Multiple sequence alignment - TraesCS2B01G319700

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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 TraesCS2B01G319700 chr2B 100.000 4316 0 0 1 4316 456016181 456020496 0.000000e+00 7971
1 TraesCS2B01G319700 chr2D 95.036 4069 144 26 274 4315 385159016 385163053 0.000000e+00 6342
2 TraesCS2B01G319700 chr2D 92.920 113 6 2 1 111 385157093 385157205 3.450000e-36 163
3 TraesCS2B01G319700 chr2A 95.907 3787 122 12 230 3998 520297732 520301503 0.000000e+00 6104
4 TraesCS2B01G319700 chr2A 91.566 249 18 2 4069 4314 520301512 520301760 1.490000e-89 340
5 TraesCS2B01G319700 chr2A 95.055 182 8 1 1 181 520297542 520297723 7.060000e-73 285
6 TraesCS2B01G319700 chr1D 73.535 495 94 25 1393 1879 366874271 366874736 2.080000e-33 154


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 TraesCS2B01G319700 chr2B 456016181 456020496 4315 False 7971.0 7971 100.000 1 4316 1 chr2B.!!$F1 4315
1 TraesCS2B01G319700 chr2D 385157093 385163053 5960 False 3252.5 6342 93.978 1 4315 2 chr2D.!!$F1 4314
2 TraesCS2B01G319700 chr2A 520297542 520301760 4218 False 2243.0 6104 94.176 1 4314 3 chr2A.!!$F1 4313

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
502 2172 1.060713 CGAACGAAATGACGAGTGCT 58.939 50.0 0.00 0.0 37.03 4.40 F
1013 2685 1.009829 GACACGATGAACCATCAGGC 58.990 55.0 7.59 0.0 40.54 4.85 F
2772 4444 0.736053 ACAACGCCAACAACGTCATT 59.264 45.0 0.00 0.0 44.30 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 3916 1.685077 CTGCTCCCTGAGGCTCTCA 60.685 63.158 16.72 5.03 38.25 3.27 R
2922 4594 1.300697 GGTAACGGCCGCTATCTGG 60.301 63.158 28.58 0.00 0.00 3.86 R
3909 5593 2.159627 GCTACATGTGGTTTCGAAGGTG 59.840 50.000 9.11 0.00 0.00 4.00 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
72 73 3.625745 GTTCAGTCAACCCCGATGT 57.374 52.632 0.00 0.00 0.00 3.06
111 114 2.078392 TCGGAAAGCGGTAAAATCCAC 58.922 47.619 8.68 0.00 0.00 4.02
112 115 1.807742 CGGAAAGCGGTAAAATCCACA 59.192 47.619 8.68 0.00 0.00 4.17
135 138 9.444534 CACATGCTATATCTCAGTACGATAATC 57.555 37.037 0.00 0.00 0.00 1.75
181 184 7.964604 AAGCTACGAAACTTCTCACTTAAAT 57.035 32.000 0.00 0.00 0.00 1.40
182 185 9.485206 AAAGCTACGAAACTTCTCACTTAAATA 57.515 29.630 0.00 0.00 0.00 1.40
183 186 9.485206 AAGCTACGAAACTTCTCACTTAAATAA 57.515 29.630 0.00 0.00 0.00 1.40
184 187 9.485206 AGCTACGAAACTTCTCACTTAAATAAA 57.515 29.630 0.00 0.00 0.00 1.40
185 188 9.526286 GCTACGAAACTTCTCACTTAAATAAAC 57.474 33.333 0.00 0.00 0.00 2.01
187 190 8.672823 ACGAAACTTCTCACTTAAATAAACCT 57.327 30.769 0.00 0.00 0.00 3.50
189 192 8.228464 CGAAACTTCTCACTTAAATAAACCTCC 58.772 37.037 0.00 0.00 0.00 4.30
190 193 7.997773 AACTTCTCACTTAAATAAACCTCCC 57.002 36.000 0.00 0.00 0.00 4.30
191 194 7.331089 ACTTCTCACTTAAATAAACCTCCCT 57.669 36.000 0.00 0.00 0.00 4.20
192 195 8.445361 ACTTCTCACTTAAATAAACCTCCCTA 57.555 34.615 0.00 0.00 0.00 3.53
193 196 8.887393 ACTTCTCACTTAAATAAACCTCCCTAA 58.113 33.333 0.00 0.00 0.00 2.69
194 197 9.907229 CTTCTCACTTAAATAAACCTCCCTAAT 57.093 33.333 0.00 0.00 0.00 1.73
207 210 7.859026 AACCTCCCTAATAATTCTCTACCTC 57.141 40.000 0.00 0.00 0.00 3.85
209 212 6.106494 ACCTCCCTAATAATTCTCTACCTCCT 59.894 42.308 0.00 0.00 0.00 3.69
211 214 7.175635 TCCCTAATAATTCTCTACCTCCTGA 57.824 40.000 0.00 0.00 0.00 3.86
212 215 7.601942 TCCCTAATAATTCTCTACCTCCTGAA 58.398 38.462 0.00 0.00 0.00 3.02
213 216 8.242325 TCCCTAATAATTCTCTACCTCCTGAAT 58.758 37.037 0.00 0.00 0.00 2.57
220 223 4.689062 TCTCTACCTCCTGAATTTCTGGT 58.311 43.478 18.52 12.93 36.89 4.00
221 224 4.467795 TCTCTACCTCCTGAATTTCTGGTG 59.532 45.833 18.52 16.27 36.89 4.17
223 226 1.355720 ACCTCCTGAATTTCTGGTGGG 59.644 52.381 30.73 26.27 46.77 4.61
224 227 1.355720 CCTCCTGAATTTCTGGTGGGT 59.644 52.381 24.83 0.00 42.12 4.51
328 1989 6.147328 ACGTACATTTTTCTAGCAAACCTCTC 59.853 38.462 0.00 0.00 0.00 3.20
334 1995 7.881775 TTTTTCTAGCAAACCTCTCTTTTCT 57.118 32.000 0.00 0.00 0.00 2.52
352 2013 8.623310 TCTTTTCTTTAATGGAAAACGTGTTC 57.377 30.769 10.16 10.16 37.63 3.18
476 2146 3.461773 CCCTCTCGGTGCCACGAT 61.462 66.667 0.14 0.00 42.62 3.73
502 2172 1.060713 CGAACGAAATGACGAGTGCT 58.939 50.000 0.00 0.00 37.03 4.40
588 2258 2.434185 CTGTAAAGGCAGCGCGGA 60.434 61.111 13.03 0.00 0.00 5.54
589 2259 2.434185 TGTAAAGGCAGCGCGGAG 60.434 61.111 13.03 1.90 0.00 4.63
590 2260 3.195698 GTAAAGGCAGCGCGGAGG 61.196 66.667 13.03 0.00 0.00 4.30
792 2464 5.426509 TGCTTTCCTCCAGAGAATGATCTTA 59.573 40.000 0.00 0.00 35.54 2.10
818 2490 8.140112 AGAAGATTCTTGGCTAGTTTTCTAGA 57.860 34.615 3.03 0.00 42.36 2.43
938 2610 2.930023 GCATCCACTCACACTCACTCTG 60.930 54.545 0.00 0.00 0.00 3.35
939 2611 2.364972 TCCACTCACACTCACTCTGA 57.635 50.000 0.00 0.00 0.00 3.27
942 2614 3.149981 CCACTCACACTCACTCTGACTA 58.850 50.000 0.00 0.00 0.00 2.59
992 2664 1.074405 TCTGGCCTGAGCTGAAACATT 59.926 47.619 8.48 0.00 39.73 2.71
1013 2685 1.009829 GACACGATGAACCATCAGGC 58.990 55.000 7.59 0.00 40.54 4.85
1677 3349 1.908793 CTCCCACACCTCGTCCACT 60.909 63.158 0.00 0.00 0.00 4.00
2001 3673 2.771943 AGACGGGTACACCATCATGAAT 59.228 45.455 0.00 0.00 40.22 2.57
2239 3911 2.433868 GAAGTACGTCTTCTGCACCA 57.566 50.000 15.92 0.00 46.36 4.17
2244 3916 2.426023 GTCTTCTGCACCACCGGT 59.574 61.111 0.00 0.00 35.62 5.28
2592 4264 2.767960 GCCCAACAAGGAAATCATGGAT 59.232 45.455 0.00 0.00 41.22 3.41
2736 4408 2.107750 CGCTCGGCCATGATGACT 59.892 61.111 2.24 0.00 0.00 3.41
2772 4444 0.736053 ACAACGCCAACAACGTCATT 59.264 45.000 0.00 0.00 44.30 2.57
3024 4696 1.000955 GTGATCCTCAACCACACGACT 59.999 52.381 0.00 0.00 0.00 4.18
3166 4838 2.643232 GGAGGCAAAGGCAGCAAGG 61.643 63.158 0.00 0.00 43.71 3.61
3422 5094 8.934507 AGAAGTAATACATAGACTGAAAGCAC 57.065 34.615 0.00 0.00 37.60 4.40
3431 5103 2.562298 AGACTGAAAGCACAGGAGAGAG 59.438 50.000 9.61 0.00 41.59 3.20
3667 5344 4.141711 TGGCTGGTATGTTCTCTATCAACC 60.142 45.833 0.00 0.00 0.00 3.77
3699 5376 5.474532 TCGGTACCAGTATACACCATACATC 59.525 44.000 13.54 0.00 41.84 3.06
3700 5377 5.336213 CGGTACCAGTATACACCATACATCC 60.336 48.000 13.54 0.00 41.84 3.51
3701 5378 5.541101 GGTACCAGTATACACCATACATCCA 59.459 44.000 7.15 0.00 41.84 3.41
3702 5379 6.042322 GGTACCAGTATACACCATACATCCAA 59.958 42.308 7.15 0.00 41.84 3.53
3712 5393 7.404671 ACACCATACATCCAAAGGTTATTTC 57.595 36.000 0.00 0.00 0.00 2.17
3772 5453 9.669353 CTTTTCCAGATGTTATTGATATTTCCG 57.331 33.333 0.00 0.00 0.00 4.30
3779 5460 6.918892 TGTTATTGATATTTCCGTGACAGG 57.081 37.500 0.00 0.00 0.00 4.00
3820 5501 4.980339 AAGGGCAAAGTGGATGATTTTT 57.020 36.364 0.00 0.00 0.00 1.94
3821 5502 6.432403 AAAGGGCAAAGTGGATGATTTTTA 57.568 33.333 0.00 0.00 0.00 1.52
3909 5593 1.996191 CGTCTAAAGCTTCACTCCAGC 59.004 52.381 0.00 0.00 37.56 4.85
3915 5599 0.036022 AGCTTCACTCCAGCACCTTC 59.964 55.000 0.00 0.00 39.99 3.46
3924 5616 0.817634 CCAGCACCTTCGAAACCACA 60.818 55.000 0.00 0.00 0.00 4.17
3963 5655 7.206687 TGAATTTTAAGTAAAGCCCACACAAG 58.793 34.615 0.00 0.00 0.00 3.16
3980 5672 4.141711 ACACAAGTTCAGAGCTCCAAACTA 60.142 41.667 24.05 0.00 31.94 2.24
3986 5678 7.010339 AGTTCAGAGCTCCAAACTAAATACT 57.990 36.000 23.04 4.56 30.47 2.12
3990 5682 6.874134 TCAGAGCTCCAAACTAAATACTGTTC 59.126 38.462 10.93 0.00 0.00 3.18
4121 5813 5.185056 TCAGACGATCACCAGAACTTTGATA 59.815 40.000 0.00 0.00 29.93 2.15
4226 5923 6.747414 ATTATTGTGCTATACCTCCTCACA 57.253 37.500 0.00 0.00 36.07 3.58
4228 5925 4.901197 TTGTGCTATACCTCCTCACAAA 57.099 40.909 3.94 0.00 42.45 2.83
4229 5926 4.471904 TGTGCTATACCTCCTCACAAAG 57.528 45.455 0.00 0.00 35.08 2.77
4230 5927 3.198872 GTGCTATACCTCCTCACAAAGC 58.801 50.000 0.00 0.00 0.00 3.51
4268 5967 2.858745 ACTCAAAGGCACGGTAAATGT 58.141 42.857 0.00 0.00 0.00 2.71
4309 6009 0.833834 ACCACTGTAGGAGCAGCTGT 60.834 55.000 16.64 1.59 39.96 4.40
4315 6015 3.325135 ACTGTAGGAGCAGCTGTAACTTT 59.675 43.478 16.64 0.00 39.96 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 114 8.845227 AGGATTATCGTACTGAGATATAGCATG 58.155 37.037 0.00 0.00 31.49 4.06
112 115 8.988546 AGGATTATCGTACTGAGATATAGCAT 57.011 34.615 0.00 0.00 31.49 3.79
135 138 0.663688 CGTGGAGTCGTGGATCTAGG 59.336 60.000 0.00 0.00 0.00 3.02
181 184 9.377238 GAGGTAGAGAATTATTAGGGAGGTTTA 57.623 37.037 0.00 0.00 0.00 2.01
182 185 7.292827 GGAGGTAGAGAATTATTAGGGAGGTTT 59.707 40.741 0.00 0.00 0.00 3.27
183 186 6.788456 GGAGGTAGAGAATTATTAGGGAGGTT 59.212 42.308 0.00 0.00 0.00 3.50
184 187 6.106494 AGGAGGTAGAGAATTATTAGGGAGGT 59.894 42.308 0.00 0.00 0.00 3.85
185 188 6.439058 CAGGAGGTAGAGAATTATTAGGGAGG 59.561 46.154 0.00 0.00 0.00 4.30
187 190 7.175635 TCAGGAGGTAGAGAATTATTAGGGA 57.824 40.000 0.00 0.00 0.00 4.20
192 195 9.844257 CAGAAATTCAGGAGGTAGAGAATTATT 57.156 33.333 0.00 0.00 39.14 1.40
193 196 8.435982 CCAGAAATTCAGGAGGTAGAGAATTAT 58.564 37.037 0.00 0.00 39.14 1.28
194 197 7.403231 ACCAGAAATTCAGGAGGTAGAGAATTA 59.597 37.037 11.51 0.00 39.14 1.40
195 198 6.216456 ACCAGAAATTCAGGAGGTAGAGAATT 59.784 38.462 11.51 0.00 41.11 2.17
196 199 5.728741 ACCAGAAATTCAGGAGGTAGAGAAT 59.271 40.000 11.51 0.00 32.45 2.40
200 203 3.519510 CCACCAGAAATTCAGGAGGTAGA 59.480 47.826 11.51 0.00 31.01 2.59
202 205 2.576191 CCCACCAGAAATTCAGGAGGTA 59.424 50.000 16.86 0.00 33.13 3.08
203 206 1.355720 CCCACCAGAAATTCAGGAGGT 59.644 52.381 16.86 6.82 33.13 3.85
204 207 1.355720 ACCCACCAGAAATTCAGGAGG 59.644 52.381 11.51 12.14 34.42 4.30
207 210 2.440409 CTCACCCACCAGAAATTCAGG 58.560 52.381 2.68 2.68 0.00 3.86
209 212 1.547675 GCCTCACCCACCAGAAATTCA 60.548 52.381 0.00 0.00 0.00 2.57
211 214 0.251787 GGCCTCACCCACCAGAAATT 60.252 55.000 0.00 0.00 0.00 1.82
212 215 1.384191 GGCCTCACCCACCAGAAAT 59.616 57.895 0.00 0.00 0.00 2.17
213 216 2.843545 GGCCTCACCCACCAGAAA 59.156 61.111 0.00 0.00 0.00 2.52
328 1989 7.305763 CGGAACACGTTTTCCATTAAAGAAAAG 60.306 37.037 28.05 7.94 44.87 2.27
334 1995 3.550436 GCCGGAACACGTTTTCCATTAAA 60.550 43.478 28.05 0.00 44.87 1.52
352 2013 0.460987 GTCTTGTGAGATCCTGCCGG 60.461 60.000 0.00 0.00 33.70 6.13
356 2017 3.683822 GCTCTTTGTCTTGTGAGATCCTG 59.316 47.826 0.00 0.00 33.70 3.86
476 2146 1.527736 CGTCATTTCGTTCGGGTCAAA 59.472 47.619 0.00 0.00 0.00 2.69
586 2256 3.303928 CGATACCCTCCGGCCTCC 61.304 72.222 0.00 0.00 0.00 4.30
587 2257 2.521224 ACGATACCCTCCGGCCTC 60.521 66.667 0.00 0.00 0.00 4.70
588 2258 2.838225 CACGATACCCTCCGGCCT 60.838 66.667 0.00 0.00 0.00 5.19
589 2259 3.925090 CCACGATACCCTCCGGCC 61.925 72.222 0.00 0.00 0.00 6.13
590 2260 3.925090 CCCACGATACCCTCCGGC 61.925 72.222 0.00 0.00 0.00 6.13
591 2261 2.123597 TCCCACGATACCCTCCGG 60.124 66.667 0.00 0.00 0.00 5.14
592 2262 2.201022 CCTCCCACGATACCCTCCG 61.201 68.421 0.00 0.00 0.00 4.63
766 2438 2.238144 TCATTCTCTGGAGGAAAGCAGG 59.762 50.000 0.00 0.00 0.00 4.85
818 2490 1.005289 ATGGAGGCCATGAGTCCCT 59.995 57.895 5.01 0.00 43.39 4.20
897 2569 2.167398 TACAAGTGGAGGGCACTCGC 62.167 60.000 10.51 5.41 44.93 5.03
916 2588 1.274728 GAGTGAGTGTGAGTGGATGCT 59.725 52.381 0.00 0.00 0.00 3.79
992 2664 2.698803 CCTGATGGTTCATCGTGTCAA 58.301 47.619 3.83 0.00 43.14 3.18
1171 2843 2.363018 CTCCTCGTCCCTGCCAGA 60.363 66.667 0.00 0.00 0.00 3.86
1500 3172 4.077184 CACGCGCCCTTCCACCTA 62.077 66.667 5.73 0.00 0.00 3.08
2094 3766 1.909700 ACACAGATTTGCCGTGGATT 58.090 45.000 0.00 0.00 34.91 3.01
2239 3911 2.681778 CCTGAGGCTCTCACCGGT 60.682 66.667 16.72 0.00 35.39 5.28
2244 3916 1.685077 CTGCTCCCTGAGGCTCTCA 60.685 63.158 16.72 5.03 38.25 3.27
2772 4444 1.672363 GATCGATTTGGCATGCTGACA 59.328 47.619 18.92 4.09 30.30 3.58
2913 4585 2.737180 GCTATCTGGCGGCTGCTA 59.263 61.111 18.85 11.13 42.25 3.49
2922 4594 1.300697 GGTAACGGCCGCTATCTGG 60.301 63.158 28.58 0.00 0.00 3.86
3111 4783 0.949105 GCGTCACCGTCACCTTCATT 60.949 55.000 0.00 0.00 36.15 2.57
3166 4838 0.106149 ACGGTGACACTGAACCCTTC 59.894 55.000 21.31 0.00 32.44 3.46
3194 4866 0.178921 TCCTGCTCTCTTCACCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
3422 5094 1.274728 CCTGGTGTGTTCTCTCTCCTG 59.725 57.143 0.00 0.00 0.00 3.86
3431 5103 2.699954 CATCAGTACCCTGGTGTGTTC 58.300 52.381 0.00 0.00 43.57 3.18
3667 5344 4.337274 TGTATACTGGTACCGATCACTGTG 59.663 45.833 7.57 0.17 0.00 3.66
3712 5393 9.414295 TCACTTTTCATCATTTTTCTTATGCAG 57.586 29.630 0.00 0.00 0.00 4.41
3772 5453 8.997621 TCTGAAGTATTATTTGTACCTGTCAC 57.002 34.615 0.00 0.00 0.00 3.67
3779 5460 8.736244 TGCCCTTTTCTGAAGTATTATTTGTAC 58.264 33.333 0.00 0.00 0.00 2.90
3909 5593 2.159627 GCTACATGTGGTTTCGAAGGTG 59.840 50.000 9.11 0.00 0.00 4.00
3915 5599 4.870426 AGTCTAATGCTACATGTGGTTTCG 59.130 41.667 9.11 0.92 0.00 3.46
3963 5655 6.651225 ACAGTATTTAGTTTGGAGCTCTGAAC 59.349 38.462 14.64 17.24 0.00 3.18
3980 5672 7.103641 TGAGCCTATTTTCTCGAACAGTATTT 58.896 34.615 0.00 0.00 32.20 1.40
3986 5678 6.222038 ACTATGAGCCTATTTTCTCGAACA 57.778 37.500 0.00 0.00 32.20 3.18
3990 5682 6.535150 TGTGAAACTATGAGCCTATTTTCTCG 59.465 38.462 0.00 0.00 38.04 4.04
4229 5926 6.137794 TGAGTTTGAGCTATGTAGAGTAGC 57.862 41.667 0.00 0.00 43.77 3.58
4230 5927 7.704472 CCTTTGAGTTTGAGCTATGTAGAGTAG 59.296 40.741 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.