Multiple sequence alignment - TraesCS1B01G281900

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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 TraesCS1B01G281900 chr1B 100.000 2549 0 0 1 2549 490564128 490561580 0 4708
1 TraesCS1B01G281900 chr1B 96.177 1988 69 7 566 2549 232740733 232742717 0 3243
2 TraesCS1B01G281900 chr1B 96.133 1991 70 7 564 2549 663786492 663788480 0 3243
3 TraesCS1B01G281900 chr7B 96.427 1987 63 7 567 2549 718488474 718486492 0 3269
4 TraesCS1B01G281900 chr3B 96.278 1988 65 7 565 2549 129332739 129330758 0 3253
5 TraesCS1B01G281900 chr2B 96.276 1987 64 8 567 2549 543889470 543887490 0 3251
6 TraesCS1B01G281900 chr2B 96.225 1987 65 8 567 2549 544319641 544317661 0 3245
7 TraesCS1B01G281900 chr2B 95.894 1997 71 9 562 2549 602077190 602075196 0 3223
8 TraesCS1B01G281900 chr2B 92.945 567 39 1 1 566 526963320 526962754 0 824
9 TraesCS1B01G281900 chr2B 91.901 568 44 1 1 566 589714179 589713612 0 793
10 TraesCS1B01G281900 chr2B 91.740 569 43 3 1 566 100407022 100406455 0 787
11 TraesCS1B01G281900 chr2B 91.373 568 47 1 1 566 387999780 387999213 0 776
12 TraesCS1B01G281900 chr5B 96.179 1989 68 7 567 2549 269389473 269391459 0 3245
13 TraesCS1B01G281900 chr5B 96.086 1993 68 9 562 2547 446193260 446191271 0 3240
14 TraesCS1B01G281900 chr5B 93.463 566 37 0 1 566 474025108 474024543 0 841
15 TraesCS1B01G281900 chr5B 90.845 568 50 1 1 566 407955585 407955018 0 760
16 TraesCS1B01G281900 chr6B 93.110 566 38 1 1 566 623250596 623250032 0 828
17 TraesCS1B01G281900 chr4B 92.430 568 41 1 1 566 540222311 540222878 0 809
18 TraesCS1B01G281900 chr4B 92.430 568 41 1 1 566 563461445 563462012 0 809


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 TraesCS1B01G281900 chr1B 490561580 490564128 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R1 2548
1 TraesCS1B01G281900 chr1B 232740733 232742717 1984 False 3243 3243 96.177 566 2549 1 chr1B.!!$F1 1983
2 TraesCS1B01G281900 chr1B 663786492 663788480 1988 False 3243 3243 96.133 564 2549 1 chr1B.!!$F2 1985
3 TraesCS1B01G281900 chr7B 718486492 718488474 1982 True 3269 3269 96.427 567 2549 1 chr7B.!!$R1 1982
4 TraesCS1B01G281900 chr3B 129330758 129332739 1981 True 3253 3253 96.278 565 2549 1 chr3B.!!$R1 1984
5 TraesCS1B01G281900 chr2B 543887490 543889470 1980 True 3251 3251 96.276 567 2549 1 chr2B.!!$R4 1982
6 TraesCS1B01G281900 chr2B 544317661 544319641 1980 True 3245 3245 96.225 567 2549 1 chr2B.!!$R5 1982
7 TraesCS1B01G281900 chr2B 602075196 602077190 1994 True 3223 3223 95.894 562 2549 1 chr2B.!!$R7 1987
8 TraesCS1B01G281900 chr2B 526962754 526963320 566 True 824 824 92.945 1 566 1 chr2B.!!$R3 565
9 TraesCS1B01G281900 chr2B 589713612 589714179 567 True 793 793 91.901 1 566 1 chr2B.!!$R6 565
10 TraesCS1B01G281900 chr2B 100406455 100407022 567 True 787 787 91.740 1 566 1 chr2B.!!$R1 565
11 TraesCS1B01G281900 chr2B 387999213 387999780 567 True 776 776 91.373 1 566 1 chr2B.!!$R2 565
12 TraesCS1B01G281900 chr5B 269389473 269391459 1986 False 3245 3245 96.179 567 2549 1 chr5B.!!$F1 1982
13 TraesCS1B01G281900 chr5B 446191271 446193260 1989 True 3240 3240 96.086 562 2547 1 chr5B.!!$R2 1985
14 TraesCS1B01G281900 chr5B 474024543 474025108 565 True 841 841 93.463 1 566 1 chr5B.!!$R3 565
15 TraesCS1B01G281900 chr5B 407955018 407955585 567 True 760 760 90.845 1 566 1 chr5B.!!$R1 565
16 TraesCS1B01G281900 chr6B 623250032 623250596 564 True 828 828 93.110 1 566 1 chr6B.!!$R1 565
17 TraesCS1B01G281900 chr4B 540222311 540222878 567 False 809 809 92.430 1 566 1 chr4B.!!$F1 565
18 TraesCS1B01G281900 chr4B 563461445 563462012 567 False 809 809 92.430 1 566 1 chr4B.!!$F2 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
321 324 0.178903 AGCCCCTGAGACACTGGTTA 60.179 55.0 0.0 0.0 36.11 2.85 F
324 327 0.246635 CCCTGAGACACTGGTTACCG 59.753 60.0 0.0 0.0 36.11 4.02 F
1119 1122 0.472471 GGAGGGTTTCTCACACACCA 59.528 55.0 0.0 0.0 44.19 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1156 2.174854 CCCCGATTCTTACCCCATTCTT 59.825 50.000 0.00 0.0 0.0 2.52 R
1498 1501 3.055385 ACAACCAGTGCGATTACCATACT 60.055 43.478 0.00 0.0 0.0 2.12 R
2416 2432 6.783708 ATCCTAAACCAAGTGAGACTCTAG 57.216 41.667 3.68 0.0 0.0 2.43 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
96 97 1.520666 GGGATTGTCCGTCACCGAT 59.479 57.895 0.00 0.0 37.43 4.18
146 147 1.063806 GCAACTATATCAGAGGCGCG 58.936 55.000 0.00 0.0 0.00 6.86
291 294 4.485554 CACGCTAGGTGTGCTCTC 57.514 61.111 0.00 0.0 41.89 3.20
314 317 3.462205 TGTAGATAGTAGCCCCTGAGACA 59.538 47.826 0.00 0.0 0.00 3.41
321 324 0.178903 AGCCCCTGAGACACTGGTTA 60.179 55.000 0.00 0.0 36.11 2.85
324 327 0.246635 CCCTGAGACACTGGTTACCG 59.753 60.000 0.00 0.0 36.11 4.02
368 371 6.789457 AGGATCATACTCCCAAGTAATGATCA 59.211 38.462 19.58 0.0 43.73 2.92
399 402 1.954382 TGTGCAGACGAGTAAGTGTCT 59.046 47.619 0.00 0.0 45.98 3.41
404 407 1.269998 AGACGAGTAAGTGTCTGGTGC 59.730 52.381 0.00 0.0 43.52 5.01
456 459 1.642037 CGACAGCTTGATGTGGCAGG 61.642 60.000 0.00 0.0 32.25 4.85
505 508 1.754803 CTTGACGAGGCACAGGGTATA 59.245 52.381 0.00 0.0 0.00 1.47
511 514 3.244215 ACGAGGCACAGGGTATATGATTG 60.244 47.826 0.00 0.0 0.00 2.67
551 554 7.861372 CAGCAAATATTTTAAGAGGAGCATGAG 59.139 37.037 0.00 0.0 0.00 2.90
601 604 1.072266 TGCCCTTAGTGGTGTCCATT 58.928 50.000 0.00 0.0 35.28 3.16
628 631 5.115480 TCAGTTTTTCCCTCAAATGCAAAC 58.885 37.500 0.00 0.0 0.00 2.93
845 848 2.074547 GCTATATTAGCGGGCGACAA 57.925 50.000 0.00 0.0 42.62 3.18
849 852 1.947597 TATTAGCGGGCGACAACGGT 61.948 55.000 0.00 0.0 43.70 4.83
908 911 2.223782 GCGAGAGAGTGAGAGCATGATT 60.224 50.000 0.00 0.0 0.00 2.57
1073 1076 1.202359 GGAGATGCCTGTCTTCGTCTC 60.202 57.143 0.00 0.0 41.99 3.36
1119 1122 0.472471 GGAGGGTTTCTCACACACCA 59.528 55.000 0.00 0.0 44.19 4.17
1153 1156 1.663388 CCGTTCTACGTGTGCAGCA 60.663 57.895 0.00 0.0 40.58 4.41
1237 1240 3.401033 TGATCTGTTCCGTGTTCATGT 57.599 42.857 0.00 0.0 0.00 3.21
1498 1501 6.291377 TGCAAATACTTTTGGGCATTTGTAA 58.709 32.000 7.49 0.0 42.09 2.41
1698 1701 7.879070 TGAGGAATTCAGAAACTTTTGATCAG 58.121 34.615 7.93 0.0 0.00 2.90
2260 2273 9.298250 GGAAGGAATGTATACATAGTGAGACTA 57.702 37.037 18.56 0.0 35.10 2.59
2475 2496 9.793252 ATAAATTTGCATGTTAGTTCATGACTC 57.207 29.630 10.28 0.0 45.41 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.744874 CTGGAAGCCGAATACTCCGA 59.255 55.000 0.00 0.0 0.00 4.55
96 97 3.299977 CCCGTCAGTGTGTCCGGA 61.300 66.667 0.00 0.0 43.01 5.14
187 188 1.698506 TCATTCAACCCGCTTTTGGT 58.301 45.000 0.00 0.0 37.85 3.67
291 294 4.076394 GTCTCAGGGGCTACTATCTACAG 58.924 52.174 0.00 0.0 0.00 2.74
314 317 3.387947 CTCGGGCCGGTAACCAGT 61.388 66.667 27.98 0.0 0.00 4.00
390 393 2.143925 GGTCAAGCACCAGACACTTAC 58.856 52.381 0.00 0.0 45.98 2.34
404 407 0.034059 AACTCAGCAGTCCGGTCAAG 59.966 55.000 0.00 0.0 29.93 3.02
433 436 0.957395 CCACATCAAGCTGTCGCCTT 60.957 55.000 0.00 0.0 36.60 4.35
456 459 4.505217 CAAGCGCGATGTCGGCAC 62.505 66.667 12.10 0.0 40.23 5.01
505 508 8.659925 TTGCTGACAATTTACAAAACAATCAT 57.340 26.923 0.00 0.0 0.00 2.45
601 604 4.740334 GCATTTGAGGGAAAAACTGAGCAA 60.740 41.667 0.00 0.0 0.00 3.91
781 784 3.073735 CGGCTCTCTGCTGGGTCT 61.074 66.667 0.00 0.0 44.06 3.85
849 852 1.744320 CTCTGTCACCGTGGTCACCA 61.744 60.000 0.00 0.0 0.00 4.17
861 864 4.724602 GCGCCGTGCTCTCTGTCA 62.725 66.667 0.00 0.0 41.73 3.58
908 911 3.003173 AGCTAGCTTCCCACCGCA 61.003 61.111 12.68 0.0 0.00 5.69
1119 1122 0.395312 ACGGACGATTGTGGTTCCTT 59.605 50.000 0.00 0.0 0.00 3.36
1153 1156 2.174854 CCCCGATTCTTACCCCATTCTT 59.825 50.000 0.00 0.0 0.00 2.52
1237 1240 3.439857 AAGAAAGAAGCATGCCACCTA 57.560 42.857 15.66 0.0 0.00 3.08
1425 1428 5.941788 TCAAGCTTCCTAACCTTCTTCTTT 58.058 37.500 0.00 0.0 0.00 2.52
1498 1501 3.055385 ACAACCAGTGCGATTACCATACT 60.055 43.478 0.00 0.0 0.00 2.12
1698 1701 7.922278 TGGAATAATTCATTAGCTGCATTTCAC 59.078 33.333 1.02 0.0 0.00 3.18
2416 2432 6.783708 ATCCTAAACCAAGTGAGACTCTAG 57.216 41.667 3.68 0.0 0.00 2.43



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

AutoCloner maintained by Alex Coulton.