Multiple sequence alignment - TraesCS1A01G395400

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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 TraesCS1A01G395400 chr1A 100.000 3434 0 0 1 3434 561279215 561282648 0.000000e+00 6342.0
1 TraesCS1A01G395400 chr1A 84.952 937 97 25 1059 1994 561202001 561202894 0.000000e+00 909.0
2 TraesCS1A01G395400 chr1A 79.438 676 112 19 2670 3336 561290445 561291102 1.450000e-123 453.0
3 TraesCS1A01G395400 chr1A 83.806 247 36 3 2392 2636 561204591 561204835 7.410000e-57 231.0
4 TraesCS1A01G395400 chr1A 92.982 114 6 2 10 123 561272897 561273008 7.620000e-37 165.0
5 TraesCS1A01G395400 chr1D 94.387 3474 111 33 1 3434 468346693 468350122 0.000000e+00 5258.0
6 TraesCS1A01G395400 chr1D 86.507 667 81 6 1345 2002 468257114 468257780 0.000000e+00 725.0
7 TraesCS1A01G395400 chr1D 80.207 677 114 15 2670 3336 468359980 468360646 1.110000e-134 490.0
8 TraesCS1A01G395400 chr1D 88.077 260 27 3 2379 2636 468257771 468258028 4.310000e-79 305.0
9 TraesCS1A01G395400 chr1D 92.982 114 6 2 10 123 468340433 468340544 7.620000e-37 165.0
10 TraesCS1A01G395400 chr1D 97.297 37 1 0 10 46 468346664 468346700 2.860000e-06 63.9
11 TraesCS1A01G395400 chr1D 97.059 34 0 1 64 97 468346835 468346867 4.790000e-04 56.5
12 TraesCS1A01G395400 chr1B 93.485 2548 134 18 668 3201 647142076 647144605 0.000000e+00 3757.0
13 TraesCS1A01G395400 chr1B 90.323 434 33 7 151 580 647141283 647141711 8.320000e-156 560.0
14 TraesCS1A01G395400 chr1B 94.853 136 4 3 10 145 647109724 647109856 3.470000e-50 209.0


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 TraesCS1A01G395400 chr1A 561279215 561282648 3433 False 6342.0 6342 100.000000 1 3434 1 chr1A.!!$F2 3433
1 TraesCS1A01G395400 chr1A 561202001 561204835 2834 False 570.0 909 84.379000 1059 2636 2 chr1A.!!$F4 1577
2 TraesCS1A01G395400 chr1A 561290445 561291102 657 False 453.0 453 79.438000 2670 3336 1 chr1A.!!$F3 666
3 TraesCS1A01G395400 chr1D 468346664 468350122 3458 False 1792.8 5258 96.247667 1 3434 3 chr1D.!!$F4 3433
4 TraesCS1A01G395400 chr1D 468257114 468258028 914 False 515.0 725 87.292000 1345 2636 2 chr1D.!!$F3 1291
5 TraesCS1A01G395400 chr1D 468359980 468360646 666 False 490.0 490 80.207000 2670 3336 1 chr1D.!!$F2 666
6 TraesCS1A01G395400 chr1B 647141283 647144605 3322 False 2158.5 3757 91.904000 151 3201 2 chr1B.!!$F2 3050

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
553 589 0.105964 TCTTCCTAGGGCTGCTCGAT 60.106 55.0 9.46 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 4121 0.172578 CGTCTTCCGTCACTGCCATA 59.827 55.0 0.0 0.0 0.0 2.74 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
25 55 2.036217 ACAATGTGTGCACCAAAGGATG 59.964 45.455 15.69 6.91 0.00 3.51
57 88 9.581099 TTTTCAGTTCTACAAAATTGAAACCTC 57.419 29.630 6.76 0.00 41.57 3.85
58 89 7.873719 TCAGTTCTACAAAATTGAAACCTCA 57.126 32.000 0.00 0.00 0.00 3.86
79 110 6.992123 CCTCACCTGCATACAAATTACTGATA 59.008 38.462 0.00 0.00 0.00 2.15
111 142 6.070656 CCCCCACATAACACATAATCTGAAT 58.929 40.000 0.00 0.00 0.00 2.57
136 167 5.216648 GGAAAACATAGCTAAACGCACAAA 58.783 37.500 0.00 0.00 42.61 2.83
137 168 5.116528 GGAAAACATAGCTAAACGCACAAAC 59.883 40.000 0.00 0.00 42.61 2.93
158 189 6.773976 AACCCCACATACAAATTACTGATG 57.226 37.500 0.00 0.00 0.00 3.07
159 190 5.200483 ACCCCACATACAAATTACTGATGG 58.800 41.667 0.00 0.00 0.00 3.51
163 194 6.376864 CCCACATACAAATTACTGATGGTGAA 59.623 38.462 0.00 0.00 0.00 3.18
225 258 3.498397 CCACGGGTATGCTGAATATGAAC 59.502 47.826 0.00 0.00 0.00 3.18
233 266 3.270027 TGCTGAATATGAACCAAGACGG 58.730 45.455 0.00 0.00 42.50 4.79
334 368 5.546526 TGCAGGGAATGAAACCAAAAATAC 58.453 37.500 0.00 0.00 0.00 1.89
348 382 7.989416 ACCAAAAATACTGTCCGAGAAAATA 57.011 32.000 0.00 0.00 0.00 1.40
349 383 8.040716 ACCAAAAATACTGTCCGAGAAAATAG 57.959 34.615 0.00 0.00 0.00 1.73
368 402 6.389830 AATAGTACTCAGATGAGAGCTGTG 57.610 41.667 16.52 0.00 44.74 3.66
378 414 4.366684 GAGCTGTGGGGTTGGGGG 62.367 72.222 0.00 0.00 0.00 5.40
381 417 2.939298 CTGTGGGGTTGGGGGAAA 59.061 61.111 0.00 0.00 0.00 3.13
383 419 0.904394 CTGTGGGGTTGGGGGAAATG 60.904 60.000 0.00 0.00 0.00 2.32
407 443 2.521451 TTGTGCCTTCCGCCTGGTA 61.521 57.895 0.00 0.00 36.24 3.25
552 588 0.753479 CTCTTCCTAGGGCTGCTCGA 60.753 60.000 9.46 0.00 0.00 4.04
553 589 0.105964 TCTTCCTAGGGCTGCTCGAT 60.106 55.000 9.46 0.00 0.00 3.59
564 600 0.106335 CTGCTCGATGGCATCTTCCT 59.894 55.000 23.97 0.00 41.63 3.36
621 657 4.436998 CCAGCGACGGTGACTCCC 62.437 72.222 27.42 0.00 32.22 4.30
726 1039 0.174162 AAACGGATTCGGGTACGGAG 59.826 55.000 0.00 0.00 39.30 4.63
757 1070 4.802051 GCCCGCTCCATCAGCCAA 62.802 66.667 0.00 0.00 46.74 4.52
829 1142 3.066900 AGCGCTAAGATTCGTGTACATCT 59.933 43.478 8.99 0.00 0.00 2.90
864 1178 4.499037 AACGGCCTGAAAGTGAAAATAC 57.501 40.909 0.00 0.00 0.00 1.89
901 1215 1.539665 TTTTTCAGGGCGGGGAACT 59.460 52.632 0.00 0.00 0.00 3.01
916 1230 5.048294 GCGGGGAACTTCTGAAATTTAGAAA 60.048 40.000 1.93 0.00 34.07 2.52
975 1305 1.811679 GTGCGGGCTACTTGCTCTC 60.812 63.158 0.00 0.00 40.82 3.20
1021 1356 3.827898 CCGCGTCACCTCTCCTCC 61.828 72.222 4.92 0.00 0.00 4.30
1852 2202 1.284408 GCGATCGAGGAGGCTGTAG 59.716 63.158 21.57 0.00 0.00 2.74
2151 3625 2.501723 GAGTGGACTTCTATTGGAGGCA 59.498 50.000 0.00 0.00 0.00 4.75
2435 4121 4.694233 CTGCAGTGCCGGCTGACT 62.694 66.667 29.70 21.12 38.70 3.41
2573 4260 0.704076 TTTTGCATCAGGGGGCTAGT 59.296 50.000 0.00 0.00 0.00 2.57
2616 4303 5.245977 TGAGATACAGATGAGTTGTTCACCA 59.754 40.000 0.00 0.00 38.99 4.17
3124 4836 4.210331 GGTGTGATCCAGCATTCCTTAAT 58.790 43.478 8.07 0.00 41.31 1.40
3147 4859 1.002033 GGGTACGTATAGTGTCCTGCG 60.002 57.143 0.00 0.00 0.00 5.18
3206 4919 7.112452 ACTTGGTTCTTTTAGTCAAATGCTT 57.888 32.000 0.00 0.00 0.00 3.91
3343 5060 0.107459 CCCTTCTTGCCTAGCCAGAC 60.107 60.000 0.00 0.00 30.06 3.51
3364 5081 2.618241 CGCTAATGCCTTCCTTGCAATA 59.382 45.455 0.00 0.00 42.92 1.90
3401 5130 2.918131 GCTAACTTTTTGCCAGACGCTG 60.918 50.000 0.52 0.52 38.78 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.317711 CCTTTGGTGCACACATTGTAGAA 59.682 43.478 20.43 3.85 0.00 2.10
4 5 1.774110 TCCTTTGGTGCACACATTGT 58.226 45.000 20.43 0.00 0.00 2.71
9 39 0.883833 CCTCATCCTTTGGTGCACAC 59.116 55.000 20.43 8.79 0.00 3.82
35 65 6.918022 GGTGAGGTTTCAATTTTGTAGAACTG 59.082 38.462 0.00 0.00 34.49 3.16
43 73 4.057406 TGCAGGTGAGGTTTCAATTTTG 57.943 40.909 0.00 0.00 34.49 2.44
57 88 8.839343 TCATTATCAGTAATTTGTATGCAGGTG 58.161 33.333 0.00 0.00 0.00 4.00
58 89 8.978874 TCATTATCAGTAATTTGTATGCAGGT 57.021 30.769 0.00 0.00 0.00 4.00
79 110 3.589735 TGTGTTATGTGGGGGTACTCATT 59.410 43.478 0.00 0.00 0.00 2.57
86 117 4.476846 TCAGATTATGTGTTATGTGGGGGT 59.523 41.667 0.00 0.00 0.00 4.95
136 167 5.200483 CCATCAGTAATTTGTATGTGGGGT 58.800 41.667 0.00 0.00 0.00 4.95
137 168 5.067674 CACCATCAGTAATTTGTATGTGGGG 59.932 44.000 0.00 0.00 0.00 4.96
158 189 6.831868 AGTAATTTGTATGTGGGGTATTCACC 59.168 38.462 0.00 0.00 44.96 4.02
159 190 7.875327 AGTAATTTGTATGTGGGGTATTCAC 57.125 36.000 0.00 0.00 35.82 3.18
163 194 6.133356 CCCAAGTAATTTGTATGTGGGGTAT 58.867 40.000 0.00 0.00 40.52 2.73
225 258 5.120208 CACTAATTTCACAGTACCGTCTTGG 59.880 44.000 0.00 0.00 46.41 3.61
233 266 5.356882 TGCTTGCACTAATTTCACAGTAC 57.643 39.130 0.00 0.00 0.00 2.73
334 368 6.438259 TCTGAGTACTATTTTCTCGGACAG 57.562 41.667 0.00 0.00 38.27 3.51
348 382 3.023119 CCACAGCTCTCATCTGAGTACT 58.977 50.000 0.00 0.00 42.60 2.73
349 383 2.100584 CCCACAGCTCTCATCTGAGTAC 59.899 54.545 7.07 1.49 42.60 2.73
368 402 2.687200 GCCATTTCCCCCAACCCC 60.687 66.667 0.00 0.00 0.00 4.95
564 600 2.279741 GGCGTGATGTTATGAAGAGCA 58.720 47.619 0.00 0.00 0.00 4.26
648 684 8.511604 GAAATCATTTCTGTAATGGAGAAGGA 57.488 34.615 2.58 0.00 43.19 3.36
757 1070 3.754068 GGGCTTCCGTCGGTTTTT 58.246 55.556 11.88 0.00 0.00 1.94
852 1166 5.067283 AGACGGCTGTTTGTATTTTCACTTT 59.933 36.000 0.00 0.00 0.00 2.66
864 1178 3.904136 AAAGAATCAGACGGCTGTTTG 57.096 42.857 19.16 9.92 42.84 2.93
893 1207 6.569179 TTTCTAAATTTCAGAAGTTCCCCG 57.431 37.500 0.00 0.00 33.72 5.73
916 1230 7.095102 GCATGAATTGTTTTGCAGTTTTCCTAT 60.095 33.333 0.00 0.00 35.22 2.57
975 1305 2.053627 GCCTGTTTGAATGCGAAGTTG 58.946 47.619 0.00 0.00 0.00 3.16
1225 1560 1.585651 GGGAGGGAGGAGAGGAGACA 61.586 65.000 0.00 0.00 0.00 3.41
1227 1562 0.556380 AAGGGAGGGAGGAGAGGAGA 60.556 60.000 0.00 0.00 0.00 3.71
1469 1804 1.519408 GTTGGCAACGTAGGTGTCAT 58.481 50.000 15.49 0.00 42.51 3.06
1852 2202 1.663379 GGCATCCCCTTAAACACCGC 61.663 60.000 0.00 0.00 0.00 5.68
2151 3625 4.279671 GTCATCCCACGTATCATCTCTTCT 59.720 45.833 0.00 0.00 0.00 2.85
2435 4121 0.172578 CGTCTTCCGTCACTGCCATA 59.827 55.000 0.00 0.00 0.00 2.74
2458 4144 0.251033 ACTGAGCTGCAATGAAGCCA 60.251 50.000 10.09 6.90 41.82 4.75
2616 4303 4.776837 TGTAATGCTGAATTTGGTCCCAAT 59.223 37.500 0.00 0.00 35.70 3.16
2680 4367 5.936956 GCAGTTCTATGGGATTCTCTAATGG 59.063 44.000 0.00 0.00 0.00 3.16
2684 4371 6.814954 AAAGCAGTTCTATGGGATTCTCTA 57.185 37.500 0.00 0.00 0.00 2.43
2691 4378 5.260424 TGCAATAAAAGCAGTTCTATGGGA 58.740 37.500 0.00 0.00 37.02 4.37
3124 4836 3.748668 GCAGGACACTATACGTACCCCTA 60.749 52.174 0.00 0.00 0.00 3.53
3147 4859 5.767168 AGCCAAACCTCAAATATCTAGCATC 59.233 40.000 0.00 0.00 0.00 3.91
3343 5060 0.810648 TTGCAAGGAAGGCATTAGCG 59.189 50.000 0.00 0.00 41.58 4.26
3410 5140 2.237143 TGCTTGATAGGAGTGAAGTGGG 59.763 50.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.