Multiple sequence alignment - TraesCS4D01G043200

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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 TraesCS4D01G043200 chr4D 100.000 2132 0 0 1 2132 19918684 19916553 0.000000e+00 3938
1 TraesCS4D01G043200 chr5D 97.197 2105 56 3 1 2102 560874660 560872556 0.000000e+00 3557
2 TraesCS4D01G043200 chr5D 96.390 2133 71 5 1 2129 6199090 6201220 0.000000e+00 3507
3 TraesCS4D01G043200 chr5D 96.208 2136 73 8 1 2132 329164366 329162235 0.000000e+00 3489
4 TraesCS4D01G043200 chr1D 96.582 2136 69 4 1 2132 254500190 254498055 0.000000e+00 3537
5 TraesCS4D01G043200 chr1D 91.334 2054 127 29 85 2129 244481977 244483988 0.000000e+00 2760
6 TraesCS4D01G043200 chr1A 95.401 2131 91 6 1 2129 168448381 168450506 0.000000e+00 3386
7 TraesCS4D01G043200 chr7A 93.533 2134 129 9 1 2129 352191834 352193963 0.000000e+00 3168
8 TraesCS4D01G043200 chr6B 95.221 1423 64 4 713 2132 22427423 22426002 0.000000e+00 2248
9 TraesCS4D01G043200 chr3B 96.754 1294 36 6 1 1290 201516871 201515580 0.000000e+00 2152
10 TraesCS4D01G043200 chr3B 94.667 1200 34 7 936 2132 201514356 201513184 0.000000e+00 1834
11 TraesCS4D01G043200 chr3B 94.231 676 34 5 1 675 524776893 524777564 0.000000e+00 1027
12 TraesCS4D01G043200 chr3D 96.896 1063 31 2 1072 2132 21905747 21904685 0.000000e+00 1779
13 TraesCS4D01G043200 chr7B 94.387 677 36 2 1 676 102631439 102632114 0.000000e+00 1038
14 TraesCS4D01G043200 chr2A 96.117 103 3 1 695 797 588453531 588453430 1.310000e-37 167


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 TraesCS4D01G043200 chr4D 19916553 19918684 2131 True 3938 3938 100.0000 1 2132 1 chr4D.!!$R1 2131
1 TraesCS4D01G043200 chr5D 560872556 560874660 2104 True 3557 3557 97.1970 1 2102 1 chr5D.!!$R2 2101
2 TraesCS4D01G043200 chr5D 6199090 6201220 2130 False 3507 3507 96.3900 1 2129 1 chr5D.!!$F1 2128
3 TraesCS4D01G043200 chr5D 329162235 329164366 2131 True 3489 3489 96.2080 1 2132 1 chr5D.!!$R1 2131
4 TraesCS4D01G043200 chr1D 254498055 254500190 2135 True 3537 3537 96.5820 1 2132 1 chr1D.!!$R1 2131
5 TraesCS4D01G043200 chr1D 244481977 244483988 2011 False 2760 2760 91.3340 85 2129 1 chr1D.!!$F1 2044
6 TraesCS4D01G043200 chr1A 168448381 168450506 2125 False 3386 3386 95.4010 1 2129 1 chr1A.!!$F1 2128
7 TraesCS4D01G043200 chr7A 352191834 352193963 2129 False 3168 3168 93.5330 1 2129 1 chr7A.!!$F1 2128
8 TraesCS4D01G043200 chr6B 22426002 22427423 1421 True 2248 2248 95.2210 713 2132 1 chr6B.!!$R1 1419
9 TraesCS4D01G043200 chr3B 201513184 201516871 3687 True 1993 2152 95.7105 1 2132 2 chr3B.!!$R1 2131
10 TraesCS4D01G043200 chr3B 524776893 524777564 671 False 1027 1027 94.2310 1 675 1 chr3B.!!$F1 674
11 TraesCS4D01G043200 chr3D 21904685 21905747 1062 True 1779 1779 96.8960 1072 2132 1 chr3D.!!$R1 1060
12 TraesCS4D01G043200 chr7B 102631439 102632114 675 False 1038 1038 94.3870 1 676 1 chr7B.!!$F1 675

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
858 1394 0.030638 CTGCACCAGTTCGTTTTGGG 59.969 55.0 6.75 0.0 38.82 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 3294 0.831307 GAGGCGGTCTCAATTAGGGT 59.169 55.0 4.4 0.0 42.02 4.34 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
186 187 3.454812 ACTAGGGCCACGATGATTTAGTT 59.545 43.478 6.18 0.00 0.00 2.24
485 489 9.689976 CTGACGAATTAGAATCATCTTGATAGT 57.310 33.333 0.00 0.00 35.76 2.12
570 575 7.703058 ATTCCAGAGATACCGAAACAAAAAT 57.297 32.000 0.00 0.00 0.00 1.82
576 581 8.673711 CAGAGATACCGAAACAAAAATATTCCA 58.326 33.333 0.00 0.00 0.00 3.53
779 1314 2.123589 TGCGATCCCCATAAAAGGAGA 58.876 47.619 0.00 0.00 35.08 3.71
793 1329 1.850755 GGAGAAGTCCCCCAACCCA 60.851 63.158 0.00 0.00 36.76 4.51
858 1394 0.030638 CTGCACCAGTTCGTTTTGGG 59.969 55.000 6.75 0.00 38.82 4.12
956 1494 8.707938 ACTATTCCGTTGTAGTTGTAAATACC 57.292 34.615 0.49 0.00 0.00 2.73
961 1499 6.096141 TCCGTTGTAGTTGTAAATACCCGATA 59.904 38.462 10.71 0.95 0.00 2.92
1034 1572 6.295123 GGAACTTTAGTCGCCATCTCCATATA 60.295 42.308 0.00 0.00 0.00 0.86
1308 2361 4.527509 TGCTTCCATAGATTCGATCCTC 57.472 45.455 0.00 0.00 0.00 3.71
1421 2475 5.665916 GGAGATGTTTCCCATGTCAAATT 57.334 39.130 2.49 0.00 43.82 1.82
1554 3145 5.649782 CTGGATCAATACCAGCAAAAACT 57.350 39.130 0.00 0.00 46.30 2.66
1596 3187 1.477700 CCATGCCAAATGTGTCCGAAT 59.522 47.619 0.00 0.00 0.00 3.34
1655 3246 2.464403 AACCCCTTGGACTGCTGCT 61.464 57.895 0.00 0.00 34.81 4.24
1665 3256 1.269723 GGACTGCTGCTAAAAACACCC 59.730 52.381 0.00 0.00 0.00 4.61
1666 3257 1.953686 GACTGCTGCTAAAAACACCCA 59.046 47.619 0.00 0.00 0.00 4.51
1679 3270 3.733443 AACACCCACAGATTTCAAAGC 57.267 42.857 0.00 0.00 0.00 3.51
1683 3274 1.614903 CCCACAGATTTCAAAGCAGCA 59.385 47.619 0.00 0.00 0.00 4.41
1703 3294 6.584563 GCAGCACGGTCTAATTCAAAAATTTA 59.415 34.615 0.00 0.00 36.49 1.40
1875 3467 6.444704 TCTAACAATTCCCTCCTCATCTACT 58.555 40.000 0.00 0.00 0.00 2.57
1928 3521 2.940410 GCATACGGCCTACAAAAAGCTA 59.060 45.455 0.00 0.00 36.11 3.32
1995 3588 2.154462 GCTATTCCATCCCCATTGTCG 58.846 52.381 0.00 0.00 0.00 4.35
2001 3594 2.240921 TCCATCCCCATTGTCGATTGAA 59.759 45.455 0.00 0.00 0.00 2.69
2041 3634 3.317993 CCCTTTTGCCGGATTATTACCAG 59.682 47.826 5.05 0.00 0.00 4.00
2069 3663 7.770801 AATCATAAAAGGCTAATTTTTCGGC 57.229 32.000 0.00 0.00 34.35 5.54
2129 3723 4.700213 GGCTAAACCATTGCTAACTCTTCA 59.300 41.667 0.00 0.00 38.86 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 4.662145 CTTGAAACTAAATCATCGTGGCC 58.338 43.478 0.00 0.00 0.00 5.36
186 187 4.442753 CCCTTGCCTTTTGTTTAGCTTGAA 60.443 41.667 0.00 0.00 0.00 2.69
289 291 7.112779 TCCTTCTAATTTTGTTTGCCCAAAAA 58.887 30.769 9.24 0.00 44.76 1.94
339 342 9.657121 CAGACTGAAAAATTCAAGTAGTTCTTC 57.343 33.333 0.00 0.00 39.58 2.87
570 575 2.445427 TGGTAGTTCGACCGTGGAATA 58.555 47.619 0.00 0.00 42.99 1.75
576 581 7.164122 TCTAGATATTATGGTAGTTCGACCGT 58.836 38.462 0.00 2.73 42.99 4.83
755 1290 2.288395 CCTTTTATGGGGATCGCAATGC 60.288 50.000 12.32 0.00 0.00 3.56
779 1314 2.863988 CCCTGGGTTGGGGGACTT 60.864 66.667 3.97 0.00 45.18 3.01
793 1329 1.217942 GGAATATGGGAAAGTGGCCCT 59.782 52.381 0.00 0.00 46.19 5.19
798 1334 6.449635 TTGAATTCGGAATATGGGAAAGTG 57.550 37.500 3.22 0.00 0.00 3.16
858 1394 6.476053 CCGTTGAAGATAGTTCTAAACCTAGC 59.524 42.308 0.00 0.00 30.38 3.42
961 1499 9.613428 TCAAGATTACAATGGATCTACGAAAAT 57.387 29.630 0.00 0.00 32.52 1.82
1010 1548 3.247006 TGGAGATGGCGACTAAAGTTC 57.753 47.619 0.00 0.00 0.00 3.01
1034 1572 6.433093 CCCAGTAAAGCTTACAAGTAAACCAT 59.567 38.462 0.00 0.00 0.00 3.55
1503 3094 5.279156 GGATGCTCAAGTTGAATTTGGAACT 60.279 40.000 7.06 0.00 33.75 3.01
1554 3145 3.250744 CGCTAGAACATTGTTCCGAGAA 58.749 45.455 22.70 6.09 0.00 2.87
1596 3187 4.455877 GCTACCTTTGCTTTGCTCTTCTTA 59.544 41.667 0.00 0.00 0.00 2.10
1655 3246 6.045955 GCTTTGAAATCTGTGGGTGTTTTTA 58.954 36.000 0.00 0.00 0.00 1.52
1665 3256 2.313234 CGTGCTGCTTTGAAATCTGTG 58.687 47.619 0.00 0.00 0.00 3.66
1666 3257 1.267806 CCGTGCTGCTTTGAAATCTGT 59.732 47.619 0.00 0.00 0.00 3.41
1679 3270 7.061789 GGTAAATTTTTGAATTAGACCGTGCTG 59.938 37.037 0.00 0.00 0.00 4.41
1683 3274 7.770366 AGGGTAAATTTTTGAATTAGACCGT 57.230 32.000 0.00 0.00 32.87 4.83
1703 3294 0.831307 GAGGCGGTCTCAATTAGGGT 59.169 55.000 4.40 0.00 42.02 4.34
1875 3467 7.900782 TTTTGAAACATTTCCGGTTGTTTTA 57.099 28.000 23.64 19.55 43.95 1.52
1916 3509 6.541111 AAGAAGGACGTTAGCTTTTTGTAG 57.459 37.500 0.00 0.00 0.00 2.74
1928 3521 7.028361 CGTCTTTAGAGATAAAGAAGGACGTT 58.972 38.462 11.03 0.00 44.65 3.99
1969 3562 2.204463 TGGGGATGGAATAGCTGTTGA 58.796 47.619 0.00 0.00 0.00 3.18
1995 3588 5.240403 GGGATTATTCAGAGCAGGTTCAATC 59.760 44.000 0.00 0.00 0.00 2.67
2001 3594 1.777272 GGGGGATTATTCAGAGCAGGT 59.223 52.381 0.00 0.00 0.00 4.00
2069 3663 9.346725 GTTTATCAGAAGCTTGGTCTAAAATTG 57.653 33.333 2.10 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.