Multiple sequence alignment - TraesCS2D01G146900

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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 TraesCS2D01G146900 chr2D 100.000 2471 0 0 1 2471 87947935 87950405 0.000000e+00 4564
1 TraesCS2D01G146900 chr2D 97.129 209 5 1 2263 2471 630079436 630079229 3.910000e-93 351
2 TraesCS2D01G146900 chr6D 96.200 2263 73 11 1 2257 257991974 257994229 0.000000e+00 3690
3 TraesCS2D01G146900 chr6D 96.670 1892 53 8 372 2257 305380477 305378590 0.000000e+00 3136
4 TraesCS2D01G146900 chr6D 96.396 222 6 2 2251 2471 257994259 257994479 5.020000e-97 364
5 TraesCS2D01G146900 chr6D 96.279 215 7 1 2257 2471 305378553 305378340 3.910000e-93 351
6 TraesCS2D01G146900 chr6D 96.172 209 7 1 2261 2469 356211460 356211253 8.460000e-90 340
7 TraesCS2D01G146900 chr5D 95.723 2268 84 12 1 2261 36561907 36564168 0.000000e+00 3639
8 TraesCS2D01G146900 chr5D 95.495 222 7 3 2251 2471 36564195 36564414 3.910000e-93 351
9 TraesCS2D01G146900 chr2B 92.032 2510 145 38 3 2469 655694285 655691788 0.000000e+00 3476
10 TraesCS2D01G146900 chr4B 91.760 2512 148 43 3 2469 15516594 15519091 0.000000e+00 3437
11 TraesCS2D01G146900 chr3B 91.600 2512 150 43 3 2469 60566604 60569099 0.000000e+00 3413
12 TraesCS2D01G146900 chr3D 91.285 2272 161 32 1 2257 305617875 305615626 0.000000e+00 3064
13 TraesCS2D01G146900 chr3D 95.283 212 9 1 2260 2471 305615587 305615377 3.940000e-88 335
14 TraesCS2D01G146900 chr5A 89.108 2286 189 44 1 2257 671452820 671455074 0.000000e+00 2787
15 TraesCS2D01G146900 chr5A 85.011 874 63 30 1 837 153575809 153574967 0.000000e+00 826
16 TraesCS2D01G146900 chr5A 90.620 597 35 16 49 627 693842569 693843162 0.000000e+00 773
17 TraesCS2D01G146900 chr1B 87.489 2270 226 43 1 2257 476681250 476683474 0.000000e+00 2566
18 TraesCS2D01G146900 chr3A 94.018 652 31 8 1 648 669776037 669775390 0.000000e+00 981
19 TraesCS2D01G146900 chr1D 98.140 215 4 0 2257 2471 383348646 383348432 2.320000e-100 375
20 TraesCS2D01G146900 chr7D 96.226 212 7 1 2260 2471 560826206 560825996 1.820000e-91 346
21 TraesCS2D01G146900 chr7A 94.144 222 10 3 2251 2471 41972681 41972900 3.940000e-88 335


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 TraesCS2D01G146900 chr2D 87947935 87950405 2470 False 4564.0 4564 100.0000 1 2471 1 chr2D.!!$F1 2470
1 TraesCS2D01G146900 chr6D 257991974 257994479 2505 False 2027.0 3690 96.2980 1 2471 2 chr6D.!!$F1 2470
2 TraesCS2D01G146900 chr6D 305378340 305380477 2137 True 1743.5 3136 96.4745 372 2471 2 chr6D.!!$R2 2099
3 TraesCS2D01G146900 chr5D 36561907 36564414 2507 False 1995.0 3639 95.6090 1 2471 2 chr5D.!!$F1 2470
4 TraesCS2D01G146900 chr2B 655691788 655694285 2497 True 3476.0 3476 92.0320 3 2469 1 chr2B.!!$R1 2466
5 TraesCS2D01G146900 chr4B 15516594 15519091 2497 False 3437.0 3437 91.7600 3 2469 1 chr4B.!!$F1 2466
6 TraesCS2D01G146900 chr3B 60566604 60569099 2495 False 3413.0 3413 91.6000 3 2469 1 chr3B.!!$F1 2466
7 TraesCS2D01G146900 chr3D 305615377 305617875 2498 True 1699.5 3064 93.2840 1 2471 2 chr3D.!!$R1 2470
8 TraesCS2D01G146900 chr5A 671452820 671455074 2254 False 2787.0 2787 89.1080 1 2257 1 chr5A.!!$F1 2256
9 TraesCS2D01G146900 chr5A 153574967 153575809 842 True 826.0 826 85.0110 1 837 1 chr5A.!!$R1 836
10 TraesCS2D01G146900 chr5A 693842569 693843162 593 False 773.0 773 90.6200 49 627 1 chr5A.!!$F2 578
11 TraesCS2D01G146900 chr1B 476681250 476683474 2224 False 2566.0 2566 87.4890 1 2257 1 chr1B.!!$F1 2256
12 TraesCS2D01G146900 chr3A 669775390 669776037 647 True 981.0 981 94.0180 1 648 1 chr3A.!!$R1 647

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
774 871 0.821711 GGTGTGCTTGGGTTGCTGTA 60.822 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2559 1.136891 TCATACGACCTGCTGACATGG 59.863 52.381 0.0 0.0 0.0 3.66 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
152 173 7.385267 AGTTGCCAAGATACAATTGCAAATTA 58.615 30.769 1.71 0.00 30.87 1.40
218 244 7.136822 AGCCATATACCAACAACTATCTCAA 57.863 36.000 0.00 0.00 0.00 3.02
238 294 5.328691 TCAACTGCAAAACGTTACTTCAAG 58.671 37.500 0.00 0.00 0.00 3.02
666 762 3.576078 TGACTTGCCTGGTTATATGGG 57.424 47.619 0.00 0.00 0.00 4.00
709 805 8.081633 TGCACTTTGAATTTCCTAGTTATGTTG 58.918 33.333 0.00 0.00 0.00 3.33
774 871 0.821711 GGTGTGCTTGGGTTGCTGTA 60.822 55.000 0.00 0.00 0.00 2.74
894 996 3.636300 TGAGCTATTTTTGGTGTGCTTGT 59.364 39.130 0.00 0.00 0.00 3.16
941 1043 5.995282 TGTATTTACTGTGCTACTTGCTTGT 59.005 36.000 0.00 0.00 43.37 3.16
1009 1111 7.765695 ATTAACAGGTTGACAATGATTGACT 57.234 32.000 12.80 0.00 0.00 3.41
1030 1132 3.063510 TGAATGAGGAACCAGCTGAAG 57.936 47.619 17.39 1.02 0.00 3.02
1040 1142 4.265073 GAACCAGCTGAAGATAATGGTGT 58.735 43.478 17.39 0.00 43.36 4.16
1136 1239 3.278668 AAGAGTCAATGCTGCTGCTAT 57.721 42.857 17.00 5.98 40.48 2.97
1210 1313 3.587797 GTACACAAGTACCTGCAGCTA 57.412 47.619 8.66 0.00 43.85 3.32
1272 1375 0.615331 CTGCAGGTGATACTGGTGGT 59.385 55.000 5.57 0.00 38.90 4.16
1295 1398 3.226777 CTGTTGGTAATGGTTTGGGTGA 58.773 45.455 0.00 0.00 0.00 4.02
1308 1411 5.170748 GGTTTGGGTGATGAAAATGATGAC 58.829 41.667 0.00 0.00 0.00 3.06
1468 1571 4.042271 ACCGGGGAGTTGATAAAACAAT 57.958 40.909 6.32 0.00 32.36 2.71
1498 1601 2.946329 TGCAACAAGTTTCGAAAGCCTA 59.054 40.909 11.66 0.00 0.00 3.93
1524 1627 0.625849 ATGACGGAGGGGCAGAAAAT 59.374 50.000 0.00 0.00 0.00 1.82
1792 1897 4.856801 CACCAAGGGATCCCGCCG 62.857 72.222 25.48 17.53 41.95 6.46
1851 1956 7.548097 TGCAATTTAACTACAGGTTTTGAACA 58.452 30.769 0.00 0.00 39.17 3.18
1854 1959 8.813282 CAATTTAACTACAGGTTTTGAACAACC 58.187 33.333 0.00 0.00 46.02 3.77
1902 2008 3.116096 AGAACCTGGACATGCCTACTA 57.884 47.619 0.00 0.00 37.63 1.82
1932 2040 4.887071 TGTTTCTTAGCCATCAACAAGTGT 59.113 37.500 0.00 0.00 0.00 3.55
1959 2068 3.713858 TTGCTTGAAACATGTCACTGG 57.286 42.857 0.00 0.00 0.00 4.00
2087 2200 5.737635 GCCTAATGTTTACCTGTTTGTTGCA 60.738 40.000 0.00 0.00 0.00 4.08
2207 2326 6.743575 ACAATAGTACTTGTTTCTGGATGC 57.256 37.500 0.00 0.00 35.90 3.91
2267 2424 2.877097 TGCATAGTTTTCCTGAGGCA 57.123 45.000 0.00 0.00 0.00 4.75
2333 2490 1.938016 GCATTTGAGTTGCCTTGCTGG 60.938 52.381 0.00 0.00 33.95 4.85
2374 2531 5.392767 TTTTGGCACTGTTTTTGTGTAGA 57.607 34.783 0.00 0.00 37.70 2.59
2401 2559 2.749621 GGATTGACCACCATTGTGACTC 59.250 50.000 0.00 0.00 45.76 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 244 4.393680 TGTCTTGAAGTAACGTTTTGCAGT 59.606 37.500 5.91 0.0 0.00 4.40
238 294 6.316140 TGTGTTTTGGATATGCTCAGTATGTC 59.684 38.462 0.00 0.0 37.40 3.06
350 422 6.774673 TGGGCATGATCGGTCTTTTATATTA 58.225 36.000 0.00 0.0 0.00 0.98
362 434 0.877071 GCAGTTATGGGCATGATCGG 59.123 55.000 0.00 0.0 0.00 4.18
559 639 9.845740 TCATGTTGTACATATAACATAGGCTTT 57.154 29.630 12.08 0.0 43.25 3.51
666 762 2.098117 GTGCACTATCAGGCAATCCAAC 59.902 50.000 10.32 0.0 42.45 3.77
739 836 4.223700 AGCACACCAGATTCACAAGATAGA 59.776 41.667 0.00 0.0 0.00 1.98
774 871 6.925165 CACACTAAATTCAGGAAGCAAACAAT 59.075 34.615 0.00 0.0 0.00 2.71
894 996 2.358957 CAAGCCAATAGCACAGCTACA 58.641 47.619 0.14 0.0 44.24 2.74
941 1043 1.871418 AGCAAGTCAGCAGAGGGATA 58.129 50.000 0.00 0.0 36.85 2.59
987 1089 6.770303 TCAAGTCAATCATTGTCAACCTGTTA 59.230 34.615 0.00 0.0 0.00 2.41
1009 1111 3.072915 TCTTCAGCTGGTTCCTCATTCAA 59.927 43.478 15.13 0.0 0.00 2.69
1040 1142 5.411361 GCATGTTGTGTACAGTAGAATGGAA 59.589 40.000 0.00 0.0 40.83 3.53
1136 1239 3.135348 CCCATCTGTCTCCATTGCTTCTA 59.865 47.826 0.00 0.0 0.00 2.10
1210 1313 0.108207 GCATCACTCCCAGCTGCTAT 59.892 55.000 8.66 0.0 0.00 2.97
1272 1375 4.141228 TCACCCAAACCATTACCAACAGTA 60.141 41.667 0.00 0.0 0.00 2.74
1295 1398 4.460382 ACCAAGCTTCGTCATCATTTTCAT 59.540 37.500 0.00 0.0 0.00 2.57
1308 1411 2.328099 GGGCTGTGACCAAGCTTCG 61.328 63.158 0.00 0.0 0.00 3.79
1498 1601 0.394352 GCCCCTCCGTCATCAACATT 60.394 55.000 0.00 0.0 0.00 2.71
1524 1627 6.191657 ACAATGTCATCTAGCATGGGAATA 57.808 37.500 0.00 0.0 0.00 1.75
1669 1774 7.062322 TGCCATCTATTACCTTCACAATCATT 58.938 34.615 0.00 0.0 0.00 2.57
1739 1844 5.359576 ACTTAGTCAAACATGGCTTGTCAAA 59.640 36.000 6.48 0.0 37.68 2.69
1813 1918 9.226345 GTAGTTAAATTGCAGTTATGAAGATGC 57.774 33.333 0.00 0.0 39.14 3.91
1902 2008 4.460263 TGATGGCTAAGAAACACACAACT 58.540 39.130 0.00 0.0 0.00 3.16
1932 2040 5.978919 GTGACATGTTTCAAGCAAAATCAGA 59.021 36.000 0.00 0.0 0.00 3.27
2087 2200 3.005791 GGCAAGTAGGAACTTTGCATTGT 59.994 43.478 10.16 0.0 43.60 2.71
2148 2266 6.352516 ACAAAGAGACTAATCATAGGCAAGG 58.647 40.000 0.00 0.0 39.88 3.61
2207 2326 3.270027 TCAATCATAGGCAAGTTGACCG 58.730 45.455 4.68 0.0 0.00 4.79
2333 2490 8.878769 TGCCAAAAATAGTTTCTTTTCTGTTTC 58.121 29.630 0.00 0.0 0.00 2.78
2401 2559 1.136891 TCATACGACCTGCTGACATGG 59.863 52.381 0.00 0.0 0.00 3.66


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

AutoCloner maintained by Alex Coulton.