Multiple sequence alignment - TraesCS5D01G475000

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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 TraesCS5D01G475000 chr5D 100.000 2457 0 0 1 2457 514948822 514946366 0.000000e+00 4538
1 TraesCS5D01G475000 chr5D 94.797 2460 121 4 1 2456 515026024 515023568 0.000000e+00 3827
2 TraesCS5D01G475000 chr5D 94.431 2460 129 5 1 2457 514996667 514994213 0.000000e+00 3777
3 TraesCS5D01G475000 chr5D 93.984 2460 134 8 1 2457 514975230 514972782 0.000000e+00 3711
4 TraesCS5D01G475000 chr5B 89.687 2463 215 20 7 2455 647781414 647778977 0.000000e+00 3105
5 TraesCS5D01G475000 chr5B 89.664 2467 211 22 7 2455 647699036 647696596 0.000000e+00 3103
6 TraesCS5D01G475000 chr5B 91.392 1975 151 10 1 1962 647405774 647403806 0.000000e+00 2687
7 TraesCS5D01G475000 chr5A 89.730 2220 205 15 247 2457 643034528 643032323 0.000000e+00 2815
8 TraesCS5D01G475000 chr5A 88.768 2306 234 17 165 2457 643042712 643040419 0.000000e+00 2800
9 TraesCS5D01G475000 chr5A 89.262 2142 211 11 165 2295 643029621 643027488 0.000000e+00 2663
10 TraesCS5D01G475000 chr4D 93.631 157 10 0 1 157 17439084 17438928 4.080000e-58 235
11 TraesCS5D01G475000 chr4D 91.250 160 14 0 1 160 69546827 69546668 4.110000e-53 219
12 TraesCS5D01G475000 chr6D 90.419 167 15 1 1 166 434815765 434815931 4.110000e-53 219


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 TraesCS5D01G475000 chr5D 514946366 514948822 2456 True 4538 4538 100.000 1 2457 1 chr5D.!!$R1 2456
1 TraesCS5D01G475000 chr5D 515023568 515026024 2456 True 3827 3827 94.797 1 2456 1 chr5D.!!$R4 2455
2 TraesCS5D01G475000 chr5D 514994213 514996667 2454 True 3777 3777 94.431 1 2457 1 chr5D.!!$R3 2456
3 TraesCS5D01G475000 chr5D 514972782 514975230 2448 True 3711 3711 93.984 1 2457 1 chr5D.!!$R2 2456
4 TraesCS5D01G475000 chr5B 647778977 647781414 2437 True 3105 3105 89.687 7 2455 1 chr5B.!!$R3 2448
5 TraesCS5D01G475000 chr5B 647696596 647699036 2440 True 3103 3103 89.664 7 2455 1 chr5B.!!$R2 2448
6 TraesCS5D01G475000 chr5B 647403806 647405774 1968 True 2687 2687 91.392 1 1962 1 chr5B.!!$R1 1961
7 TraesCS5D01G475000 chr5A 643040419 643042712 2293 True 2800 2800 88.768 165 2457 1 chr5A.!!$R1 2292
8 TraesCS5D01G475000 chr5A 643027488 643034528 7040 True 2739 2815 89.496 165 2457 2 chr5A.!!$R2 2292

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
89 90 0.555769 TCTTTGGCTCCCCTTGTGTT 59.444 50.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2049 1.359848 CCTCAATCCGACAAGAACCG 58.64 55.0 0.0 0.0 0.0 4.44 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
89 90 0.555769 TCTTTGGCTCCCCTTGTGTT 59.444 50.000 0.00 0.00 0.00 3.32
94 95 1.707989 TGGCTCCCCTTGTGTTGAATA 59.292 47.619 0.00 0.00 0.00 1.75
99 100 5.067805 GGCTCCCCTTGTGTTGAATAAATAG 59.932 44.000 0.00 0.00 0.00 1.73
172 173 8.153221 TGAGGGTTATAAGTAGTTCATTCCAA 57.847 34.615 0.00 0.00 0.00 3.53
180 181 5.046910 AGTAGTTCATTCCAATTTGTGCG 57.953 39.130 0.00 0.00 0.00 5.34
222 223 2.846039 TTTCGTCGATCAGGAGTAGC 57.154 50.000 0.00 0.00 0.00 3.58
264 271 1.757699 GCCCTTAAGGTCATCGTCTCT 59.242 52.381 20.22 0.00 38.26 3.10
289 299 3.476552 CCAAGTGGCTACAAGTTCTTGA 58.523 45.455 17.75 2.96 35.69 3.02
314 324 6.874288 AAGTCTCACAAATTTTCCTCTCAG 57.126 37.500 0.00 0.00 0.00 3.35
334 344 6.549364 TCTCAGTTAGATCCTTCTGAATCTCC 59.451 42.308 10.86 0.00 36.67 3.71
383 394 3.989817 CGGGGCTCTTTTCTTTTTCAATG 59.010 43.478 0.00 0.00 0.00 2.82
736 760 3.575965 AAATGCCTCGTTCATTTCCAC 57.424 42.857 6.50 0.00 39.21 4.02
772 796 9.892130 ATCGGATTATATAAGTTGGAGGATTTC 57.108 33.333 1.02 0.00 0.00 2.17
871 895 9.979578 TGAGCACATTAAAACAATGATTTTAGT 57.020 25.926 4.10 0.00 35.88 2.24
901 925 7.390996 CCGCCTATATATATCATACGAGAAGGT 59.609 40.741 0.00 0.00 0.00 3.50
917 941 4.072088 GTGACCGAACGCAAGCCG 62.072 66.667 0.00 0.00 45.62 5.52
952 981 7.548075 GGAATCGACCACTATTTCACTTTTCTA 59.452 37.037 0.00 0.00 0.00 2.10
1274 1303 1.871039 CAGTGTTCAAGTACAACCCGG 59.129 52.381 0.00 0.00 0.00 5.73
1466 1495 5.734786 GCTGTCACTGCTTAATAGATCTCGT 60.735 44.000 0.00 0.00 0.00 4.18
1489 1518 5.799936 GTGCATATGCGTGTCTTTGTATTTT 59.200 36.000 22.21 0.00 45.83 1.82
1523 1552 3.941483 CCAAGTCTTTATGGTGTGCTAGG 59.059 47.826 0.00 0.00 31.84 3.02
1571 1604 6.382869 AATAAATTGATCCTAGTGCAGTGC 57.617 37.500 8.58 8.58 0.00 4.40
1572 1605 3.354948 AATTGATCCTAGTGCAGTGCA 57.645 42.857 15.37 15.37 35.60 4.57
1697 1730 5.606348 ACTTTGAACATTAAGGGCAAACA 57.394 34.783 6.39 0.00 0.00 2.83
2132 2166 4.251103 TGGAGCTGGAGTAACATCTAGA 57.749 45.455 0.00 0.00 29.74 2.43
2189 2223 1.212935 GCTCCACTTCACCCACCATAT 59.787 52.381 0.00 0.00 0.00 1.78
2191 2225 2.774234 CTCCACTTCACCCACCATATCT 59.226 50.000 0.00 0.00 0.00 1.98
2192 2226 2.505407 TCCACTTCACCCACCATATCTG 59.495 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 3.093717 CGCGATAGTGTTCAAGGGTAT 57.906 47.619 0.00 0.00 42.91 2.73
157 158 5.240623 TCGCACAAATTGGAATGAACTACTT 59.759 36.000 0.00 0.00 0.00 2.24
163 164 3.153130 TCCTCGCACAAATTGGAATGAA 58.847 40.909 0.00 0.00 0.00 2.57
172 173 3.350219 ACTAACCATCCTCGCACAAAT 57.650 42.857 0.00 0.00 0.00 2.32
180 181 5.625568 TTAGCCCTAAACTAACCATCCTC 57.374 43.478 0.00 0.00 0.00 3.71
222 223 1.291877 CCTCCGTGAAAACTCCGCAG 61.292 60.000 0.00 0.00 0.00 5.18
250 257 1.187087 GGGACAGAGACGATGACCTT 58.813 55.000 0.00 0.00 33.68 3.50
264 271 1.136828 ACTTGTAGCCACTTGGGACA 58.863 50.000 0.00 0.00 40.01 4.02
289 299 8.160106 ACTGAGAGGAAAATTTGTGAGACTTAT 58.840 33.333 0.00 0.00 0.00 1.73
314 324 5.278758 CCGAGGAGATTCAGAAGGATCTAAC 60.279 48.000 0.00 0.00 33.50 2.34
334 344 4.319984 GGTTAACAAAGCAGTAAACCCGAG 60.320 45.833 8.10 0.00 32.09 4.63
383 394 7.470935 TTTTAGGCTAGGTTAATTTGGAACC 57.529 36.000 0.97 0.97 45.76 3.62
502 520 6.458206 GCCATGATTTGCGATTGTTTAGTCTA 60.458 38.462 0.00 0.00 0.00 2.59
554 574 7.458170 AGGAGAAGTCCCTAATCTTGACTTTTA 59.542 37.037 5.69 0.00 46.37 1.52
701 721 6.093633 ACGAGGCATTTATTTCCTACTTTCAC 59.906 38.462 0.00 0.00 0.00 3.18
772 796 8.515473 TGCAACATTAGTTAGTATATGCTACG 57.485 34.615 0.00 0.00 35.85 3.51
871 895 7.935210 TCTCGTATGATATATATAGGCGGTCAA 59.065 37.037 0.00 0.00 0.00 3.18
901 925 4.595538 ACGGCTTGCGTTCGGTCA 62.596 61.111 0.00 0.00 0.00 4.02
917 941 2.028930 AGTGGTCGATTCCTCAAGTGAC 60.029 50.000 0.00 0.00 0.00 3.67
952 981 6.406370 TGTTGATACCGAAGATCACAAGAAT 58.594 36.000 0.00 0.00 0.00 2.40
1005 1034 2.672295 GGTACCATGGTTGCCCGA 59.328 61.111 25.38 0.00 0.00 5.14
1466 1495 5.559427 AAATACAAAGACACGCATATGCA 57.441 34.783 26.52 4.04 42.21 3.96
1523 1552 8.442632 TTCTTCTATCACCAATTCATCATGAC 57.557 34.615 0.00 0.00 0.00 3.06
1571 1604 6.280643 AGATTCCATGAAAACATGATGCATG 58.719 36.000 2.46 13.92 46.18 4.06
1572 1605 6.479972 AGATTCCATGAAAACATGATGCAT 57.520 33.333 0.00 0.00 34.66 3.96
1639 1672 9.047947 AGAATGGTAGGAACTTATGTCTACTTT 57.952 33.333 0.00 0.00 41.75 2.66
1640 1673 8.611051 AGAATGGTAGGAACTTATGTCTACTT 57.389 34.615 0.00 0.00 41.75 2.24
1655 1688 4.150359 AGTATGGTCGGTAGAATGGTAGG 58.850 47.826 0.00 0.00 0.00 3.18
2015 2049 1.359848 CCTCAATCCGACAAGAACCG 58.640 55.000 0.00 0.00 0.00 4.44
2132 2166 6.259608 CCATTTCTCTGCTCGAGTAAAATGAT 59.740 38.462 26.98 10.13 41.67 2.45
2143 2177 1.446907 AGCAACCATTTCTCTGCTCG 58.553 50.000 0.00 0.00 41.18 5.03
2189 2223 1.228894 AACTCCGAGGGCAGACAGA 60.229 57.895 0.00 0.00 0.00 3.41
2191 2225 2.283529 GGAACTCCGAGGGCAGACA 61.284 63.158 0.00 0.00 0.00 3.41
2192 2226 1.545706 AAGGAACTCCGAGGGCAGAC 61.546 60.000 0.00 0.00 38.49 3.51
2370 2411 8.142994 AGTTACCACTAATCAATGATTTAGCG 57.857 34.615 14.15 3.03 33.95 4.26
2407 2448 7.387119 TGCGTGTATCTCTTACTTTTCTAGA 57.613 36.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.