200358987 3624 False 6191.000000 6191 97.422 1 3643 1 chr7B.!!$F1 3642
7 TraesCS4B01G156600 chr7B 27329972 27333077 3105 True 4855.000000 4855 94.904 170 3275 1 chr7B.!!$R1 3105
8 TraesCS4B01G156600 chr7B 577214686 577217826 3140 True 4774.000000 4774 94.101 127 3278 1 chr7B.!!$R3 3151
9 TraesCS4B01G156600 chr7B 130335885 130340569 4684 True 2058.333333 5675 97.262 1 3476 3 chr7B.!!$R4 3475
10 TraesCS4B01G156600 chr6B 661055222 661058519 3297 True 5214.000000 5214 95.313 1 3278 1 chr6B.!!$R1 3277

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
747 756 2.736144 ATCGACGGACAAGCTGTTAA 57.264 45.000 0.00 0.0 35.85 2.01 F
1641 1652 1.961394 TCGAGTGGCACTTTGTAGACT 59.039 47.619 22.98 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1785 0.244450 ATGCACGGGACAAAGCATTG 59.756 50.0 0.00 0.0 44.63 2.82 R
3196 3290 0.106519 GGCGTCTGGTACCTACCCTA 60.107 60.0 14.36 0.0 45.87 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
166 167 6.600822 AGATGATGTTGGTATGTTTGAGAAGG 59.399 38.462 0.00 0.00 0.00 3.46
230 234 6.773976 TGTTTGAGAAGAATGGTTTGTTCT 57.226 33.333 0.00 0.00 45.33 3.01
747 756 2.736144 ATCGACGGACAAGCTGTTAA 57.264 45.000 0.00 0.00 35.85 2.01
850 860 3.097461 CGATACCGGAGAGTGAGGT 57.903 57.895 9.46 0.00 41.73 3.85
1199 1209 4.590647 GGAGATACATCCTCATTGTCTGGA 59.409 45.833 0.00 0.00 36.35 3.86
1283 1293 2.755469 CCCCTCATGGCAAACCCG 60.755 66.667 0.00 0.00 35.87 5.28
1411 1421 4.123497 ACAAGTGCTATATGAACGAGCA 57.877 40.909 0.00 0.00 43.74 4.26
1641 1652 1.961394 TCGAGTGGCACTTTGTAGACT 59.039 47.619 22.98 0.00 0.00 3.24
1821 1834 2.281762 GGTTCGATCGAAGGAACAATCG 59.718 50.000 29.79 12.67 43.29 3.34
1882 1895 9.705103 TGGATAGAAATTTGGAATCAAAGAGAT 57.295 29.630 0.00 0.00 44.87 2.75
2015 2028 0.963962 GTGGTCGGAGTTGGTGTCTA 59.036 55.000 0.00 0.00 0.00 2.59
2225 2238 0.376852 GTTGCTTCTGTGCGTCAACA 59.623 50.000 0.00 0.00 37.53 3.33
2544 2557 1.988107 AGGTCAATGAAGAGGAGCCAA 59.012 47.619 0.00 0.00 0.00 4.52
2704 2718 5.810095 AGGCAAAGAAATAGCTAAGACACT 58.190 37.500 0.00 0.00 0.00 3.55
2843 2857 0.033011 AGGCTAGCGAAGAGGAGGAA 60.033 55.000 9.00 0.00 0.00 3.36
3030 3069 5.236911 ACTTGTTGCCGTTCGAATTAAGTTA 59.763 36.000 0.00 0.00 0.00 2.24
3066 3105 6.917477 GTGAAGTTGCTATGAATGTTTGACAA 59.083 34.615 0.00 0.00 0.00 3.18
3268 3404 0.821711 CCAAACGCCAGGTTCCTTGA 60.822 55.000 0.00 0.00 38.08 3.02
3394 4579 2.224159 ATGGACCTTGGCGTCTGGT 61.224 57.895 5.03 5.03 36.70 4.00
3504 4689 2.338620 CGTCAGCAGGTCAACGGA 59.661 61.111 0.00 0.00 0.00 4.69
3571 4803 3.423154 GCTTCGCAACCCAGACGG 61.423 66.667 0.00 0.00 37.81 4.79
3626 4858 9.974528 CAGAATCGAAATTTCTTTTAAAACGAC 57.025 29.630 15.92 0.72 31.11 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 9.049523 TCTTCTTCTTCATATGCACACATAATC 57.950 33.333 0.00 0.00 41.99 1.75
230 234 8.593945 ATTTTCTTCTCCAAGTTATGCCATAA 57.406 30.769 0.00 0.00 0.00 1.90
301 306 3.576078 TCATCCGCCATCCTACAAAAT 57.424 42.857 0.00 0.00 0.00 1.82
747 756 4.678269 CGACGCTGACACGACCGT 62.678 66.667 0.00 0.00 36.70 4.83
850 860 7.399191 TCCTCTGACTAGTTTTAGCCAAGAATA 59.601 37.037 0.00 0.00 0.00 1.75
1199 1209 3.016736 CACGGATAGGCTCCAAACAAAT 58.983 45.455 0.00 0.00 45.24 2.32
1283 1293 1.597027 CCCGTCATGATTACCCCGC 60.597 63.158 0.00 0.00 0.00 6.13
1411 1421 0.683973 CTCAGCAGTCAAGGTGTCCT 59.316 55.000 0.00 0.00 38.15 3.85
1641 1652 2.382882 TCCAAATTGTCTTGCCACACA 58.617 42.857 0.00 0.00 0.00 3.72
1772 1785 0.244450 ATGCACGGGACAAAGCATTG 59.756 50.000 0.00 0.00 44.63 2.82
1821 1834 3.644966 TTGCCCAATCCGATATATCCC 57.355 47.619 7.15 0.00 0.00 3.85
1882 1895 8.144478 GGTCTATTCTCTGATTGCACTAATGTA 58.856 37.037 0.00 0.00 0.00 2.29
1885 1898 7.070447 TGAGGTCTATTCTCTGATTGCACTAAT 59.930 37.037 0.00 0.00 32.78 1.73
2015 2028 1.371558 GTGCAGTCTCCGGGTCTTT 59.628 57.895 0.00 0.00 0.00 2.52
2128 2141 8.400186 CAACATGATGCAAGTATGTTAGAATCA 58.600 33.333 19.56 3.82 41.60 2.57
2225 2238 1.965643 ACTCAGTGCAACATTGGCATT 59.034 42.857 0.00 0.00 44.11 3.56
2325 2338 5.700846 TGCAAATAACTAATCCGCGAAAAA 58.299 33.333 8.23 0.00 0.00 1.94
2544 2557 1.421268 TGTTGGCTCCTCTTGATGTGT 59.579 47.619 0.00 0.00 0.00 3.72
2689 2703 2.576191 TGGCCCAGTGTCTTAGCTATTT 59.424 45.455 0.00 0.00 0.00 1.40
2704 2718 2.344592 TCTTTCTACCTTTCTGGCCCA 58.655 47.619 0.00 0.00 40.22 5.36
2843 2857 0.749649 CCTCTTCGCTAGCCTCATGT 59.250 55.000 9.66 0.00 0.00 3.21
3030 3069 1.508632 CAACTTCACGAATCCGGTGT 58.491 50.000 0.00 0.00 40.78 4.16
3118 3157 7.854557 TGAATTCATAGACATCACAGGAAAG 57.145 36.000 3.38 0.00 0.00 2.62
3156 3248 4.543590 TGAGTCCTCCTTTTGACAGATC 57.456 45.455 0.00 0.00 33.89 2.75
3196 3290 0.106519 GGCGTCTGGTACCTACCCTA 60.107 60.000 14.36 0.00 45.87 3.53
3268 3404 0.733729 GTCAGTCGATAGCCAGACGT 59.266 55.000 0.00 0.00 41.86 4.34
3571 4803 2.359850 TGACGCCAACATCCCTGC 60.360 61.111 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.