Multiple sequence alignment - TraesCS2B01G496100

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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 TraesCS2B01G496100 chr2B 100.000 2549 0 0 1 2549 692955329 692957877 0 4708
1 TraesCS2B01G496100 chr2B 95.785 1993 77 6 560 2549 458657414 458659402 0 3208
2 TraesCS2B01G496100 chr2B 95.585 1993 76 9 566 2549 492636662 492638651 0 3182
3 TraesCS2B01G496100 chr4A 96.185 1992 70 6 560 2549 705529259 705527272 0 3253
4 TraesCS2B01G496100 chr7B 96.088 1994 71 6 561 2549 720989199 720987208 0 3243
5 TraesCS2B01G496100 chr7B 93.110 566 39 0 3 568 413480417 413480982 0 830
6 TraesCS2B01G496100 chr1B 95.982 1991 71 7 566 2549 581717564 581715576 0 3225
7 TraesCS2B01G496100 chr1B 95.919 1985 74 6 568 2549 671392209 671394189 0 3210
8 TraesCS2B01G496100 chr1B 95.915 1983 75 5 569 2549 520844119 520842141 0 3208
9 TraesCS2B01G496100 chr1B 94.014 568 33 1 1 568 302877335 302877901 0 859
10 TraesCS2B01G496100 chr3B 95.976 1988 75 5 566 2549 108092315 108090329 0 3223
11 TraesCS2B01G496100 chr3B 93.134 568 39 0 1 568 432816325 432815758 0 833
12 TraesCS2B01G496100 chr3B 92.606 568 42 0 1 568 394001299 394000732 0 817
13 TraesCS2B01G496100 chr5B 95.785 1993 79 4 560 2549 497276157 497278147 0 3210
14 TraesCS2B01G496100 chr6B 94.014 568 34 0 1 568 645313930 645313363 0 861
15 TraesCS2B01G496100 chr6B 92.782 568 41 0 1 568 475342625 475343192 0 822
16 TraesCS2B01G496100 chrUn 93.310 568 38 0 1 568 396329805 396329238 0 839
17 TraesCS2B01G496100 chr2D 93.863 554 34 0 15 568 39544957 39544404 0 835
18 TraesCS2B01G496100 chr6D 92.958 568 40 0 1 568 461034582 461035149 0 828


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 TraesCS2B01G496100 chr2B 692955329 692957877 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F3 2548
1 TraesCS2B01G496100 chr2B 458657414 458659402 1988 False 3208 3208 95.785 560 2549 1 chr2B.!!$F1 1989
2 TraesCS2B01G496100 chr2B 492636662 492638651 1989 False 3182 3182 95.585 566 2549 1 chr2B.!!$F2 1983
3 TraesCS2B01G496100 chr4A 705527272 705529259 1987 True 3253 3253 96.185 560 2549 1 chr4A.!!$R1 1989
4 TraesCS2B01G496100 chr7B 720987208 720989199 1991 True 3243 3243 96.088 561 2549 1 chr7B.!!$R1 1988
5 TraesCS2B01G496100 chr7B 413480417 413480982 565 False 830 830 93.110 3 568 1 chr7B.!!$F1 565
6 TraesCS2B01G496100 chr1B 581715576 581717564 1988 True 3225 3225 95.982 566 2549 1 chr1B.!!$R2 1983
7 TraesCS2B01G496100 chr1B 671392209 671394189 1980 False 3210 3210 95.919 568 2549 1 chr1B.!!$F2 1981
8 TraesCS2B01G496100 chr1B 520842141 520844119 1978 True 3208 3208 95.915 569 2549 1 chr1B.!!$R1 1980
9 TraesCS2B01G496100 chr1B 302877335 302877901 566 False 859 859 94.014 1 568 1 chr1B.!!$F1 567
10 TraesCS2B01G496100 chr3B 108090329 108092315 1986 True 3223 3223 95.976 566 2549 1 chr3B.!!$R1 1983
11 TraesCS2B01G496100 chr3B 432815758 432816325 567 True 833 833 93.134 1 568 1 chr3B.!!$R3 567
12 TraesCS2B01G496100 chr3B 394000732 394001299 567 True 817 817 92.606 1 568 1 chr3B.!!$R2 567
13 TraesCS2B01G496100 chr5B 497276157 497278147 1990 False 3210 3210 95.785 560 2549 1 chr5B.!!$F1 1989
14 TraesCS2B01G496100 chr6B 645313363 645313930 567 True 861 861 94.014 1 568 1 chr6B.!!$R1 567
15 TraesCS2B01G496100 chr6B 475342625 475343192 567 False 822 822 92.782 1 568 1 chr6B.!!$F1 567
16 TraesCS2B01G496100 chrUn 396329238 396329805 567 True 839 839 93.310 1 568 1 chrUn.!!$R1 567
17 TraesCS2B01G496100 chr2D 39544404 39544957 553 True 835 835 93.863 15 568 1 chr2D.!!$R1 553
18 TraesCS2B01G496100 chr6D 461034582 461035149 567 False 828 828 92.958 1 568 1 chr6D.!!$F1 567

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
233 234 0.041535 TTCTTGCTGCCCCCATTGAT 59.958 50.0 0.00 0.0 0.0 2.57 F
474 475 0.751277 TCCCATTATTGCGGCCAGTG 60.751 55.0 2.24 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1103 1107 0.105964 CCTCGGTGTGTGAGAAACCA 59.894 55.0 0.0 0.0 35.43 3.67 R
2409 2601 0.107831 ACTAAACCAAGTGCCGCTCA 59.892 50.0 0.0 0.0 0.00 4.26 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
133 134 7.147949 GGCCATCCCTTTATATCAAATGATGAG 60.148 40.741 0.00 0.10 42.53 2.90
195 196 3.066481 GGCATTTGAGGATCTGAAGAAGC 59.934 47.826 0.00 0.00 34.92 3.86
213 214 3.315949 AGTTAGCCGAACCGCCCA 61.316 61.111 0.00 0.00 39.02 5.36
233 234 0.041535 TTCTTGCTGCCCCCATTGAT 59.958 50.000 0.00 0.00 0.00 2.57
248 249 4.202182 CCCATTGATAAGGAACCATTGCTG 60.202 45.833 0.00 0.00 0.00 4.41
255 256 7.342581 TGATAAGGAACCATTGCTGTTATACA 58.657 34.615 0.00 0.00 0.00 2.29
259 260 4.499696 GGAACCATTGCTGTTATACATGGC 60.500 45.833 0.00 0.00 0.00 4.40
266 267 3.876914 TGCTGTTATACATGGCTGCTAAC 59.123 43.478 0.00 0.00 0.00 2.34
269 270 3.131396 GTTATACATGGCTGCTAACGCT 58.869 45.455 0.00 0.00 36.97 5.07
305 306 2.829206 CGTTGTGGTGGAGCGCAAA 61.829 57.895 11.47 0.00 0.00 3.68
318 319 0.955919 GCGCAAAGAGGCAGGTAAGT 60.956 55.000 0.30 0.00 0.00 2.24
399 400 2.578021 AGATACCCACATTGGCAGAAGT 59.422 45.455 0.00 0.00 35.79 3.01
409 410 2.949177 TGGCAGAAGTTGGTGTATGT 57.051 45.000 0.00 0.00 0.00 2.29
469 470 1.290009 GCCATCCCATTATTGCGGC 59.710 57.895 0.00 0.00 0.00 6.53
474 475 0.751277 TCCCATTATTGCGGCCAGTG 60.751 55.000 2.24 0.00 0.00 3.66
503 504 7.339177 TCCATTGGGAGATATCATTCAGAAT 57.661 36.000 5.32 0.00 38.64 2.40
505 506 8.546322 TCCATTGGGAGATATCATTCAGAATAG 58.454 37.037 5.32 0.00 38.64 1.73
511 512 6.900186 GGAGATATCATTCAGAATAGGGAGGA 59.100 42.308 5.32 0.00 0.00 3.71
603 604 4.463050 TTTTCCCTTAGTGGTGTCCATT 57.537 40.909 0.00 0.00 35.28 3.16
647 648 3.196463 CAAATTGTGCTCAGTTTTGCCA 58.804 40.909 6.53 0.00 32.55 4.92
858 862 2.261671 GACAGCGACGGTGACCAT 59.738 61.111 31.66 10.81 34.87 3.55
937 941 3.774528 CTAGCTGTGGAGGGCGCA 61.775 66.667 10.83 0.00 0.00 6.09
1036 1040 2.662596 GCACCACCTCACGGATGA 59.337 61.111 0.00 0.00 0.00 2.92
1103 1107 1.819632 GGGCGAGCGTTGATTGGAT 60.820 57.895 0.00 0.00 0.00 3.41
1285 1307 1.078567 GCTCTGGCCAAGACTCTGG 60.079 63.158 7.01 0.00 39.71 3.86
1495 1671 5.938438 TTGCAAATACTTTTGGGCATTTC 57.062 34.783 0.00 0.00 42.09 2.17
1537 1713 8.402798 ACTGGTTGTGATGTTGAAAATGTATA 57.597 30.769 0.00 0.00 0.00 1.47
2041 2226 4.410400 GGGCTGCGCTGGTAACCT 62.410 66.667 16.47 0.00 0.00 3.50
2055 2240 3.271225 TGGTAACCTCTAGGACAGATGGA 59.729 47.826 2.23 0.00 38.94 3.41
2057 2242 4.902448 GGTAACCTCTAGGACAGATGGAAT 59.098 45.833 2.23 0.00 38.94 3.01
2076 2261 4.567747 GGAATGAGTTTGACATGGGTAGGT 60.568 45.833 0.00 0.00 0.00 3.08
2103 2288 7.786030 AGCAATGTATACATAGTGAGACTGTT 58.214 34.615 18.56 6.18 35.10 3.16
2113 2298 8.324163 ACATAGTGAGACTGTTAAATTTGTCC 57.676 34.615 0.00 0.00 0.00 4.02
2322 2514 0.938008 TGAATGTTTGCACACGCGTA 59.062 45.000 13.44 0.00 42.97 4.42
2409 2601 0.174617 CTGCCACGTGGTTTTGGTTT 59.825 50.000 33.92 0.00 37.57 3.27
2413 2605 1.555477 CACGTGGTTTTGGTTTGAGC 58.445 50.000 7.95 0.00 0.00 4.26
2443 2635 3.746492 GGTTTAGTGTTAGAGTGGCACTG 59.254 47.826 27.45 0.00 42.60 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.533491 TGATACACGCCGGTTTAGCT 59.467 50.000 1.90 0.00 0.00 3.32
176 177 5.176741 ACTGCTTCTTCAGATCCTCAAAT 57.823 39.130 0.00 0.00 37.51 2.32
213 214 0.041535 TCAATGGGGGCAGCAAGAAT 59.958 50.000 0.00 0.00 0.00 2.40
233 234 6.545666 CCATGTATAACAGCAATGGTTCCTTA 59.454 38.462 0.00 0.00 0.00 2.69
248 249 3.521524 GCGTTAGCAGCCATGTATAAC 57.478 47.619 0.00 0.00 44.35 1.89
288 289 1.008538 CTTTGCGCTCCACCACAAC 60.009 57.895 9.73 0.00 0.00 3.32
305 306 3.488363 CGGATACTACTTACCTGCCTCT 58.512 50.000 0.00 0.00 0.00 3.69
366 367 5.692115 TGTGGGTATCTCTGCTTTGATTA 57.308 39.130 0.00 0.00 0.00 1.75
367 368 4.574674 TGTGGGTATCTCTGCTTTGATT 57.425 40.909 0.00 0.00 0.00 2.57
399 400 7.526142 TTGCCATAAAAACTACATACACCAA 57.474 32.000 0.00 0.00 0.00 3.67
409 410 3.074675 TCCGGCTTGCCATAAAAACTA 57.925 42.857 12.45 0.00 0.00 2.24
437 438 1.683385 GGATGGCCCTGAAAGTATTGC 59.317 52.381 0.00 0.00 0.00 3.56
469 470 3.136123 CCAATGGAGCGGCACTGG 61.136 66.667 1.45 0.00 0.00 4.00
503 504 2.279073 CGGCCAGTCTCCTCCCTA 59.721 66.667 2.24 0.00 0.00 3.53
511 512 2.185310 CTTAGCAACCCGGCCAGTCT 62.185 60.000 2.24 0.00 0.00 3.24
585 586 2.554344 GCAAATGGACACCACTAAGGGA 60.554 50.000 0.00 0.00 43.89 4.20
603 604 1.133823 TCTGAGGGCAAAACTGAGCAA 60.134 47.619 0.00 0.00 0.00 3.91
647 648 2.258591 CAGTGCGCACGGACTAGT 59.741 61.111 32.96 12.72 44.89 2.57
858 862 4.056125 CCGTGCTCTCTGTCGCCA 62.056 66.667 0.00 0.00 0.00 5.69
912 916 0.835941 CTCCACAGCTAGCTTCCCAT 59.164 55.000 16.46 0.00 0.00 4.00
937 941 2.685380 AGCTAGCTTCCCACCGCT 60.685 61.111 12.68 0.00 40.15 5.52
1099 1103 1.542328 CGGTGTGTGAGAAACCATCCA 60.542 52.381 0.00 0.00 33.30 3.41
1103 1107 0.105964 CCTCGGTGTGTGAGAAACCA 59.894 55.000 0.00 0.00 35.43 3.67
1285 1307 5.362556 TGCTCTTCTTGCAGTTCATTTAC 57.637 39.130 0.00 0.00 35.31 2.01
1495 1671 3.321111 ACCAGTGCGATTACCATACCTAG 59.679 47.826 0.00 0.00 0.00 3.02
1521 1697 9.241317 CATGCCTTTCTATACATTTTCAACATC 57.759 33.333 0.00 0.00 0.00 3.06
1537 1713 5.393068 TCCTCCATAATTCATGCCTTTCT 57.607 39.130 0.00 0.00 32.84 2.52
1668 1849 9.978044 CTGAATTCTTCATTTCTTCTCCTTTTT 57.022 29.630 7.05 0.00 39.30 1.94
2041 2226 5.721480 TCAAACTCATTCCATCTGTCCTAGA 59.279 40.000 0.00 0.00 40.37 2.43
2055 2240 4.657814 ACCTACCCATGTCAAACTCATT 57.342 40.909 0.00 0.00 0.00 2.57
2057 2242 4.564821 GCTTACCTACCCATGTCAAACTCA 60.565 45.833 0.00 0.00 0.00 3.41
2076 2261 8.914011 ACAGTCTCACTATGTATACATTGCTTA 58.086 33.333 22.90 9.44 37.76 3.09
2298 2490 2.052891 CGTGTGCAAACATTCATGGTG 58.947 47.619 8.00 0.00 0.00 4.17
2302 2494 0.310543 ACGCGTGTGCAAACATTCAT 59.689 45.000 12.93 0.00 42.97 2.57
2322 2514 3.603158 AAACAAAGGAAAACCACGCTT 57.397 38.095 0.00 0.00 0.00 4.68
2325 2517 2.996621 TGCAAAACAAAGGAAAACCACG 59.003 40.909 0.00 0.00 0.00 4.94
2409 2601 0.107831 ACTAAACCAAGTGCCGCTCA 59.892 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.