Multiple sequence alignment - TraesCS5B01G067900

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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 TraesCS5B01G067900 chr5B 100.000 2548 0 0 1 2548 76432496 76429949 0.000000e+00 4706
1 TraesCS5B01G067900 chr5B 94.960 377 17 2 597 971 317969014 317969390 7.850000e-165 590
2 TraesCS5B01G067900 chr6B 95.284 1972 81 8 588 2548 527993586 527991616 0.000000e+00 3116
3 TraesCS5B01G067900 chr3B 95.127 1970 77 14 593 2548 792939411 792941375 0.000000e+00 3088
4 TraesCS5B01G067900 chr3B 93.872 1991 82 23 598 2548 108092312 108090322 0.000000e+00 2964
5 TraesCS5B01G067900 chr3B 95.652 368 14 2 598 963 594400316 594399949 7.850000e-165 590
6 TraesCS5B01G067900 chr3B 94.681 376 18 2 598 971 330378561 330378936 1.310000e-162 582
7 TraesCS5B01G067900 chr1B 94.756 1964 76 14 597 2548 189219499 189221447 0.000000e+00 3031
8 TraesCS5B01G067900 chr1B 94.372 1990 73 12 596 2548 520844121 520842134 0.000000e+00 3018
9 TraesCS5B01G067900 chr1B 94.132 1994 73 25 598 2548 581717561 581715569 0.000000e+00 2994
10 TraesCS5B01G067900 chr1B 94.041 386 19 4 587 969 663786484 663786868 1.310000e-162 582
11 TraesCS5B01G067900 chr4A 94.076 1992 75 27 597 2548 705529253 705527265 0.000000e+00 2985
12 TraesCS5B01G067900 chr2B 94.070 1990 77 11 598 2548 692955897 692957884 0.000000e+00 2983
13 TraesCS5B01G067900 chr2B 94.737 380 17 3 595 971 546410282 546410661 2.820000e-164 588
14 TraesCS5B01G067900 chr7B 96.289 1617 49 8 942 2548 708942881 708941266 0.000000e+00 2643
15 TraesCS5B01G067900 chr3A 88.663 1129 88 13 598 1720 120653865 120654959 0.000000e+00 1339
16 TraesCS5B01G067900 chr6D 96.817 597 19 0 1 597 102040192 102039596 0.000000e+00 998
17 TraesCS5B01G067900 chr6D 96.817 597 19 0 1 597 439983767 439983171 0.000000e+00 998
18 TraesCS5B01G067900 chr6D 96.817 597 19 0 1 597 442539645 442539049 0.000000e+00 998
19 TraesCS5B01G067900 chr5D 96.817 597 19 0 1 597 207766803 207766207 0.000000e+00 998
20 TraesCS5B01G067900 chr5D 96.817 597 19 0 1 597 456854309 456854905 0.000000e+00 998
21 TraesCS5B01G067900 chr4D 96.817 597 19 0 1 597 393595388 393595984 0.000000e+00 998
22 TraesCS5B01G067900 chr1D 96.817 597 19 0 1 597 102171596 102171000 0.000000e+00 998
23 TraesCS5B01G067900 chr1D 96.817 597 19 0 1 597 419344910 419345506 0.000000e+00 998
24 TraesCS5B01G067900 chr1D 96.817 597 19 0 1 597 470242205 470242801 0.000000e+00 998
25 TraesCS5B01G067900 chr2A 90.018 541 48 3 597 1136 695806753 695806218 0.000000e+00 695


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 TraesCS5B01G067900 chr5B 76429949 76432496 2547 True 4706 4706 100.000 1 2548 1 chr5B.!!$R1 2547
1 TraesCS5B01G067900 chr6B 527991616 527993586 1970 True 3116 3116 95.284 588 2548 1 chr6B.!!$R1 1960
2 TraesCS5B01G067900 chr3B 792939411 792941375 1964 False 3088 3088 95.127 593 2548 1 chr3B.!!$F2 1955
3 TraesCS5B01G067900 chr3B 108090322 108092312 1990 True 2964 2964 93.872 598 2548 1 chr3B.!!$R1 1950
4 TraesCS5B01G067900 chr1B 189219499 189221447 1948 False 3031 3031 94.756 597 2548 1 chr1B.!!$F1 1951
5 TraesCS5B01G067900 chr1B 520842134 520844121 1987 True 3018 3018 94.372 596 2548 1 chr1B.!!$R1 1952
6 TraesCS5B01G067900 chr1B 581715569 581717561 1992 True 2994 2994 94.132 598 2548 1 chr1B.!!$R2 1950
7 TraesCS5B01G067900 chr4A 705527265 705529253 1988 True 2985 2985 94.076 597 2548 1 chr4A.!!$R1 1951
8 TraesCS5B01G067900 chr2B 692955897 692957884 1987 False 2983 2983 94.070 598 2548 1 chr2B.!!$F2 1950
9 TraesCS5B01G067900 chr7B 708941266 708942881 1615 True 2643 2643 96.289 942 2548 1 chr7B.!!$R1 1606
10 TraesCS5B01G067900 chr3A 120653865 120654959 1094 False 1339 1339 88.663 598 1720 1 chr3A.!!$F1 1122
11 TraesCS5B01G067900 chr6D 102039596 102040192 596 True 998 998 96.817 1 597 1 chr6D.!!$R1 596
12 TraesCS5B01G067900 chr6D 439983171 439983767 596 True 998 998 96.817 1 597 1 chr6D.!!$R2 596
13 TraesCS5B01G067900 chr6D 442539049 442539645 596 True 998 998 96.817 1 597 1 chr6D.!!$R3 596
14 TraesCS5B01G067900 chr5D 207766207 207766803 596 True 998 998 96.817 1 597 1 chr5D.!!$R1 596
15 TraesCS5B01G067900 chr5D 456854309 456854905 596 False 998 998 96.817 1 597 1 chr5D.!!$F1 596
16 TraesCS5B01G067900 chr4D 393595388 393595984 596 False 998 998 96.817 1 597 1 chr4D.!!$F1 596
17 TraesCS5B01G067900 chr1D 102171000 102171596 596 True 998 998 96.817 1 597 1 chr1D.!!$R1 596
18 TraesCS5B01G067900 chr1D 419344910 419345506 596 False 998 998 96.817 1 597 1 chr1D.!!$F1 596
19 TraesCS5B01G067900 chr1D 470242205 470242801 596 False 998 998 96.817 1 597 1 chr1D.!!$F2 596
20 TraesCS5B01G067900 chr2A 695806218 695806753 535 True 695 695 90.018 597 1136 1 chr2A.!!$R1 539

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
230 231 0.035317 ACGAACTGATTCAGGCAGCA 59.965 50.0 17.66 0.0 36.86 4.41 F
357 358 0.038166 TTGGAGACCAACAGGGATGC 59.962 55.0 0.00 0.0 38.75 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1367 0.952984 TGCGCAACCATTCGTCATGA 60.953 50.000 8.16 0.0 34.31 3.07 R
2292 2367 1.333308 TGTGCAAACATTCACGGTCTG 59.667 47.619 0.00 0.0 36.06 3.51 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
47 48 4.038282 CCATAATGCTGGCAAGATGCTTAA 59.962 41.667 0.00 0.00 44.28 1.85
163 164 0.603569 GTCCTTCAGCTTCCTGTCGA 59.396 55.000 0.00 0.00 40.09 4.20
230 231 0.035317 ACGAACTGATTCAGGCAGCA 59.965 50.000 17.66 0.00 36.86 4.41
260 261 1.134098 AGTTTGTGCCAGCAGTAGTGT 60.134 47.619 0.00 0.00 0.00 3.55
277 278 2.691526 AGTGTCCAGTAACTCGAACACA 59.308 45.455 13.47 0.00 39.48 3.72
304 305 1.202770 AGACAGGACTTTTGGGTTCCG 60.203 52.381 0.00 0.00 0.00 4.30
357 358 0.038166 TTGGAGACCAACAGGGATGC 59.962 55.000 0.00 0.00 38.75 3.91
430 431 6.713450 ACGTGGTACTGTTCTCCAATATTTTT 59.287 34.615 0.00 0.00 32.82 1.94
477 478 3.120338 CGGACACATCACATGTTTACCAC 60.120 47.826 0.00 0.00 42.70 4.16
481 482 4.336993 ACACATCACATGTTTACCACGTTT 59.663 37.500 0.00 0.00 42.70 3.60
852 856 2.263741 GCATAGAGCCATTGCGGGG 61.264 63.158 0.00 0.00 44.33 5.73
900 904 0.250166 TGACCACGACGACAGAGAGA 60.250 55.000 0.00 0.00 0.00 3.10
963 1025 0.978146 GGAAGCTAGCTGTGGAGGGA 60.978 60.000 20.16 0.00 0.00 4.20
1010 1072 0.173481 CCGAGCTTCATGTCTTCCGA 59.827 55.000 0.00 0.00 0.00 4.55
1071 1133 0.976641 TGGAGATGCCTGTCTTCGTT 59.023 50.000 0.00 0.00 37.63 3.85
1083 1145 1.083015 CTTCGTTTGTTCGCGGTGG 60.083 57.895 6.13 0.00 0.00 4.61
1141 1203 1.804748 GGAACCACAATCGTCTGTTCC 59.195 52.381 4.18 4.18 42.46 3.62
1238 1300 2.289631 TGATCTGTTCCGTGTTCATGCT 60.290 45.455 0.00 0.00 0.00 3.79
1267 1329 3.486383 TGCTTCTTTCTTTGGGTCGATT 58.514 40.909 0.00 0.00 0.00 3.34
1305 1367 7.828223 ACTCTGATAAATGAACTGCAAGAAGAT 59.172 33.333 0.00 0.00 37.43 2.40
1508 1571 5.772004 TGGGCATTTGTAGGTATGGTAATT 58.228 37.500 0.00 0.00 0.00 1.40
1738 1804 5.616424 GCAGCTAATGAATTATTCCAGAGCG 60.616 44.000 12.89 10.34 33.91 5.03
2080 2150 2.311542 TGACATGGGTAGGGAAGCAATT 59.688 45.455 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 9.736023 CAAACAAGAGAAAGTTAATAAGCTTGT 57.264 29.630 9.86 0.00 44.42 3.16
230 231 3.429410 GCTGGCACAAACTCTTTGAACTT 60.429 43.478 1.75 0.00 43.26 2.66
260 261 3.804786 TGTTGTGTTCGAGTTACTGGA 57.195 42.857 0.00 0.00 0.00 3.86
277 278 3.891366 CCCAAAAGTCCTGTCTTGATGTT 59.109 43.478 0.00 0.00 0.00 2.71
357 358 5.988561 GCAGATAAGGTTCAAGATAGTGAGG 59.011 44.000 0.00 0.00 0.00 3.86
400 401 4.084287 TGGAGAACAGTACCACGTTATCT 58.916 43.478 12.18 0.43 34.55 1.98
430 431 6.627395 TTGTTTCTCTTTTAGAATGCGGAA 57.373 33.333 0.00 0.00 43.75 4.30
776 777 6.529829 GCATGCAACGGTCTGAATAAAATTAA 59.470 34.615 14.21 0.00 0.00 1.40
777 778 6.033341 GCATGCAACGGTCTGAATAAAATTA 58.967 36.000 14.21 0.00 0.00 1.40
844 845 3.350219 CTAATATAGCACCCCCGCAAT 57.650 47.619 0.00 0.00 0.00 3.56
889 893 2.561885 CGCCGTTCTCTCTGTCGT 59.438 61.111 0.00 0.00 0.00 4.34
938 1000 1.609501 ACAGCTAGCTTCCCACCGA 60.610 57.895 16.46 0.00 0.00 4.69
1083 1145 4.520846 CAATCAACGCTCGCCCGC 62.521 66.667 0.00 0.00 0.00 6.13
1141 1203 1.131218 CATTCTCGCTGCACACGTG 59.869 57.895 15.48 15.48 0.00 4.49
1190 1252 3.840831 CTCAAAGATCCCGAGCACA 57.159 52.632 0.00 0.00 0.00 4.57
1194 1256 1.863454 CGATTGCTCAAAGATCCCGAG 59.137 52.381 0.00 0.00 0.00 4.63
1238 1300 3.318839 CCAAAGAAAGAAGCATGTCACCA 59.681 43.478 0.00 0.00 0.00 4.17
1267 1329 6.665248 TCATTTATCAGAGTCTTGGTCAGAGA 59.335 38.462 0.00 0.00 29.34 3.10
1305 1367 0.952984 TGCGCAACCATTCGTCATGA 60.953 50.000 8.16 0.00 34.31 3.07
1389 1451 3.358111 ACAGCTAGCTCTCTGTCAGTA 57.642 47.619 16.15 0.00 39.11 2.74
1456 1519 6.619329 ATTTGCAAATGGGTATTGGTAGTT 57.381 33.333 23.54 0.00 0.00 2.24
1508 1571 4.991153 TTTCAACATTACAACCAGTGCA 57.009 36.364 0.00 0.00 0.00 4.57
1844 1911 1.891150 CCAGAGCTGAGGCACATTTTT 59.109 47.619 0.00 0.00 41.70 1.94
2292 2367 1.333308 TGTGCAAACATTCACGGTCTG 59.667 47.619 0.00 0.00 36.06 3.51


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

AutoCloner maintained by Alex Coulton.