Multiple sequence alignment - TraesCS6B01G233000

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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 TraesCS6B01G233000 chr6B 100.000 2342 0 0 1 2342 388287137 388284796 0 4325
1 TraesCS6B01G233000 chr6B 95.455 1056 34 3 1300 2342 388038509 388037455 0 1672
2 TraesCS6B01G233000 chr5A 97.326 2356 49 3 1 2342 16544454 16546809 0 3989
3 TraesCS6B01G233000 chr5A 96.647 2356 53 5 1 2342 420185602 420187945 0 3890
4 TraesCS6B01G233000 chr7B 97.241 2356 51 3 1 2342 716784507 716786862 0 3978
5 TraesCS6B01G233000 chr7B 97.071 2356 55 3 1 2342 742948838 742946483 0 3956
6 TraesCS6B01G233000 chr7B 94.589 2310 117 7 38 2342 139608300 139610606 0 3567
7 TraesCS6B01G233000 chr7A 97.241 2356 51 3 1 2342 60084836 60087191 0 3978
8 TraesCS6B01G233000 chr7A 97.156 2356 53 3 1 2342 60168867 60166512 0 3967
9 TraesCS6B01G233000 chr7A 96.336 1201 31 2 1155 2342 708248560 708249760 0 1962
10 TraesCS6B01G233000 chr1D 95.844 2358 76 9 1 2342 275778828 275781179 0 3792
11 TraesCS6B01G233000 chr2D 94.230 2357 100 17 1 2342 291773519 291775854 0 3567
12 TraesCS6B01G233000 chrUn 96.314 1058 24 3 1300 2342 396261128 396262185 0 1724
13 TraesCS6B01G233000 chrUn 96.128 1059 25 4 1300 2342 209407075 209408133 0 1714
14 TraesCS6B01G233000 chr7D 96.314 1058 24 3 1300 2342 579000820 578999763 0 1724


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 TraesCS6B01G233000 chr6B 388284796 388287137 2341 True 4325 4325 100.000 1 2342 1 chr6B.!!$R2 2341
1 TraesCS6B01G233000 chr6B 388037455 388038509 1054 True 1672 1672 95.455 1300 2342 1 chr6B.!!$R1 1042
2 TraesCS6B01G233000 chr5A 16544454 16546809 2355 False 3989 3989 97.326 1 2342 1 chr5A.!!$F1 2341
3 TraesCS6B01G233000 chr5A 420185602 420187945 2343 False 3890 3890 96.647 1 2342 1 chr5A.!!$F2 2341
4 TraesCS6B01G233000 chr7B 716784507 716786862 2355 False 3978 3978 97.241 1 2342 1 chr7B.!!$F2 2341
5 TraesCS6B01G233000 chr7B 742946483 742948838 2355 True 3956 3956 97.071 1 2342 1 chr7B.!!$R1 2341
6 TraesCS6B01G233000 chr7B 139608300 139610606 2306 False 3567 3567 94.589 38 2342 1 chr7B.!!$F1 2304
7 TraesCS6B01G233000 chr7A 60084836 60087191 2355 False 3978 3978 97.241 1 2342 1 chr7A.!!$F1 2341
8 TraesCS6B01G233000 chr7A 60166512 60168867 2355 True 3967 3967 97.156 1 2342 1 chr7A.!!$R1 2341
9 TraesCS6B01G233000 chr7A 708248560 708249760 1200 False 1962 1962 96.336 1155 2342 1 chr7A.!!$F2 1187
10 TraesCS6B01G233000 chr1D 275778828 275781179 2351 False 3792 3792 95.844 1 2342 1 chr1D.!!$F1 2341
11 TraesCS6B01G233000 chr2D 291773519 291775854 2335 False 3567 3567 94.230 1 2342 1 chr2D.!!$F1 2341
12 TraesCS6B01G233000 chrUn 396261128 396262185 1057 False 1724 1724 96.314 1300 2342 1 chrUn.!!$F2 1042
13 TraesCS6B01G233000 chrUn 209407075 209408133 1058 False 1714 1714 96.128 1300 2342 1 chrUn.!!$F1 1042
14 TraesCS6B01G233000 chr7D 578999763 579000820 1057 True 1724 1724 96.314 1300 2342 1 chr7D.!!$R1 1042

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
78 80 0.542938 AGACAGGTGCAGGTAGCTCA 60.543 55.000 0.0 0.0 45.94 4.26 F
233 235 1.403647 CGTTGGCTTATCCGTCAGTCA 60.404 52.381 0.0 0.0 37.80 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1155 2.598565 TCCAATACCGATAGCAGCTCT 58.401 47.619 0.0 0.0 0.0 4.09 R
2115 2152 2.593026 CCAAAGTCAAGTAAAGCCCCA 58.407 47.619 0.0 0.0 0.0 4.96 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
78 80 0.542938 AGACAGGTGCAGGTAGCTCA 60.543 55.000 0.00 0.00 45.94 4.26
201 203 4.058817 AGCTCTTTTATCGCGGAATTAGG 58.941 43.478 6.13 0.00 0.00 2.69
205 207 2.623878 TTATCGCGGAATTAGGCCAA 57.376 45.000 6.13 0.00 0.00 4.52
233 235 1.403647 CGTTGGCTTATCCGTCAGTCA 60.404 52.381 0.00 0.00 37.80 3.41
570 572 6.918067 AAATCCTTCTTAGAAAAAGGTGGG 57.082 37.500 0.00 0.00 42.28 4.61
718 720 3.704061 TGAACCCCAATAGGCTATTTTGC 59.296 43.478 16.95 5.04 0.00 3.68
768 770 4.846779 ATTTTCGTGCCATGTGTAAACT 57.153 36.364 0.00 0.00 0.00 2.66
863 865 1.914764 GGTTGACGGACCCCCTACA 60.915 63.158 0.00 0.00 33.41 2.74
959 961 8.694540 ACAAGCCTTGCAAATTGTGATAATATA 58.305 29.630 18.38 0.00 34.71 0.86
1033 1035 4.018050 AGGCCCAAGTACTTCAAATCATCT 60.018 41.667 4.77 0.00 0.00 2.90
1152 1154 3.350833 AGCTGCTACAATTGCTTTAGCT 58.649 40.909 20.79 19.00 42.66 3.32
1153 1155 4.517285 AGCTGCTACAATTGCTTTAGCTA 58.483 39.130 20.79 10.87 42.66 3.32
1179 1181 3.864243 TGCTATCGGTATTGGAAACGTT 58.136 40.909 0.00 0.00 0.00 3.99
1207 1209 1.737236 CTTTGATTCATTCCGTGGCGA 59.263 47.619 0.00 0.00 0.00 5.54
1214 1216 1.207089 TCATTCCGTGGCGAGAAATCT 59.793 47.619 0.00 0.00 0.00 2.40
1222 1224 3.804325 CGTGGCGAGAAATCTATCATTGT 59.196 43.478 0.00 0.00 0.00 2.71
1490 1493 3.173668 CGGAATTTCAGTACCGGATCA 57.826 47.619 9.46 0.00 41.41 2.92
1547 1550 7.228906 GTGTATGTCTGTGTTAGATAGGCTCTA 59.771 40.741 0.00 0.00 37.83 2.43
1661 1666 1.593196 TTTTCTTCGGCTGTCACCAG 58.407 50.000 0.00 0.00 41.91 4.00
1734 1739 4.502604 CCGGGTTCAGAGAAGTTTGTAAGA 60.503 45.833 0.00 0.00 0.00 2.10
1856 1865 1.410648 GCATGGGATCCTGAACACCAT 60.411 52.381 12.58 1.42 42.36 3.55
1940 1949 4.475051 TTAGGCGTAGAAAAGGCATACA 57.525 40.909 0.00 0.00 40.84 2.29
2018 2027 1.447489 CCTCTGTCGGAGCAAGCTG 60.447 63.158 0.00 0.00 40.57 4.24
2024 2033 0.037790 GTCGGAGCAAGCTGAAGAGT 60.038 55.000 0.00 0.00 0.00 3.24
2066 2090 2.093973 CAGGTAAGGCACTCGATCAAGT 60.094 50.000 0.00 0.00 38.49 3.16
2115 2152 1.001633 CTTTGCTGCATTTCTTGGGCT 59.998 47.619 1.84 0.00 0.00 5.19
2130 2167 0.965866 GGGCTGGGGCTTTACTTGAC 60.966 60.000 0.00 0.00 38.73 3.18
2211 2260 4.019858 GCCCCTTCTTGCTCTTATTCTTT 58.980 43.478 0.00 0.00 0.00 2.52
2213 2262 5.047021 GCCCCTTCTTGCTCTTATTCTTTTT 60.047 40.000 0.00 0.00 0.00 1.94
2214 2263 6.625362 CCCCTTCTTGCTCTTATTCTTTTTC 58.375 40.000 0.00 0.00 0.00 2.29
2215 2264 6.435591 CCCCTTCTTGCTCTTATTCTTTTTCT 59.564 38.462 0.00 0.00 0.00 2.52
2216 2265 7.039434 CCCCTTCTTGCTCTTATTCTTTTTCTT 60.039 37.037 0.00 0.00 0.00 2.52
2217 2266 9.014297 CCCTTCTTGCTCTTATTCTTTTTCTTA 57.986 33.333 0.00 0.00 0.00 2.10
2261 2310 5.062528 AGAGTTCTGAAGCTCCTTTCTTTG 58.937 41.667 12.99 0.00 32.47 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 43 1.546923 TCTGGTCCGATTGTTTAGCGA 59.453 47.619 0.00 0.00 0.00 4.93
205 207 5.014808 ACGGATAAGCCAACGTTAATAGT 57.985 39.130 0.00 0.00 35.90 2.12
570 572 8.013947 GGTTCCATCTTTCTTTCGTTAGTTAAC 58.986 37.037 0.00 0.00 0.00 2.01
746 748 5.195001 AGTTTACACATGGCACGAAAATT 57.805 34.783 0.00 0.00 0.00 1.82
761 763 7.336427 GGTAGACTCTCAGTAGCTTAGTTTACA 59.664 40.741 0.00 0.00 32.36 2.41
768 770 3.526430 TGGGGTAGACTCTCAGTAGCTTA 59.474 47.826 0.00 0.00 0.00 3.09
959 961 6.430000 GGTTATGCGGACCACTAATTTGATAT 59.570 38.462 0.00 0.00 37.14 1.63
1033 1035 6.293407 CGCTGTTCTTTCTTGGATTTCTTGTA 60.293 38.462 0.00 0.00 0.00 2.41
1152 1154 3.763057 TCCAATACCGATAGCAGCTCTA 58.237 45.455 0.00 0.00 0.00 2.43
1153 1155 2.598565 TCCAATACCGATAGCAGCTCT 58.401 47.619 0.00 0.00 0.00 4.09
1162 1164 4.181578 CTGAGAACGTTTCCAATACCGAT 58.818 43.478 0.46 0.00 0.00 4.18
1179 1181 5.409520 CACGGAATGAATCAAAGAACTGAGA 59.590 40.000 0.00 0.00 0.00 3.27
1470 1473 3.173668 TGATCCGGTACTGAAATTCCG 57.826 47.619 2.31 0.00 42.22 4.30
1472 1475 3.930848 ACGTTGATCCGGTACTGAAATTC 59.069 43.478 2.31 0.00 0.00 2.17
1490 1493 5.313712 AGGACACAGAAATAAATGGACGTT 58.686 37.500 0.00 0.00 0.00 3.99
1547 1550 5.546887 ACCTGTTAGTAAAGTAAGGCCTTCT 59.453 40.000 24.49 16.06 0.00 2.85
1661 1666 3.084786 AGGGACTAGCATTGAACAAAGC 58.915 45.455 6.65 6.65 36.02 3.51
1856 1865 7.542534 TTGAAAAGTAGTACGCTTTCTTTCA 57.457 32.000 21.52 13.17 35.38 2.69
1940 1949 9.525826 ACCTCTTTTCAATCAATCTTTCATACT 57.474 29.630 0.00 0.00 0.00 2.12
2018 2027 6.057627 TCGACGATATAAAGTGGACTCTTC 57.942 41.667 0.00 0.00 0.00 2.87
2024 2033 6.183360 ACCTGAAATCGACGATATAAAGTGGA 60.183 38.462 11.42 0.00 0.00 4.02
2066 2090 4.319911 CGTCTTTGGTTTGGAGCGAAATTA 60.320 41.667 0.00 0.00 0.00 1.40
2115 2152 2.593026 CCAAAGTCAAGTAAAGCCCCA 58.407 47.619 0.00 0.00 0.00 4.96
2130 2167 3.496898 GGCCTTTCTTTCGCCAAAG 57.503 52.632 0.00 0.00 42.52 2.77
2211 2260 9.893634 TGTATTCCACCGATTAAGAATAAGAAA 57.106 29.630 0.00 0.00 34.06 2.52
2213 2262 9.542462 CTTGTATTCCACCGATTAAGAATAAGA 57.458 33.333 0.00 0.00 34.06 2.10
2214 2263 9.542462 TCTTGTATTCCACCGATTAAGAATAAG 57.458 33.333 0.00 0.00 34.06 1.73
2215 2264 9.542462 CTCTTGTATTCCACCGATTAAGAATAA 57.458 33.333 0.00 0.00 34.06 1.40
2216 2265 8.701895 ACTCTTGTATTCCACCGATTAAGAATA 58.298 33.333 0.00 0.00 31.63 1.75
2217 2266 7.565680 ACTCTTGTATTCCACCGATTAAGAAT 58.434 34.615 0.00 0.00 33.66 2.40
2218 2267 6.942976 ACTCTTGTATTCCACCGATTAAGAA 58.057 36.000 0.00 0.00 0.00 2.52
2219 2268 6.540438 ACTCTTGTATTCCACCGATTAAGA 57.460 37.500 0.00 0.00 0.00 2.10
2220 2269 7.010552 CAGAACTCTTGTATTCCACCGATTAAG 59.989 40.741 0.00 0.00 0.00 1.85
2221 2270 6.816640 CAGAACTCTTGTATTCCACCGATTAA 59.183 38.462 0.00 0.00 0.00 1.40
2222 2271 6.153851 TCAGAACTCTTGTATTCCACCGATTA 59.846 38.462 0.00 0.00 0.00 1.75
2223 2272 5.046591 TCAGAACTCTTGTATTCCACCGATT 60.047 40.000 0.00 0.00 0.00 3.34
2224 2273 4.466370 TCAGAACTCTTGTATTCCACCGAT 59.534 41.667 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.