Multiple sequence alignment - TraesCS4A01G434400

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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 TraesCS4A01G434400 chr4A 100.000 2475 0 0 1 2475 705057494 705055020 0.000000e+00 4571
1 TraesCS4A01G434400 chr4A 95.572 2484 97 11 1 2475 704810224 704807745 0.000000e+00 3965
2 TraesCS4A01G434400 chr5D 94.723 1971 92 8 1 1965 365120439 365118475 0.000000e+00 3053
3 TraesCS4A01G434400 chr5D 94.608 1966 96 10 1 1962 12933483 12931524 0.000000e+00 3035
4 TraesCS4A01G434400 chr6D 94.630 1974 91 9 1 1962 31859059 31861029 0.000000e+00 3044
5 TraesCS4A01G434400 chr2D 94.425 1973 97 10 1 1966 588796858 588794892 0.000000e+00 3022
6 TraesCS4A01G434400 chr2D 94.461 1968 98 9 1 1962 476878769 476880731 0.000000e+00 3020
7 TraesCS4A01G434400 chr2D 94.309 1968 103 7 1 1962 16904393 16906357 0.000000e+00 3005
8 TraesCS4A01G434400 chr7D 94.320 1972 98 10 1 1965 384052920 384050956 0.000000e+00 3009
9 TraesCS4A01G434400 chr7D 84.381 557 23 21 1964 2475 22510210 22509673 2.860000e-134 488
10 TraesCS4A01G434400 chr7D 88.485 330 12 11 2167 2475 22270428 22270104 2.320000e-100 375
11 TraesCS4A01G434400 chr1D 94.264 1970 100 10 1 1962 471280900 471282864 0.000000e+00 3000
12 TraesCS4A01G434400 chr7A 88.788 330 16 9 2167 2475 22898542 22898213 3.860000e-103 385
13 TraesCS4A01G434400 chr7A 81.040 327 20 24 2166 2475 22916650 22916349 3.200000e-54 222
14 TraesCS4A01G434400 chr5B 92.562 121 8 1 2356 2475 469337832 469337952 3.270000e-39 172


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 TraesCS4A01G434400 chr4A 705055020 705057494 2474 True 4571 4571 100.000 1 2475 1 chr4A.!!$R2 2474
1 TraesCS4A01G434400 chr4A 704807745 704810224 2479 True 3965 3965 95.572 1 2475 1 chr4A.!!$R1 2474
2 TraesCS4A01G434400 chr5D 365118475 365120439 1964 True 3053 3053 94.723 1 1965 1 chr5D.!!$R2 1964
3 TraesCS4A01G434400 chr5D 12931524 12933483 1959 True 3035 3035 94.608 1 1962 1 chr5D.!!$R1 1961
4 TraesCS4A01G434400 chr6D 31859059 31861029 1970 False 3044 3044 94.630 1 1962 1 chr6D.!!$F1 1961
5 TraesCS4A01G434400 chr2D 588794892 588796858 1966 True 3022 3022 94.425 1 1966 1 chr2D.!!$R1 1965
6 TraesCS4A01G434400 chr2D 476878769 476880731 1962 False 3020 3020 94.461 1 1962 1 chr2D.!!$F2 1961
7 TraesCS4A01G434400 chr2D 16904393 16906357 1964 False 3005 3005 94.309 1 1962 1 chr2D.!!$F1 1961
8 TraesCS4A01G434400 chr7D 384050956 384052920 1964 True 3009 3009 94.320 1 1965 1 chr7D.!!$R3 1964
9 TraesCS4A01G434400 chr7D 22509673 22510210 537 True 488 488 84.381 1964 2475 1 chr7D.!!$R2 511
10 TraesCS4A01G434400 chr1D 471280900 471282864 1964 False 3000 3000 94.264 1 1962 1 chr1D.!!$F1 1961

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
875 880 0.108615 CTCCAGTCGTCGCCATCTTT 60.109 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2255 1.610673 GTGGCAGAGAGAGGTGGGA 60.611 63.158 0.0 0.0 0.0 4.37 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 1.258676 GTCGTCTTCTCCTGTTCCCT 58.741 55.000 0.00 0.00 0.00 4.20
55 56 4.271816 CCTGAGCCGCGTCGCTAT 62.272 66.667 16.36 0.02 39.87 2.97
131 132 2.352805 CGCCCTTCTTTCCCTGCT 59.647 61.111 0.00 0.00 0.00 4.24
172 173 2.189521 CGTCCCCTCCCAAATCCG 59.810 66.667 0.00 0.00 0.00 4.18
471 475 2.249535 CCGCCATGATCTCTTGCCG 61.250 63.158 0.00 0.00 0.00 5.69
481 485 1.672356 CTCTTGCCGTTCCCCTGTG 60.672 63.158 0.00 0.00 0.00 3.66
668 672 2.409870 GCCACTCCCTTTCCATGCG 61.410 63.158 0.00 0.00 0.00 4.73
690 694 2.435938 CCCATGCTACACCGCGTT 60.436 61.111 4.92 0.00 0.00 4.84
875 880 0.108615 CTCCAGTCGTCGCCATCTTT 60.109 55.000 0.00 0.00 0.00 2.52
884 889 3.381136 GCCATCTTTTGCCGGCCA 61.381 61.111 26.77 11.12 38.67 5.36
1089 1094 0.178921 AGAAGGTGTGGAGAGGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
1133 1138 2.814097 GCTGTGGTGGAGGTGTTTATGT 60.814 50.000 0.00 0.00 0.00 2.29
1169 1174 4.168101 AGTGGAAGGAGAGGTCACAATTA 58.832 43.478 0.00 0.00 0.00 1.40
1179 1184 7.038017 AGGAGAGGTCACAATTAGAAAGAATCA 60.038 37.037 0.00 0.00 0.00 2.57
1182 1189 7.389053 AGAGGTCACAATTAGAAAGAATCACAC 59.611 37.037 0.00 0.00 0.00 3.82
1252 1264 5.945784 TCAATGTAGGGGTGATTTCTTTCAG 59.054 40.000 0.00 0.00 0.00 3.02
1569 1586 7.947282 TCCGTTTCCTGAAAATCTGTTATTTT 58.053 30.769 0.00 0.00 34.30 1.82
1808 1825 5.646360 GGAGAGAAAAATAAACCGATGGACA 59.354 40.000 0.00 0.00 0.00 4.02
1824 1841 2.863988 CAAGGGTGGGAGGGGGTT 60.864 66.667 0.00 0.00 0.00 4.11
1845 1864 2.037251 TGTGGGAGGAGAGACGAAAAAG 59.963 50.000 0.00 0.00 0.00 2.27
1900 1919 0.325671 GGATGGTGGGAGGAGAGACA 60.326 60.000 0.00 0.00 0.00 3.41
2026 2055 7.931578 ATGAATACACGATTTGGGTAAGAAA 57.068 32.000 0.00 0.00 0.00 2.52
2063 2092 4.063335 CCACCTGCAGGGAGAGAT 57.937 61.111 35.42 11.84 40.27 2.75
2203 2255 3.838795 CCATTTTCTTGGCGCCAAT 57.161 47.368 40.03 23.82 35.20 3.16
2247 2313 3.132289 CGCCTCTCTTCCACCTATAAACA 59.868 47.826 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.842698 CTCTATAGCGACGCGGCTCA 61.843 60.000 11.76 0.88 43.54 4.26
131 132 1.690633 GAGGAGTGAGGCCATGGGA 60.691 63.158 15.13 0.00 0.00 4.37
172 173 1.876263 GCGAGCGAGAAGGAGAAGC 60.876 63.158 0.00 0.00 0.00 3.86
205 206 1.006571 GGCGTCTGACTTCGTCCAA 60.007 57.895 6.21 0.00 0.00 3.53
471 475 1.134438 AGAGGGGAACACAGGGGAAC 61.134 60.000 0.00 0.00 0.00 3.62
481 485 0.321996 AGAGCAAACGAGAGGGGAAC 59.678 55.000 0.00 0.00 0.00 3.62
809 813 1.153168 GGCGAGCAAAGGATAGGCA 60.153 57.895 0.00 0.00 31.08 4.75
1089 1094 3.637273 GACACCGCCCCAGACCTT 61.637 66.667 0.00 0.00 0.00 3.50
1133 1138 1.984570 CCACTCCGGCTCCTTCTCA 60.985 63.158 0.00 0.00 0.00 3.27
1191 1201 3.637229 TGAACTGAGATCTCCGGGTTATC 59.363 47.826 20.03 11.24 0.00 1.75
1252 1264 8.630037 CCAATATTTCCTATGTTTTCCACCTAC 58.370 37.037 0.00 0.00 0.00 3.18
1304 1316 8.533569 TCAGTTCAAAAATCCTAACTTTCCTT 57.466 30.769 0.00 0.00 29.93 3.36
1676 1693 7.930865 CCTTTTATTGGTTCAATTTGTCTTGGA 59.069 33.333 0.00 0.00 35.54 3.53
1808 1825 2.863988 CAACCCCCTCCCACCCTT 60.864 66.667 0.00 0.00 0.00 3.95
1824 1841 1.712056 TTTTCGTCTCTCCTCCCACA 58.288 50.000 0.00 0.00 0.00 4.17
1845 1864 1.789054 CGCGGTTTATTTTCGCTGGTC 60.789 52.381 0.00 0.00 46.23 4.02
1883 1902 2.044793 TTTGTCTCTCCTCCCACCAT 57.955 50.000 0.00 0.00 0.00 3.55
1938 1961 5.296283 GTCTCTACTCCTAATGCACGAGTTA 59.704 44.000 11.47 0.00 37.93 2.24
1996 2020 5.101628 CCCAAATCGTGTATTCATTTGTGG 58.898 41.667 0.00 0.00 32.18 4.17
2063 2092 3.134804 GCTTTCCTTCACCTATCCAGCTA 59.865 47.826 0.00 0.00 0.00 3.32
2203 2255 1.610673 GTGGCAGAGAGAGGTGGGA 60.611 63.158 0.00 0.00 0.00 4.37
2263 2331 2.427002 GGAGGGGATGGATGAGAGAGAA 60.427 54.545 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.