Multiple sequence alignment - TraesCS1A01G232100

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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 TraesCS1A01G232100 chr1A 100.000 2925 0 0 1 2925 405541319 405544243 0.000000e+00 5402
1 TraesCS1A01G232100 chr1A 84.952 2924 428 12 6 2923 461264169 461261252 0.000000e+00 2952
2 TraesCS1A01G232100 chr7D 92.723 2927 210 3 1 2925 605089393 605086468 0.000000e+00 4222
3 TraesCS1A01G232100 chr7D 90.303 2413 222 9 517 2925 417915727 417918131 0.000000e+00 3149
4 TraesCS1A01G232100 chr2D 95.672 2611 106 5 317 2925 11503054 11500449 0.000000e+00 4189
5 TraesCS1A01G232100 chr3D 92.347 2927 216 6 1 2925 606146649 606143729 0.000000e+00 4157
6 TraesCS1A01G232100 chr7A 91.656 2433 193 7 495 2925 78843067 78845491 0.000000e+00 3360
7 TraesCS1A01G232100 chr6B 87.046 2918 368 8 2 2916 15778944 15776034 0.000000e+00 3286
8 TraesCS1A01G232100 chr4A 86.114 2931 385 17 6 2923 531310630 531307709 0.000000e+00 3138
9 TraesCS1A01G232100 chr5B 86.898 2137 258 11 2 2119 396817764 396819897 0.000000e+00 2375
10 TraesCS1A01G232100 chr4D 91.908 1483 100 3 1 1483 73405999 73407461 0.000000e+00 2056
11 TraesCS1A01G232100 chr4D 94.609 371 18 1 2557 2925 73417235 73417605 9.090000e-160 573


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 TraesCS1A01G232100 chr1A 405541319 405544243 2924 False 5402 5402 100.000 1 2925 1 chr1A.!!$F1 2924
1 TraesCS1A01G232100 chr1A 461261252 461264169 2917 True 2952 2952 84.952 6 2923 1 chr1A.!!$R1 2917
2 TraesCS1A01G232100 chr7D 605086468 605089393 2925 True 4222 4222 92.723 1 2925 1 chr7D.!!$R1 2924
3 TraesCS1A01G232100 chr7D 417915727 417918131 2404 False 3149 3149 90.303 517 2925 1 chr7D.!!$F1 2408
4 TraesCS1A01G232100 chr2D 11500449 11503054 2605 True 4189 4189 95.672 317 2925 1 chr2D.!!$R1 2608
5 TraesCS1A01G232100 chr3D 606143729 606146649 2920 True 4157 4157 92.347 1 2925 1 chr3D.!!$R1 2924
6 TraesCS1A01G232100 chr7A 78843067 78845491 2424 False 3360 3360 91.656 495 2925 1 chr7A.!!$F1 2430
7 TraesCS1A01G232100 chr6B 15776034 15778944 2910 True 3286 3286 87.046 2 2916 1 chr6B.!!$R1 2914
8 TraesCS1A01G232100 chr4A 531307709 531310630 2921 True 3138 3138 86.114 6 2923 1 chr4A.!!$R1 2917
9 TraesCS1A01G232100 chr5B 396817764 396819897 2133 False 2375 2375 86.898 2 2119 1 chr5B.!!$F1 2117
10 TraesCS1A01G232100 chr4D 73405999 73407461 1462 False 2056 2056 91.908 1 1483 1 chr4D.!!$F1 1482

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
185 186 0.17668 CGAATCTGGAGGTCCCACAG 59.823 60.0 4.41 4.41 40.82 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2045 1.212935 GCCAAAGCCAGATCCTTAGGA 59.787 52.381 2.37 2.37 35.55 2.94 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
23 24 3.302740 GCGCTGAATTGATCGTTAAGGAG 60.303 47.826 0.00 0.00 0.00 3.69
110 111 2.115427 TCTTATGAATCTGCGGGTCCA 58.885 47.619 0.00 0.00 0.00 4.02
185 186 0.176680 CGAATCTGGAGGTCCCACAG 59.823 60.000 4.41 4.41 40.82 3.66
216 217 3.959975 CACAACCACCGCCGTTGG 61.960 66.667 0.00 0.00 43.95 3.77
244 245 2.621526 GTCGTGTGGTTGGGAAGAAAAT 59.378 45.455 0.00 0.00 0.00 1.82
266 267 3.436359 TGGGTCGTAAAAATACGCTTTCC 59.564 43.478 3.64 4.17 42.62 3.13
278 279 3.334583 ACGCTTTCCATTTCTGCTAGA 57.665 42.857 0.00 0.00 0.00 2.43
322 323 2.317371 TTTTATGGCCAGCTTTGGGA 57.683 45.000 13.05 0.00 0.00 4.37
510 511 9.886132 TTGATCCAACTCCTACTATCTTTAAAC 57.114 33.333 0.00 0.00 0.00 2.01
519 520 7.186972 TCCTACTATCTTTAAACTCTCCACCA 58.813 38.462 0.00 0.00 0.00 4.17
525 526 9.284968 CTATCTTTAAACTCTCCACCAAGAAAA 57.715 33.333 0.00 0.00 0.00 2.29
562 563 2.287368 CGTTTGTTGAGGTGGTTAAGGC 60.287 50.000 0.00 0.00 0.00 4.35
683 687 4.802051 GCTGCTCCATTGGCGGGA 62.802 66.667 0.00 0.00 36.65 5.14
863 891 3.407967 CCGGGGCACTATGTGGGT 61.408 66.667 0.00 0.00 33.64 4.51
952 980 2.831526 GGGCAAAACCACATCCTACAAT 59.168 45.455 0.00 0.00 42.05 2.71
1004 1032 5.068987 CCTGGGGTTTTACCATATTGATGTG 59.931 44.000 0.00 0.00 41.02 3.21
1234 1263 3.494332 AGAGTTTCCTGCATTTGAGCTT 58.506 40.909 0.00 0.00 34.99 3.74
1245 1274 4.221041 TGCATTTGAGCTTCCAATTGATGA 59.779 37.500 7.12 0.00 32.27 2.92
1274 1303 0.247460 CAAGATCTGCGAGTGGGTGA 59.753 55.000 0.00 0.00 0.00 4.02
1423 1452 8.429641 GTGGACTGGAATGGTATATTTAAGAGA 58.570 37.037 0.00 0.00 0.00 3.10
1553 1582 2.838637 AGGGTTTGAACAACTGGGAA 57.161 45.000 0.00 0.00 0.00 3.97
1605 1638 7.040823 CCCAGATTTAGACAATATGGAGAAAGC 60.041 40.741 9.36 0.00 40.49 3.51
1923 1958 3.040477 TGATCCCATGTCAGCACATCTA 58.960 45.455 0.00 0.00 41.69 1.98
2014 2049 5.508567 TGGATGAAATGCATTGTCTTCCTA 58.491 37.500 30.08 22.42 40.85 2.94
2129 2164 1.915078 AATTCTCCTGTCTGGGGGCG 61.915 60.000 0.00 0.00 36.78 6.13
2192 2227 5.948162 ACATTAAGATCATGGACAAAGCTGT 59.052 36.000 0.00 0.00 38.98 4.40
2271 2306 3.106827 TGCTGTCCTTGATCCTGATGTA 58.893 45.455 0.00 0.00 0.00 2.29
2395 2431 6.830324 TGCCTTAAGTTTGCTGATGATAATCT 59.170 34.615 0.97 0.00 0.00 2.40
2494 2530 1.629861 TGATGGTTCAGATGGCACTGA 59.370 47.619 13.41 13.41 43.83 3.41
2563 2601 1.476488 GGCTTGTCGCACCCATTTAAT 59.524 47.619 0.00 0.00 41.67 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.781324 AATGGAAGTGGAGTCACAAATAATT 57.219 32.000 0.00 0.00 45.91 1.40
128 129 2.126307 GCAGAAGCGAGCTCGTCA 60.126 61.111 34.46 0.00 42.22 4.35
163 164 0.902531 TGGGACCTCCAGATTCGAAC 59.097 55.000 0.00 0.00 41.46 3.95
200 201 4.493049 ACCAACGGCGGTGGTTGT 62.493 61.111 41.77 22.15 42.42 3.32
216 217 1.644913 CAACCACACGACCCGAAAC 59.355 57.895 0.00 0.00 0.00 2.78
244 245 3.436359 GGAAAGCGTATTTTTACGACCCA 59.564 43.478 9.52 0.00 45.45 4.51
266 267 1.202580 CCGTCCCCTCTAGCAGAAATG 60.203 57.143 0.00 0.00 0.00 2.32
278 279 3.612607 ACTTCCTCCCCGTCCCCT 61.613 66.667 0.00 0.00 0.00 4.79
445 446 1.083489 CGGGAAACAATCTTGCGCTA 58.917 50.000 9.73 0.00 0.00 4.26
478 479 5.365021 AGTAGGAGTTGGATCAAATCTGG 57.635 43.478 7.79 0.00 38.32 3.86
510 511 6.901081 AAAACCTATTTTCTTGGTGGAGAG 57.099 37.500 0.00 0.00 32.29 3.20
525 526 6.488683 TCAACAAACGATCAAGGAAAACCTAT 59.511 34.615 0.00 0.00 0.00 2.57
537 538 2.631160 ACCACCTCAACAAACGATCA 57.369 45.000 0.00 0.00 0.00 2.92
562 563 4.864334 GCCCCCGCTCCATCACTG 62.864 72.222 0.00 0.00 0.00 3.66
863 891 4.022935 CACTTCTTTGGCTCAATGCAGTTA 60.023 41.667 0.00 0.00 45.15 2.24
891 919 0.535335 TTATGACCTCCCGCACAGAC 59.465 55.000 0.00 0.00 0.00 3.51
896 924 1.199615 TGACATTATGACCTCCCGCA 58.800 50.000 0.00 0.00 0.00 5.69
952 980 0.970640 TGCGCTACCAAAGTAGGTCA 59.029 50.000 9.73 0.00 45.29 4.02
1234 1263 6.716173 TCTTGACAGAAACATCATCAATTGGA 59.284 34.615 5.42 0.00 0.00 3.53
1245 1274 3.930336 TCGCAGATCTTGACAGAAACAT 58.070 40.909 0.00 0.00 30.76 2.71
1274 1303 6.060788 GTCCTCCAAATTCATCTAGCATTCT 58.939 40.000 0.00 0.00 0.00 2.40
1312 1341 4.402616 AGGAATCCCCTCAATTTGAACA 57.597 40.909 0.00 0.00 43.31 3.18
1448 1477 1.839994 CCTGGGATCTCTACAAGCCAA 59.160 52.381 0.00 0.00 0.00 4.52
1553 1582 4.589798 CAGATCATCTCCATCAGAGTCCTT 59.410 45.833 0.00 0.00 43.71 3.36
1605 1638 5.359756 TGTCCTCATTGTTATCTTCATCCG 58.640 41.667 0.00 0.00 0.00 4.18
1923 1958 6.881065 TGCTTAGTTGTTCAGAGCAATATTCT 59.119 34.615 2.68 0.00 40.09 2.40
2004 2039 3.454858 AGCCAGATCCTTAGGAAGACAA 58.545 45.455 4.56 0.00 34.34 3.18
2010 2045 1.212935 GCCAAAGCCAGATCCTTAGGA 59.787 52.381 2.37 2.37 35.55 2.94
2014 2049 1.829222 CATTGCCAAAGCCAGATCCTT 59.171 47.619 0.00 0.00 38.69 3.36
2192 2227 7.500227 CCAAGTTCTTCCTCTTCATATATGCAA 59.500 37.037 7.92 3.18 0.00 4.08
2271 2306 9.841295 TCAACCTTACTAGTATTTGAAACAAGT 57.159 29.630 14.95 0.00 0.00 3.16
2418 2454 9.481340 CTCATCGACCATCATTTCTAAATCTAA 57.519 33.333 0.00 0.00 0.00 2.10
2475 2511 2.408271 TCAGTGCCATCTGAACCATC 57.592 50.000 1.75 0.00 40.82 3.51
2512 2548 3.534357 TTTTTGTATTCAGGGCAGGGA 57.466 42.857 0.00 0.00 0.00 4.20
2563 2601 6.928202 TCCAAAAGGCCCCTATCATTTAATA 58.072 36.000 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.