Multiple sequence alignment - TraesCS1D01G395400

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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 TraesCS1D01G395400 chr1D 100.000 2312 0 0 1 2312 464034375 464032064 0.000000e+00 4270.0
1 TraesCS1D01G395400 chr1D 100.000 46 0 0 1 46 71164344 71164299 4.090000e-13 86.1
2 TraesCS1D01G395400 chr1D 84.375 64 6 4 143 202 292706730 292706667 2.480000e-05 60.2
3 TraesCS1D01G395400 chr1B 91.834 2143 136 22 57 2186 640078961 640076845 0.000000e+00 2952.0
4 TraesCS1D01G395400 chr1A 96.002 1701 46 3 18 1716 556188242 556186562 0.000000e+00 2745.0
5 TraesCS1D01G395400 chr1A 93.485 614 31 6 1704 2310 556186384 556185773 0.000000e+00 904.0
6 TraesCS1D01G395400 chr1A 97.368 114 3 0 57 170 257583977 257583864 6.520000e-46 195.0
7 TraesCS1D01G395400 chr1A 100.000 46 0 0 1 46 32617337 32617292 4.090000e-13 86.1
8 TraesCS1D01G395400 chr4D 98.261 115 2 0 57 171 413774395 413774281 3.900000e-48 202.0
9 TraesCS1D01G395400 chr4D 96.581 117 4 0 54 170 127572943 127573059 6.520000e-46 195.0
10 TraesCS1D01G395400 chr4D 100.000 46 0 0 1 46 404068409 404068454 4.090000e-13 86.1
11 TraesCS1D01G395400 chr4D 100.000 46 0 0 1 46 498089157 498089202 4.090000e-13 86.1
12 TraesCS1D01G395400 chr7B 97.368 114 3 0 57 170 565715852 565715739 6.520000e-46 195.0
13 TraesCS1D01G395400 chr2D 96.581 117 4 0 54 170 275869878 275869994 6.520000e-46 195.0
14 TraesCS1D01G395400 chr2D 100.000 46 0 0 1 46 543791772 543791817 4.090000e-13 86.1
15 TraesCS1D01G395400 chr3D 96.552 116 4 0 57 172 441588151 441588036 2.340000e-45 193.0
16 TraesCS1D01G395400 chr3D 100.000 46 0 0 1 46 581416207 581416252 4.090000e-13 86.1
17 TraesCS1D01G395400 chr3D 85.246 61 5 4 143 202 253401256 253401313 2.480000e-05 60.2
18 TraesCS1D01G395400 chr5D 95.041 121 6 0 54 174 242109079 242109199 8.430000e-45 191.0
19 TraesCS1D01G395400 chr5D 100.000 46 0 0 1 46 136283554 136283599 4.090000e-13 86.1
20 TraesCS1D01G395400 chr6B 100.000 46 0 0 1 46 697866041 697865996 4.090000e-13 86.1
21 TraesCS1D01G395400 chr4B 100.000 28 0 0 2271 2298 82279755 82279728 4.000000e-03 52.8


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 TraesCS1D01G395400 chr1D 464032064 464034375 2311 True 4270.0 4270 100.0000 1 2312 1 chr1D.!!$R3 2311
1 TraesCS1D01G395400 chr1B 640076845 640078961 2116 True 2952.0 2952 91.8340 57 2186 1 chr1B.!!$R1 2129
2 TraesCS1D01G395400 chr1A 556185773 556188242 2469 True 1824.5 2745 94.7435 18 2310 2 chr1A.!!$R3 2292

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
245 246 1.771255 AGCCTTTCCAGCGGAGATTAT 59.229 47.619 0.0 0.0 31.21 1.28 F
1218 1224 3.447586 TCGCAAAAGATCTACAGGCTACT 59.552 43.478 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1233 0.329261 CATGCACCCCTTTCTCCTCA 59.671 55.0 0.00 0.00 0.00 3.86 R
2172 2376 5.518128 TGAACATGTTTTGGAAACACGAATG 59.482 36.0 13.36 6.01 42.67 2.67 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
245 246 1.771255 AGCCTTTCCAGCGGAGATTAT 59.229 47.619 0.00 0.00 31.21 1.28
486 487 8.124430 TCTTTCTAGACACCTATTAAACCCCTA 58.876 37.037 0.00 0.00 0.00 3.53
583 588 9.591792 CAATGAATGTCTACATCGATGGTATAT 57.408 33.333 28.09 13.72 35.10 0.86
873 879 8.874744 ACTAACAACTACTCTTACTCATACCA 57.125 34.615 0.00 0.00 0.00 3.25
874 880 9.305555 ACTAACAACTACTCTTACTCATACCAA 57.694 33.333 0.00 0.00 0.00 3.67
1216 1222 4.672587 ATCGCAAAAGATCTACAGGCTA 57.327 40.909 0.00 0.00 0.00 3.93
1218 1224 3.447586 TCGCAAAAGATCTACAGGCTACT 59.552 43.478 0.00 0.00 0.00 2.57
1238 1244 1.202806 TGCCAACACTGAGGAGAAAGG 60.203 52.381 0.00 0.00 0.00 3.11
1362 1368 7.201600 GCTTGTTGTTGTGATGTTAATTGGTTT 60.202 33.333 0.00 0.00 0.00 3.27
1535 1542 8.970020 TGATATTATTGCTTAATTATGGGCCAG 58.030 33.333 13.78 0.00 32.66 4.85
1537 1544 2.380064 TGCTTAATTATGGGCCAGGG 57.620 50.000 13.78 0.00 0.00 4.45
1549 1556 1.342975 GGGCCAGGGGAACAATGTAAT 60.343 52.381 4.39 0.00 0.00 1.89
1658 1665 3.085533 CACGGAACATACCAAAATGGGA 58.914 45.455 0.87 0.00 43.37 4.37
1681 1688 1.273887 GCGGCATCGACAAATCTCG 59.726 57.895 0.00 0.00 39.00 4.04
1745 1943 2.775032 TAACCGTGAGCTCCAACGCC 62.775 60.000 18.40 0.00 0.00 5.68
1768 1966 2.414994 ATGTCCTTCATCTGCACCAG 57.585 50.000 0.00 0.00 29.76 4.00
1802 2000 5.232463 TGCTGCAAAAAGAGGATGATTTTC 58.768 37.500 0.00 0.00 0.00 2.29
1849 2047 3.955471 GGATCACCCACTCAATTCTGAA 58.045 45.455 0.00 0.00 34.14 3.02
2203 2408 6.475076 TGTTTCCAAAACATGTTCAGAATTCG 59.525 34.615 12.39 0.00 0.00 3.34
2224 2429 3.242706 CGTGAACAATGCTTGAACTCACA 60.243 43.478 18.16 0.00 37.74 3.58
2228 2433 4.989279 ACAATGCTTGAACTCACAAACT 57.011 36.364 3.37 0.00 0.00 2.66
2269 2475 9.424659 GAACATTGTTTATTTTTGCTCACTTTG 57.575 29.630 3.08 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.423209 GGAGGGAGGAGGGGCTGT 62.423 72.222 0.00 0.00 0.00 4.40
1 2 2.332258 TATGGAGGGAGGAGGGGCTG 62.332 65.000 0.00 0.00 0.00 4.85
2 3 2.027059 TATGGAGGGAGGAGGGGCT 61.027 63.158 0.00 0.00 0.00 5.19
3 4 1.537643 CTATGGAGGGAGGAGGGGC 60.538 68.421 0.00 0.00 0.00 5.80
4 5 0.796255 ATCTATGGAGGGAGGAGGGG 59.204 60.000 0.00 0.00 0.00 4.79
5 6 2.731339 AATCTATGGAGGGAGGAGGG 57.269 55.000 0.00 0.00 0.00 4.30
6 7 4.757692 ACTAAATCTATGGAGGGAGGAGG 58.242 47.826 0.00 0.00 0.00 4.30
7 8 5.841237 TCAACTAAATCTATGGAGGGAGGAG 59.159 44.000 0.00 0.00 0.00 3.69
8 9 5.788430 TCAACTAAATCTATGGAGGGAGGA 58.212 41.667 0.00 0.00 0.00 3.71
9 10 6.694445 ATCAACTAAATCTATGGAGGGAGG 57.306 41.667 0.00 0.00 0.00 4.30
10 11 8.429237 ACTATCAACTAAATCTATGGAGGGAG 57.571 38.462 0.00 0.00 0.00 4.30
43 44 3.735746 GCTGTTTTCAACATTAGCACACC 59.264 43.478 0.00 0.00 41.26 4.16
245 246 4.374518 GGGGGTGGGGAGGGGTTA 62.375 72.222 0.00 0.00 0.00 2.85
460 461 6.964086 AGGGGTTTAATAGGTGTCTAGAAAGA 59.036 38.462 0.00 0.00 0.00 2.52
486 487 4.456662 AAGGATAGGGATGTCGACTAGT 57.543 45.455 17.92 0.00 0.00 2.57
583 588 8.498575 TGGATATAATAGATGGGTTTTGTCACA 58.501 33.333 0.00 0.00 0.00 3.58
939 945 2.102109 TTTGTTGGGCGAGCTCGGTA 62.102 55.000 35.10 6.71 40.23 4.02
1216 1222 1.131638 TTCTCCTCAGTGTTGGCAGT 58.868 50.000 0.00 0.00 0.00 4.40
1218 1224 1.202806 CCTTTCTCCTCAGTGTTGGCA 60.203 52.381 0.00 0.00 0.00 4.92
1227 1233 0.329261 CATGCACCCCTTTCTCCTCA 59.671 55.000 0.00 0.00 0.00 3.86
1238 1244 2.725221 ATCCTTCTCTTCATGCACCC 57.275 50.000 0.00 0.00 0.00 4.61
1288 1294 2.040412 ACTTTTCCTCGAAGGCTGGAAT 59.960 45.455 5.01 0.00 39.30 3.01
1535 1542 9.203421 CTTTTGTTCTAAATTACATTGTTCCCC 57.797 33.333 0.00 0.00 0.00 4.81
1537 1544 8.708742 GCCTTTTGTTCTAAATTACATTGTTCC 58.291 33.333 0.00 0.00 0.00 3.62
1549 1556 4.887071 TCTGCTTGAGCCTTTTGTTCTAAA 59.113 37.500 0.00 0.00 41.18 1.85
1638 1645 3.443145 TCCCATTTTGGTATGTTCCGT 57.557 42.857 0.00 0.00 35.17 4.69
1658 1665 0.810648 ATTTGTCGATGCCGCATGTT 59.189 45.000 11.49 0.00 35.37 2.71
1681 1688 3.031013 CAACCCAAACCCCTATGAATCC 58.969 50.000 0.00 0.00 0.00 3.01
1745 1943 3.201290 GGTGCAGATGAAGGACATACAG 58.799 50.000 0.00 0.00 39.56 2.74
1768 1966 1.868469 TTTGCAGCAATTGAAGCCAC 58.132 45.000 9.12 0.00 0.00 5.01
1802 2000 7.793888 CCTAAACAATTGATTGATCGTATGTCG 59.206 37.037 13.59 0.00 40.14 4.35
1847 2045 4.573607 GTCGATGGGGTTAGGTACAAATTC 59.426 45.833 0.00 0.00 0.00 2.17
1849 2047 3.118149 GGTCGATGGGGTTAGGTACAAAT 60.118 47.826 0.00 0.00 0.00 2.32
2172 2376 5.518128 TGAACATGTTTTGGAAACACGAATG 59.482 36.000 13.36 6.01 42.67 2.67
2250 2455 9.986833 ATTTGAACAAAGTGAGCAAAAATAAAC 57.013 25.926 6.18 0.00 33.32 2.01


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

AutoCloner maintained by Alex Coulton.