Multiple sequence alignment - TraesCS6B01G293800

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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 TraesCS6B01G293800 chr6B 100.000 2549 0 0 1 2549 527994174 527991626 0.000000e+00 4708
1 TraesCS6B01G293800 chr3B 95.765 1960 73 8 593 2549 792939413 792941365 0.000000e+00 3151
2 TraesCS6B01G293800 chr3B 94.655 1983 73 18 598 2549 108092312 108090332 0.000000e+00 3044
3 TraesCS6B01G293800 chr5B 95.260 1962 81 8 589 2549 76431909 76429959 0.000000e+00 3097
4 TraesCS6B01G293800 chr5B 93.678 1993 79 27 590 2549 269389464 269391442 0.000000e+00 2939
5 TraesCS6B01G293800 chr5B 94.805 385 18 1 589 971 317969006 317969390 1.310000e-167 599
6 TraesCS6B01G293800 chr1B 94.962 1985 65 11 598 2549 581717561 581715579 0.000000e+00 3079
7 TraesCS6B01G293800 chr1B 95.197 1957 72 12 597 2549 189219499 189221437 0.000000e+00 3073
8 TraesCS6B01G293800 chr1B 93.995 383 22 1 589 971 307939697 307940078 1.700000e-161 579
9 TraesCS6B01G293800 chr2B 94.753 1982 70 5 598 2549 692955897 692957874 0.000000e+00 3053
10 TraesCS6B01G293800 chr2B 94.601 1982 72 15 598 2549 458657423 458659399 0.000000e+00 3035
11 TraesCS6B01G293800 chr2B 93.830 389 22 1 581 967 596962052 596962440 3.650000e-163 584
12 TraesCS6B01G293800 chr7B 94.456 1984 74 6 598 2549 720989190 720987211 0.000000e+00 3022
13 TraesCS6B01G293800 chr7B 94.791 1958 69 7 622 2549 708943230 708941276 0.000000e+00 3020
14 TraesCS6B01G293800 chr7B 94.041 386 20 2 584 967 677862803 677862419 1.310000e-162 582
15 TraesCS6B01G293800 chr3A 89.065 1134 88 10 591 1721 120653859 120654959 0.000000e+00 1375
16 TraesCS6B01G293800 chr5D 95.060 587 28 1 1 586 561437742 561437156 0.000000e+00 922
17 TraesCS6B01G293800 chr5D 94.872 585 30 0 2 586 211156958 211157542 0.000000e+00 915
18 TraesCS6B01G293800 chr2D 95.051 586 29 0 1 586 173030527 173029942 0.000000e+00 922
19 TraesCS6B01G293800 chr2D 94.881 586 29 1 1 586 362602735 362602151 0.000000e+00 915
20 TraesCS6B01G293800 chr2D 94.728 588 29 2 1 586 615763494 615762907 0.000000e+00 913
21 TraesCS6B01G293800 chr7D 94.898 588 23 3 1 586 265231106 265230524 0.000000e+00 913
22 TraesCS6B01G293800 chr4D 94.737 589 28 3 1 586 56182173 56181585 0.000000e+00 913
23 TraesCS6B01G293800 chr4D 94.710 586 31 0 1 586 320609459 320610044 0.000000e+00 911
24 TraesCS6B01G293800 chr7A 94.719 587 30 1 1 586 230346501 230347087 0.000000e+00 911
25 TraesCS6B01G293800 chr2A 90.055 543 48 3 597 1138 695806753 695806216 0.000000e+00 699


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 TraesCS6B01G293800 chr6B 527991626 527994174 2548 True 4708 4708 100.000 1 2549 1 chr6B.!!$R1 2548
1 TraesCS6B01G293800 chr3B 792939413 792941365 1952 False 3151 3151 95.765 593 2549 1 chr3B.!!$F1 1956
2 TraesCS6B01G293800 chr3B 108090332 108092312 1980 True 3044 3044 94.655 598 2549 1 chr3B.!!$R1 1951
3 TraesCS6B01G293800 chr5B 76429959 76431909 1950 True 3097 3097 95.260 589 2549 1 chr5B.!!$R1 1960
4 TraesCS6B01G293800 chr5B 269389464 269391442 1978 False 2939 2939 93.678 590 2549 1 chr5B.!!$F1 1959
5 TraesCS6B01G293800 chr1B 581715579 581717561 1982 True 3079 3079 94.962 598 2549 1 chr1B.!!$R1 1951
6 TraesCS6B01G293800 chr1B 189219499 189221437 1938 False 3073 3073 95.197 597 2549 1 chr1B.!!$F1 1952
7 TraesCS6B01G293800 chr2B 692955897 692957874 1977 False 3053 3053 94.753 598 2549 1 chr2B.!!$F3 1951
8 TraesCS6B01G293800 chr2B 458657423 458659399 1976 False 3035 3035 94.601 598 2549 1 chr2B.!!$F1 1951
9 TraesCS6B01G293800 chr7B 720987211 720989190 1979 True 3022 3022 94.456 598 2549 1 chr7B.!!$R3 1951
10 TraesCS6B01G293800 chr7B 708941276 708943230 1954 True 3020 3020 94.791 622 2549 1 chr7B.!!$R2 1927
11 TraesCS6B01G293800 chr3A 120653859 120654959 1100 False 1375 1375 89.065 591 1721 1 chr3A.!!$F1 1130
12 TraesCS6B01G293800 chr5D 561437156 561437742 586 True 922 922 95.060 1 586 1 chr5D.!!$R1 585
13 TraesCS6B01G293800 chr5D 211156958 211157542 584 False 915 915 94.872 2 586 1 chr5D.!!$F1 584
14 TraesCS6B01G293800 chr2D 173029942 173030527 585 True 922 922 95.051 1 586 1 chr2D.!!$R1 585
15 TraesCS6B01G293800 chr2D 362602151 362602735 584 True 915 915 94.881 1 586 1 chr2D.!!$R2 585
16 TraesCS6B01G293800 chr2D 615762907 615763494 587 True 913 913 94.728 1 586 1 chr2D.!!$R3 585
17 TraesCS6B01G293800 chr7D 265230524 265231106 582 True 913 913 94.898 1 586 1 chr7D.!!$R1 585
18 TraesCS6B01G293800 chr4D 56181585 56182173 588 True 913 913 94.737 1 586 1 chr4D.!!$R1 585
19 TraesCS6B01G293800 chr4D 320609459 320610044 585 False 911 911 94.710 1 586 1 chr4D.!!$F1 585
20 TraesCS6B01G293800 chr7A 230346501 230347087 586 False 911 911 94.719 1 586 1 chr7A.!!$F1 585
21 TraesCS6B01G293800 chr2A 695806216 695806753 537 True 699 699 90.055 597 1138 1 chr2A.!!$R1 541

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
904 915 0.249447 CACGGTGACAGAGAGCACAA 60.249 55.0 0.74 0.0 36.76 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2043 1.606313 CCCATGCGGTCTTGGGTTT 60.606 57.895 12.27 0.0 46.96 3.27 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
203 205 7.609918 TGGTGCATTATTCAGTGTTAGTTATGT 59.390 33.333 0.00 0.00 0.00 2.29
356 363 7.710579 AGTCCACTATACCTACCTATATGCTT 58.289 38.462 0.00 0.00 0.00 3.91
390 397 5.861787 GCCGTTCTAAGCAAATTTGTATGTT 59.138 36.000 19.03 10.27 0.00 2.71
465 473 2.919043 GGTAGGGGGTGGCTGATG 59.081 66.667 0.00 0.00 0.00 3.07
485 493 4.439305 TGTTTTTCCATGCTAGATGTGC 57.561 40.909 0.00 0.00 0.00 4.57
510 518 8.272176 GCTATTCTCAAGATGAGTGTTTATTCG 58.728 37.037 7.21 0.00 44.58 3.34
574 582 5.547276 TCCCAGTCCCAAAATGAAAAATGAT 59.453 36.000 0.00 0.00 0.00 2.45
730 738 2.126424 GCGTCTCCGTCAGGTCAC 60.126 66.667 0.00 0.00 39.05 3.67
791 799 3.299503 AGGCGGCCAATTTTATTCAGAT 58.700 40.909 23.09 0.00 0.00 2.90
796 804 6.039616 GCGGCCAATTTTATTCAGATTGTTA 58.960 36.000 2.24 0.00 0.00 2.41
903 914 1.363807 CACGGTGACAGAGAGCACA 59.636 57.895 0.74 0.00 36.76 4.57
904 915 0.249447 CACGGTGACAGAGAGCACAA 60.249 55.000 0.74 0.00 36.76 3.33
1124 1164 1.605712 GGTTTCTCACACACCGAGGAG 60.606 57.143 0.00 0.00 0.00 3.69
1133 1173 1.296392 CACCGAGGAGCCACAATCA 59.704 57.895 0.00 0.00 0.00 2.57
1152 1192 0.601558 ATCCGTTCTACGTGTGCAGT 59.398 50.000 0.00 0.00 40.58 4.40
1171 1211 4.384647 GCAGTGAGAATGGGGTAAGAATCT 60.385 45.833 0.00 0.00 0.00 2.40
1344 1384 3.365265 CTGCCCCAAACCGCAGTC 61.365 66.667 0.91 0.00 45.97 3.51
1751 1797 5.665916 ATTCCAGAGCCAAACAATTAAGG 57.334 39.130 0.00 0.00 0.00 2.69
1860 1906 3.229293 TGTCATGGAAAATGTGCCTCAA 58.771 40.909 0.00 0.00 0.00 3.02
1992 2043 3.075005 GGTGCGGCTAGGGACTCA 61.075 66.667 0.00 0.00 41.75 3.41
2108 2159 9.973450 ATGTATACATAGTGAGACTGTGAAATC 57.027 33.333 16.85 0.00 39.34 2.17
2178 2232 1.664306 GACTCGAACCCAAGACCGT 59.336 57.895 0.00 0.00 0.00 4.83
2197 2251 2.163815 CGTGTGGGTTTGTGGTGTTTAA 59.836 45.455 0.00 0.00 0.00 1.52
2212 2266 1.743394 GTTTAAGGCTGCGCTGGTAAT 59.257 47.619 16.47 0.00 0.00 1.89
2227 2281 3.562182 TGGTAATCGCTAGGACAGATGA 58.438 45.455 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 3.620488 TGCATAGGGAATCACAAACCTC 58.380 45.455 0.00 0.00 34.59 3.85
356 363 5.440234 TGCTTAGAACGGCACAAAAATAA 57.560 34.783 0.00 0.00 33.23 1.40
404 411 8.404765 AGCACACAAAAAGGAAATTTATTTTGG 58.595 29.630 24.85 18.83 43.54 3.28
465 473 4.708726 AGCACATCTAGCATGGAAAAAC 57.291 40.909 0.00 0.00 0.00 2.43
510 518 1.151668 ACTCTCGTGCAATGACAAGC 58.848 50.000 0.00 0.00 0.00 4.01
590 598 9.674068 GGCAAAAGGATAATTAACCCAAATAAA 57.326 29.630 8.09 0.00 0.00 1.40
591 599 8.268605 GGGCAAAAGGATAATTAACCCAAATAA 58.731 33.333 8.09 0.00 34.82 1.40
791 799 0.039617 GCAAGCCATGCGTGTAACAA 60.040 50.000 4.96 0.00 46.87 2.83
890 901 4.343581 GCGTTGTGCTCTCTGTCA 57.656 55.556 0.00 0.00 41.73 3.58
967 978 3.659089 AACGGGATCTCAACGCCGG 62.659 63.158 0.00 0.00 0.00 6.13
1124 1164 1.593006 CGTAGAACGGATGATTGTGGC 59.407 52.381 0.00 0.00 38.08 5.01
1152 1192 3.459598 CCCAGATTCTTACCCCATTCTCA 59.540 47.826 0.00 0.00 0.00 3.27
1171 1211 1.607509 CGAAAATGGTGCAATTGCCCA 60.608 47.619 30.42 30.42 42.56 5.36
1675 1720 9.755804 AAAGTTTCTGAATTCTTCATTTCTTCC 57.244 29.630 7.05 0.00 39.30 3.46
1751 1797 8.880878 TTTAACAGCTCCCAAAAATTTCTAAC 57.119 30.769 0.00 0.00 0.00 2.34
1860 1906 6.153000 CACTAGGTGTAAACATCTACCAGAGT 59.847 42.308 0.00 0.00 38.47 3.24
1943 1993 4.821260 GTGCATTTTCCACCCTTCATTTTT 59.179 37.500 0.00 0.00 0.00 1.94
1992 2043 1.606313 CCCATGCGGTCTTGGGTTT 60.606 57.895 12.27 0.00 46.96 3.27
2178 2232 2.761208 CCTTAAACACCACAAACCCACA 59.239 45.455 0.00 0.00 0.00 4.17
2212 2266 2.685388 CTCTTGTCATCTGTCCTAGCGA 59.315 50.000 0.00 0.00 0.00 4.93
2227 2281 3.244911 CCCTACCCATGTCAAACTCTTGT 60.245 47.826 0.00 0.00 33.94 3.16


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

AutoCloner maintained by Alex Coulton.