Multiple sequence alignment - TraesCS2D01G060900

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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 TraesCS2D01G060900 chr2D 100.000 2882 0 0 1 2882 25177288 25174407 0.000000e+00 5323.0
1 TraesCS2D01G060900 chr2A 95.826 2252 85 5 636 2881 27606961 27604713 0.000000e+00 3629.0
2 TraesCS2D01G060900 chr2A 96.040 404 12 1 246 649 27607695 27607296 0.000000e+00 654.0
3 TraesCS2D01G060900 chr2A 94.694 245 11 2 3 247 27616226 27615984 2.100000e-101 379.0
4 TraesCS2D01G060900 chr2B 92.517 1724 91 14 1168 2878 40908944 40907246 0.000000e+00 2435.0
5 TraesCS2D01G060900 chr2B 84.634 1217 163 14 964 2164 40855771 40856979 0.000000e+00 1190.0
6 TraesCS2D01G060900 chr2B 91.374 313 26 1 878 1189 40909336 40909024 7.380000e-116 427.0
7 TraesCS2D01G060900 chr2B 91.949 236 9 2 498 733 40910130 40909905 3.580000e-84 322.0
8 TraesCS2D01G060900 chr2B 95.588 136 5 1 3 138 40913039 40912905 1.740000e-52 217.0
9 TraesCS2D01G060900 chr2B 93.137 102 3 1 303 400 40912583 40912482 2.310000e-31 147.0
10 TraesCS2D01G060900 chr2B 90.000 110 6 2 394 502 40912458 40912353 1.390000e-28 137.0
11 TraesCS2D01G060900 chr2B 91.667 84 6 1 759 841 40909563 40909480 6.530000e-22 115.0
12 TraesCS2D01G060900 chr1D 76.344 465 98 11 1654 2114 283551797 283552253 3.710000e-59 239.0
13 TraesCS2D01G060900 chr1A 75.901 444 91 13 1667 2104 355322019 355322452 2.250000e-51 213.0
14 TraesCS2D01G060900 chr1B 75.161 467 101 12 1653 2114 385159859 385160315 3.760000e-49 206.0
15 TraesCS2D01G060900 chr1B 77.844 167 36 1 1667 1832 2086697 2086531 5.080000e-18 102.0
16 TraesCS2D01G060900 chr1B 77.246 167 37 1 1667 1832 2064070 2063904 2.360000e-16 97.1
17 TraesCS2D01G060900 chr1B 77.246 167 37 1 1667 1832 2109456 2109290 2.360000e-16 97.1


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 TraesCS2D01G060900 chr2D 25174407 25177288 2881 True 5323.000000 5323 100.000000 1 2882 1 chr2D.!!$R1 2881
1 TraesCS2D01G060900 chr2A 27604713 27607695 2982 True 2141.500000 3629 95.933000 246 2881 2 chr2A.!!$R2 2635
2 TraesCS2D01G060900 chr2B 40855771 40856979 1208 False 1190.000000 1190 84.634000 964 2164 1 chr2B.!!$F1 1200
3 TraesCS2D01G060900 chr2B 40907246 40913039 5793 True 542.857143 2435 92.318857 3 2878 7 chr2B.!!$R1 2875

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
229 264 0.388649 AAACTAGTCTCGCGCCACTG 60.389 55.0 17.19 10.82 0.00 3.66 F
1460 4782 1.246056 GCTCTGAGCATGTGCCCAAA 61.246 55.0 24.02 0.00 41.89 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 4963 0.907486 CATCTGAAGAGGAGGTGGCA 59.093 55.000 0.0 0.0 0.0 4.92 R
2773 6120 3.156288 AGAAAACCTGGAACCTTAGCC 57.844 47.619 0.0 0.0 0.0 3.93 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
40 41 5.862924 ATTTGTGGAGTGTTGTAGAATCG 57.137 39.130 0.00 0.00 0.00 3.34
74 75 6.375455 AGCCGAGAGATCATGTTATTGTTTTT 59.625 34.615 0.00 0.00 0.00 1.94
75 76 6.688813 GCCGAGAGATCATGTTATTGTTTTTC 59.311 38.462 0.00 0.00 0.00 2.29
76 77 7.414540 GCCGAGAGATCATGTTATTGTTTTTCT 60.415 37.037 0.00 0.00 0.00 2.52
77 78 8.119226 CCGAGAGATCATGTTATTGTTTTTCTC 58.881 37.037 0.00 0.00 0.00 2.87
78 79 8.119226 CGAGAGATCATGTTATTGTTTTTCTCC 58.881 37.037 0.00 0.00 0.00 3.71
121 122 4.424061 TTTGCCATGAGATCTTGAAACG 57.576 40.909 0.00 0.00 0.00 3.60
122 123 3.057969 TGCCATGAGATCTTGAAACGT 57.942 42.857 0.00 0.00 0.00 3.99
138 139 1.226974 CGTGCGGGGTGTCATCTAG 60.227 63.158 0.00 0.00 0.00 2.43
148 183 7.783119 TGCGGGGTGTCATCTAGTTATATATAT 59.217 37.037 0.00 0.00 0.00 0.86
181 216 1.076777 GCCCCAGCATACCATGTGT 60.077 57.895 0.00 0.00 39.53 3.72
183 218 1.851304 CCCCAGCATACCATGTGTTT 58.149 50.000 0.00 0.00 0.00 2.83
185 220 2.094078 CCCCAGCATACCATGTGTTTTG 60.094 50.000 0.00 0.00 0.00 2.44
192 227 2.888834 ACCATGTGTTTTGGTTGCTC 57.111 45.000 0.00 0.00 45.19 4.26
200 235 6.841443 TGTGTTTTGGTTGCTCAATTATTG 57.159 33.333 0.00 0.00 0.00 1.90
213 248 7.319646 TGCTCAATTATTGTGGGTCATTAAAC 58.680 34.615 4.77 0.00 0.00 2.01
214 249 7.178274 TGCTCAATTATTGTGGGTCATTAAACT 59.822 33.333 4.77 0.00 0.00 2.66
215 250 8.682710 GCTCAATTATTGTGGGTCATTAAACTA 58.317 33.333 4.77 0.00 0.00 2.24
217 252 9.747898 TCAATTATTGTGGGTCATTAAACTAGT 57.252 29.630 4.77 0.00 0.00 2.57
219 254 9.975218 AATTATTGTGGGTCATTAAACTAGTCT 57.025 29.630 0.00 0.00 0.00 3.24
220 255 9.614792 ATTATTGTGGGTCATTAAACTAGTCTC 57.385 33.333 0.00 0.00 0.00 3.36
221 256 5.068234 TGTGGGTCATTAAACTAGTCTCG 57.932 43.478 0.00 0.00 0.00 4.04
222 257 3.864003 GTGGGTCATTAAACTAGTCTCGC 59.136 47.826 0.00 0.00 0.00 5.03
223 258 3.114065 GGGTCATTAAACTAGTCTCGCG 58.886 50.000 0.00 0.00 0.00 5.87
224 259 2.534757 GGTCATTAAACTAGTCTCGCGC 59.465 50.000 0.00 0.00 0.00 6.86
225 260 2.534757 GTCATTAAACTAGTCTCGCGCC 59.465 50.000 0.00 0.00 0.00 6.53
226 261 2.164827 TCATTAAACTAGTCTCGCGCCA 59.835 45.455 0.00 0.00 0.00 5.69
227 262 1.986698 TTAAACTAGTCTCGCGCCAC 58.013 50.000 0.00 0.00 0.00 5.01
228 263 1.171308 TAAACTAGTCTCGCGCCACT 58.829 50.000 13.39 13.39 0.00 4.00
229 264 0.388649 AAACTAGTCTCGCGCCACTG 60.389 55.000 17.19 10.82 0.00 3.66
230 265 2.103143 CTAGTCTCGCGCCACTGG 59.897 66.667 17.19 11.86 0.00 4.00
464 675 7.124298 GGTATGCTCCTCCAGTATGATGTATTA 59.876 40.741 0.00 0.00 39.69 0.98
465 676 6.346477 TGCTCCTCCAGTATGATGTATTAC 57.654 41.667 0.00 0.00 39.69 1.89
466 677 6.077993 TGCTCCTCCAGTATGATGTATTACT 58.922 40.000 0.00 0.00 39.69 2.24
467 678 6.209589 TGCTCCTCCAGTATGATGTATTACTC 59.790 42.308 0.00 0.00 39.69 2.59
604 3042 9.998106 GTAGCTATTCCTTAATCAGTTTCCATA 57.002 33.333 0.00 0.00 0.00 2.74
621 3059 2.421775 CCATAGCTACATCGATCTCGCT 59.578 50.000 14.08 14.08 39.60 4.93
633 3071 4.869440 CTCGCTGGCCGCTCTCTG 62.869 72.222 15.78 2.47 36.73 3.35
755 3541 3.341043 CATTCATCTCGGCGCCGG 61.341 66.667 44.95 34.43 40.25 6.13
771 3874 3.799232 GCGCCGGAGATTTGTAAGTCTAT 60.799 47.826 10.31 0.00 0.00 1.98
941 4152 2.670905 TCAACAGTCGGCGTCAATAATG 59.329 45.455 6.85 0.00 0.00 1.90
1081 4292 2.281761 AGCCCGTGAAACTGCCAG 60.282 61.111 0.00 0.00 33.40 4.85
1107 4318 3.865745 CACTATTGGAGGACATCACGAAC 59.134 47.826 0.00 0.00 0.00 3.95
1149 4360 2.361104 GGCATCGGAGGGTTTGCA 60.361 61.111 3.28 0.00 36.82 4.08
1398 4720 3.655777 ACAAGGGGAAATGGAAGACTACA 59.344 43.478 0.00 0.00 0.00 2.74
1460 4782 1.246056 GCTCTGAGCATGTGCCCAAA 61.246 55.000 24.02 0.00 41.89 3.28
1923 5248 4.385358 TCTTCTCTTTGGTGGCAAAAAC 57.615 40.909 0.00 0.00 0.00 2.43
2006 5331 0.832135 TTGCTCCGGAACTCCTGAGT 60.832 55.000 15.94 0.00 45.60 3.41
2086 5411 5.575157 ACTGACAGGAGAGAAGAGTTATCA 58.425 41.667 7.51 0.00 0.00 2.15
2087 5412 6.013379 ACTGACAGGAGAGAAGAGTTATCAA 58.987 40.000 7.51 0.00 0.00 2.57
2120 5445 8.494016 AGAAGGTAACAACAAGTTATGCTATC 57.506 34.615 0.00 0.00 44.06 2.08
2189 5514 9.646427 CACTCTAGTTTAGCAAATATATCTCCC 57.354 37.037 0.00 0.00 0.00 4.30
2196 5521 9.178758 GTTTAGCAAATATATCTCCCCCATTAG 57.821 37.037 0.00 0.00 0.00 1.73
2247 5572 4.722526 TTTTGATCCGACCCATCCATAT 57.277 40.909 0.00 0.00 0.00 1.78
2342 5672 6.042093 TCTGTGTGGTTAGTGAGAGAAGAAAT 59.958 38.462 0.00 0.00 0.00 2.17
2480 5812 7.904094 TGCTTCAAATAACAACATTTTGACAC 58.096 30.769 0.00 0.00 38.65 3.67
2542 5886 9.802039 ATTTTGATTTCCTACTACTACCAAACA 57.198 29.630 0.00 0.00 0.00 2.83
2567 5911 6.769608 ATACAACTATACATGTGATGCACG 57.230 37.500 9.11 0.00 37.14 5.34
2573 5917 2.420628 ACATGTGATGCACGGTTTTG 57.579 45.000 0.00 0.00 37.14 2.44
2773 6120 9.892130 ATTAACCCTTTAGTGAAGTCATTAGAG 57.108 33.333 0.00 0.00 33.29 2.43
2820 6167 5.597430 TGCCCCCATCAGATTTGATATTA 57.403 39.130 0.00 0.00 42.12 0.98
2827 6174 6.881065 CCCATCAGATTTGATATTATGGACGT 59.119 38.462 0.00 0.00 42.12 4.34
2856 6203 6.656693 ACATTGGTTGGTTTTCACAAAAATCA 59.343 30.769 0.00 0.00 42.35 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.449588 CCACAAATTTCGGATCAGATCTTGG 60.450 44.000 10.36 1.00 0.00 3.61
40 41 5.047660 ACATGATCTCTCGGCTTATCCTAAC 60.048 44.000 0.00 0.00 0.00 2.34
121 122 0.249398 AACTAGATGACACCCCGCAC 59.751 55.000 0.00 0.00 0.00 5.34
122 123 1.855295 TAACTAGATGACACCCCGCA 58.145 50.000 0.00 0.00 0.00 5.69
138 139 6.643770 CGGCGGGTGTAATCCATATATATAAC 59.356 42.308 0.00 0.00 0.00 1.89
148 183 4.476752 GGCGGCGGGTGTAATCCA 62.477 66.667 9.78 0.00 0.00 3.41
160 195 4.586235 ATGGTATGCTGGGGCGGC 62.586 66.667 0.00 0.00 42.25 6.53
181 216 5.163258 ACCCACAATAATTGAGCAACCAAAA 60.163 36.000 0.00 0.00 0.00 2.44
183 218 3.900601 ACCCACAATAATTGAGCAACCAA 59.099 39.130 0.00 0.00 0.00 3.67
185 220 3.509575 TGACCCACAATAATTGAGCAACC 59.490 43.478 0.00 0.00 0.00 3.77
200 235 3.864003 GCGAGACTAGTTTAATGACCCAC 59.136 47.826 0.00 0.00 0.00 4.61
213 248 2.103143 CCAGTGGCGCGAGACTAG 59.897 66.667 12.10 0.00 42.42 2.57
214 249 4.129737 GCCAGTGGCGCGAGACTA 62.130 66.667 20.55 0.00 42.42 2.59
221 256 7.971859 AGTATAATACTCTTGCCAGTGGCGC 62.972 48.000 28.56 7.06 43.43 6.53
222 257 4.501571 AGTATAATACTCTTGCCAGTGGCG 60.502 45.833 28.56 16.77 43.43 5.69
223 258 4.962155 AGTATAATACTCTTGCCAGTGGC 58.038 43.478 28.01 28.01 41.66 5.01
224 259 6.015010 AGCTAGTATAATACTCTTGCCAGTGG 60.015 42.308 4.20 4.20 40.14 4.00
225 260 6.865726 CAGCTAGTATAATACTCTTGCCAGTG 59.134 42.308 0.00 0.00 40.14 3.66
226 261 6.517529 GCAGCTAGTATAATACTCTTGCCAGT 60.518 42.308 0.00 0.00 40.14 4.00
227 262 5.866633 GCAGCTAGTATAATACTCTTGCCAG 59.133 44.000 0.00 0.00 40.14 4.85
228 263 5.304357 TGCAGCTAGTATAATACTCTTGCCA 59.696 40.000 0.00 1.55 40.14 4.92
229 264 5.784177 TGCAGCTAGTATAATACTCTTGCC 58.216 41.667 0.00 0.00 40.14 4.52
230 265 6.926272 ACTTGCAGCTAGTATAATACTCTTGC 59.074 38.462 7.83 0.00 40.14 4.01
301 477 1.202746 CCTCCAGGCTCCAGCTAATTC 60.203 57.143 0.00 0.00 41.70 2.17
464 675 5.091552 TGGGACCAAATAGTAAGAGTGAGT 58.908 41.667 0.00 0.00 0.00 3.41
465 676 5.677319 TGGGACCAAATAGTAAGAGTGAG 57.323 43.478 0.00 0.00 0.00 3.51
466 677 5.724370 TCATGGGACCAAATAGTAAGAGTGA 59.276 40.000 0.00 0.00 0.00 3.41
467 678 5.989477 TCATGGGACCAAATAGTAAGAGTG 58.011 41.667 0.00 0.00 0.00 3.51
621 3059 2.036414 AGAGACAGAGAGCGGCCA 59.964 61.111 2.24 0.00 0.00 5.36
633 3071 3.241701 CGCAACAGAAAGAGAGAGAGAC 58.758 50.000 0.00 0.00 0.00 3.36
790 3893 6.985059 AGTTTCAGTCCAACTTCACTACTTAC 59.015 38.462 0.00 0.00 29.75 2.34
1081 4292 5.009710 TCGTGATGTCCTCCAATAGTGATAC 59.990 44.000 0.00 0.00 0.00 2.24
1107 4318 3.887621 TGGTTATCAGGAGAGAAACGG 57.112 47.619 0.00 0.00 35.45 4.44
1398 4720 3.152341 CTGACATGACAAGCTTTCCCTT 58.848 45.455 0.00 0.00 0.00 3.95
1460 4782 6.295349 CGGTAATATGCTTATCAAGACTCCCT 60.295 42.308 0.00 0.00 0.00 4.20
1635 4960 1.152030 TGAAGAGGAGGTGGCAGGT 60.152 57.895 0.00 0.00 0.00 4.00
1638 4963 0.907486 CATCTGAAGAGGAGGTGGCA 59.093 55.000 0.00 0.00 0.00 4.92
2035 5360 4.141846 CCATGATTATGACGCCTAGGCTAT 60.142 45.833 30.55 22.32 36.29 2.97
2086 5411 7.283329 ACTTGTTGTTACCTTCTCATCTTCTT 58.717 34.615 0.00 0.00 0.00 2.52
2087 5412 6.831976 ACTTGTTGTTACCTTCTCATCTTCT 58.168 36.000 0.00 0.00 0.00 2.85
2120 5445 3.955650 TTCCTTCGACTAACTTGGAGG 57.044 47.619 0.00 0.00 0.00 4.30
2183 5508 5.162637 TGTATTAGTGCTAATGGGGGAGAT 58.837 41.667 13.09 0.00 36.52 2.75
2189 5514 8.567948 CCTTGTATTTGTATTAGTGCTAATGGG 58.432 37.037 13.09 0.00 36.52 4.00
2196 5521 6.753107 ACCACCTTGTATTTGTATTAGTGC 57.247 37.500 0.00 0.00 0.00 4.40
2247 5572 4.021807 TCGTGAGTGGTTGCTGAAAGTATA 60.022 41.667 0.00 0.00 35.30 1.47
2389 5719 5.126061 GCACAATCCAAGAGAATGTACCAAT 59.874 40.000 0.00 0.00 36.43 3.16
2421 5753 8.635765 ATGTACATTTTCAAGGAAGTGTACAT 57.364 30.769 24.90 24.90 46.15 2.29
2542 5886 7.545615 CCGTGCATCACATGTATAGTTGTATAT 59.454 37.037 0.00 0.00 33.40 0.86
2567 5911 7.444487 GGGTGGAGTAGTCAATATATCAAAACC 59.556 40.741 0.00 0.00 0.00 3.27
2573 5917 9.003658 CATTTTGGGTGGAGTAGTCAATATATC 57.996 37.037 0.00 0.00 0.00 1.63
2737 6081 9.444600 TTCACTAAAGGGTTAATCACATACTTC 57.555 33.333 0.00 0.00 0.00 3.01
2773 6120 3.156288 AGAAAACCTGGAACCTTAGCC 57.844 47.619 0.00 0.00 0.00 3.93
2820 6167 3.892588 ACCAACCAATGTTAAACGTCCAT 59.107 39.130 0.00 0.00 32.09 3.41
2827 6174 7.979444 TTTGTGAAAACCAACCAATGTTAAA 57.021 28.000 0.00 0.00 32.09 1.52


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

AutoCloner maintained by Alex Coulton.