Multiple sequence alignment - TraesCS5B01G261600

Loading Multiple Alignment...

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 TraesCS5B01G261600 chr5B 100.000 2549 0 0 1 2549 446193820 446191272 0 4708
1 TraesCS5B01G261600 chr5B 96.235 1992 70 4 561 2549 269389467 269391456 0 3258
2 TraesCS5B01G261600 chr5B 94.533 567 30 1 1 566 673029555 673028989 0 874
3 TraesCS5B01G261600 chr5B 94.004 567 33 1 1 566 369906386 369905820 0 857
4 TraesCS5B01G261600 chr2B 96.436 1992 66 5 561 2549 596962064 596964053 0 3280
5 TraesCS5B01G261600 chr2B 96.389 1994 65 5 561 2549 602077190 602075199 0 3277
6 TraesCS5B01G261600 chr2B 96.138 1994 66 8 558 2549 543889477 543887493 0 3245
7 TraesCS5B01G261600 chr7B 96.436 1992 64 4 560 2549 718488481 718486495 0 3278
8 TraesCS5B01G261600 chr7B 96.376 1987 65 5 567 2549 621924192 621926175 0 3264
9 TraesCS5B01G261600 chr7B 94.876 566 27 2 3 566 287023204 287022639 0 883
10 TraesCS5B01G261600 chr1B 96.427 1987 63 4 565 2549 498442421 498440441 0 3269
11 TraesCS5B01G261600 chr1B 96.187 1993 70 5 559 2549 663786489 663788477 0 3254
12 TraesCS5B01G261600 chr3B 96.291 1995 64 9 558 2549 703251160 703253147 0 3265
13 TraesCS5B01G261600 chr3B 94.533 567 30 1 1 566 731251746 731251180 0 874
14 TraesCS5B01G261600 chr3B 94.366 568 30 2 1 566 496929932 496930499 0 870
15 TraesCS5B01G261600 chr6B 94.709 567 29 1 1 566 595418277 595417711 0 880
16 TraesCS5B01G261600 chr6B 94.004 567 33 1 1 566 719925936 719926502 0 857
17 TraesCS5B01G261600 chr4A 94.180 567 32 1 1 566 718728539 718729105 0 863
18 TraesCS5B01G261600 chr4B 94.004 567 33 1 1 566 645955378 645954812 0 857


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 TraesCS5B01G261600 chr5B 446191272 446193820 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R2 2548
1 TraesCS5B01G261600 chr5B 269389467 269391456 1989 False 3258 3258 96.235 561 2549 1 chr5B.!!$F1 1988
2 TraesCS5B01G261600 chr5B 673028989 673029555 566 True 874 874 94.533 1 566 1 chr5B.!!$R3 565
3 TraesCS5B01G261600 chr5B 369905820 369906386 566 True 857 857 94.004 1 566 1 chr5B.!!$R1 565
4 TraesCS5B01G261600 chr2B 596962064 596964053 1989 False 3280 3280 96.436 561 2549 1 chr2B.!!$F1 1988
5 TraesCS5B01G261600 chr2B 602075199 602077190 1991 True 3277 3277 96.389 561 2549 1 chr2B.!!$R2 1988
6 TraesCS5B01G261600 chr2B 543887493 543889477 1984 True 3245 3245 96.138 558 2549 1 chr2B.!!$R1 1991
7 TraesCS5B01G261600 chr7B 718486495 718488481 1986 True 3278 3278 96.436 560 2549 1 chr7B.!!$R2 1989
8 TraesCS5B01G261600 chr7B 621924192 621926175 1983 False 3264 3264 96.376 567 2549 1 chr7B.!!$F1 1982
9 TraesCS5B01G261600 chr7B 287022639 287023204 565 True 883 883 94.876 3 566 1 chr7B.!!$R1 563
10 TraesCS5B01G261600 chr1B 498440441 498442421 1980 True 3269 3269 96.427 565 2549 1 chr1B.!!$R1 1984
11 TraesCS5B01G261600 chr1B 663786489 663788477 1988 False 3254 3254 96.187 559 2549 1 chr1B.!!$F1 1990
12 TraesCS5B01G261600 chr3B 703251160 703253147 1987 False 3265 3265 96.291 558 2549 1 chr3B.!!$F2 1991
13 TraesCS5B01G261600 chr3B 731251180 731251746 566 True 874 874 94.533 1 566 1 chr3B.!!$R1 565
14 TraesCS5B01G261600 chr3B 496929932 496930499 567 False 870 870 94.366 1 566 1 chr3B.!!$F1 565
15 TraesCS5B01G261600 chr6B 595417711 595418277 566 True 880 880 94.709 1 566 1 chr6B.!!$R1 565
16 TraesCS5B01G261600 chr6B 719925936 719926502 566 False 857 857 94.004 1 566 1 chr6B.!!$F1 565
17 TraesCS5B01G261600 chr4A 718728539 718729105 566 False 863 863 94.180 1 566 1 chr4A.!!$F1 565
18 TraesCS5B01G261600 chr4B 645954812 645955378 566 True 857 857 94.004 1 566 1 chr4B.!!$R1 565

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
603 606 1.134371 GCCCTTAGTGGTGTCCATCTC 60.134 57.143 0.0 0.0 35.28 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 1977 1.460689 TGGGTTCGAGTCCCCAGTT 60.461 57.895 20.23 0.0 46.06 3.16 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
46 47 6.746364 GCTCTCTTTATGCTTCAATTCTTGTG 59.254 38.462 0.00 0.00 0.00 3.33
201 204 9.778741 ACTCTCTGTTTAGATGTGTTTTTATCA 57.221 29.630 0.00 0.00 31.21 2.15
410 413 9.939802 TTGGTAGGATTTTTAGAGTTCTAGAAC 57.060 33.333 25.24 25.24 41.45 3.01
470 473 8.237949 TGTTTTTGACAGATTCTGTTTTTCGTA 58.762 29.630 19.88 3.93 45.44 3.43
603 606 1.134371 GCCCTTAGTGGTGTCCATCTC 60.134 57.143 0.00 0.00 35.28 2.75
770 773 2.442212 TTATTCAGACCGTTGCACGA 57.558 45.000 9.75 0.00 46.05 4.35
1008 1011 1.342819 GCTCCGAGCTCCATGTATTCT 59.657 52.381 13.42 0.00 38.45 2.40
1073 1076 2.025155 GGAGATGCCTGTCTTCGTCTA 58.975 52.381 0.00 0.00 0.00 2.59
1085 1088 4.201679 CGTCTATCCGCGGTGCCA 62.202 66.667 27.15 5.72 0.00 4.92
1296 1299 6.070251 TGGCCAAGACTCTGATAAATGAACTA 60.070 38.462 0.61 0.00 0.00 2.24
1890 1897 9.077885 ACACCTAGTGACAAAATAAATGAACAT 57.922 29.630 0.96 0.00 36.96 2.71
2156 2165 3.691342 CGGCTGGGGACTCGAACA 61.691 66.667 0.00 0.00 0.00 3.18
2200 2209 1.550130 TTAGGGCTGCGCTGGTAACT 61.550 55.000 27.01 3.65 37.61 2.24
2246 2255 4.080919 TGACATGAGTAGGGAAGGAATGTG 60.081 45.833 0.00 0.00 0.00 3.21
2359 2370 3.628832 AATTTTGGAGGGTTGGAAGGA 57.371 42.857 0.00 0.00 0.00 3.36
2511 2527 1.128188 AAACGGAGGGCTTCTCACCT 61.128 55.000 9.20 0.00 44.19 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 8.922058 AGATTTCAATGATGCTCACATAAAAC 57.078 30.769 0.00 0.00 36.35 2.43
216 219 8.376270 GTTTATCCTATAGGTTCTACTTGGCAT 58.624 37.037 18.51 2.89 36.34 4.40
341 344 9.801714 CAATTTGTTTATTGATCAGAAGCAAAC 57.198 29.630 23.96 17.34 36.52 2.93
405 408 7.359765 GCAATCTGTAACTAACGCAAAGTTCTA 60.360 37.037 1.38 0.00 43.06 2.10
410 413 5.283060 AGCAATCTGTAACTAACGCAAAG 57.717 39.130 0.00 0.00 0.00 2.77
470 473 7.604927 AGATGCATTGAAATAAGCAAACAACAT 59.395 29.630 0.00 0.00 40.76 2.71
569 572 6.833933 ACCACTAAGGGCAAAAGGATAATTAG 59.166 38.462 0.00 0.00 43.89 1.73
603 606 2.751806 GCATCTGAGGGAAAAACTGAGG 59.248 50.000 0.00 0.00 0.00 3.86
635 638 1.276989 CACGGACTAGGGGCAAAACTA 59.723 52.381 0.00 0.00 0.00 2.24
770 773 3.177884 TGGGTCCTGCAAGCCACT 61.178 61.111 5.20 0.00 41.74 4.00
812 815 0.611200 TATAGCACACACCCGCAACT 59.389 50.000 0.00 0.00 0.00 3.16
967 970 2.552585 GAACGGGATCTCAACGCCGA 62.553 60.000 12.02 0.00 0.00 5.54
1085 1088 3.417275 CTCCGATCAACGCTCGCCT 62.417 63.158 0.00 0.00 41.07 5.52
1296 1299 3.005554 CCATTCGTCATGCTCTTCTTGT 58.994 45.455 0.00 0.00 0.00 3.16
1463 1466 8.043710 CCCAAAAGTATTTGCAAATGGGTATTA 58.956 33.333 30.43 9.45 43.11 0.98
1968 1977 1.460689 TGGGTTCGAGTCCCCAGTT 60.461 57.895 20.23 0.00 46.06 3.16
1969 1978 2.203182 TGGGTTCGAGTCCCCAGT 59.797 61.111 20.23 0.00 46.06 4.00
2200 2209 1.483827 CTCTTGCCATCTGTCCTAGCA 59.516 52.381 0.00 0.00 0.00 3.49
2230 2239 6.098409 CACTATGTACACATTCCTTCCCTACT 59.902 42.308 0.00 0.00 37.76 2.57
2246 2255 8.311650 ACAAATTTCACAGTCTCACTATGTAC 57.688 34.615 0.00 0.00 0.00 2.90
2359 2370 3.980775 GCAGTGCAAACATACGTTTTCAT 59.019 39.130 11.09 0.00 42.82 2.57
2511 2527 4.531854 TGTGGTTGTCATTCAAAAGAGGA 58.468 39.130 0.00 0.00 37.81 3.71


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

AutoCloner maintained by Alex Coulton.