Multiple sequence alignment - TraesCS7D01G195600

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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 TraesCS7D01G195600 chr7D 100.000 3073 0 0 1 3073 151941640 151938568 0.000000e+00 5675.0
1 TraesCS7D01G195600 chr7D 96.836 1612 35 7 1 1604 151857616 151856013 0.000000e+00 2680.0
2 TraesCS7D01G195600 chr7D 97.847 1486 29 2 1588 3073 151855998 151854516 0.000000e+00 2564.0
3 TraesCS7D01G195600 chr7D 95.821 1005 27 4 597 1591 152099390 152098391 0.000000e+00 1609.0
4 TraesCS7D01G195600 chr7D 93.260 638 36 4 1601 2237 152098348 152097717 0.000000e+00 933.0
5 TraesCS7D01G195600 chr7D 81.427 1163 147 41 970 2100 152120440 152121565 0.000000e+00 887.0
6 TraesCS7D01G195600 chr7D 95.238 399 12 5 185 580 152100952 152100558 2.600000e-175 625.0
7 TraesCS7D01G195600 chr7D 96.373 193 4 1 1 190 152101412 152101220 6.400000e-82 315.0
8 TraesCS7D01G195600 chr7D 98.246 57 1 0 2913 2969 304976529 304976473 1.950000e-17 100.0
9 TraesCS7D01G195600 chr7D 77.848 158 35 0 1400 1557 538895308 538895151 7.010000e-17 99.0
10 TraesCS7D01G195600 chr7B 91.358 1782 95 26 511 2263 113770024 113771775 0.000000e+00 2383.0
11 TraesCS7D01G195600 chr7B 79.915 1414 194 60 731 2100 114178288 114179655 0.000000e+00 955.0
12 TraesCS7D01G195600 chr7B 83.601 561 45 13 2314 2861 113772125 113772651 1.660000e-132 483.0
13 TraesCS7D01G195600 chr7B 85.799 338 31 11 1865 2188 113772649 113772983 2.930000e-90 342.0
14 TraesCS7D01G195600 chr7B 77.215 158 36 0 1400 1557 581395681 581395524 3.260000e-15 93.5
15 TraesCS7D01G195600 chr7B 95.745 47 2 0 141 187 144071034 144071080 3.290000e-10 76.8
16 TraesCS7D01G195600 chr7B 92.308 52 3 1 137 187 371966474 371966525 4.250000e-09 73.1
17 TraesCS7D01G195600 chr7B 87.931 58 7 0 128 185 90799139 90799196 5.500000e-08 69.4
18 TraesCS7D01G195600 chrUn 90.072 977 58 13 1 952 85642119 85641157 0.000000e+00 1230.0
19 TraesCS7D01G195600 chr7A 82.293 1169 141 37 970 2114 152540367 152541493 0.000000e+00 952.0
20 TraesCS7D01G195600 chr7A 77.848 158 35 0 1400 1557 620412450 620412293 7.010000e-17 99.0
21 TraesCS7D01G195600 chr6A 98.246 57 1 0 2913 2969 375844374 375844318 1.950000e-17 100.0
22 TraesCS7D01G195600 chr6A 92.308 52 3 1 138 188 213553469 213553520 4.250000e-09 73.1
23 TraesCS7D01G195600 chr5D 98.246 57 1 0 2913 2969 58707128 58707072 1.950000e-17 100.0
24 TraesCS7D01G195600 chr5D 90.566 53 4 1 137 188 273121468 273121416 5.500000e-08 69.4
25 TraesCS7D01G195600 chr3D 98.246 57 1 0 2913 2969 498475580 498475636 1.950000e-17 100.0
26 TraesCS7D01G195600 chr3A 98.246 57 1 0 2913 2969 640146620 640146564 1.950000e-17 100.0
27 TraesCS7D01G195600 chr2A 98.246 57 1 0 2913 2969 588460040 588460096 1.950000e-17 100.0
28 TraesCS7D01G195600 chr2A 98.246 57 1 0 2913 2969 755488661 755488605 1.950000e-17 100.0
29 TraesCS7D01G195600 chr1A 98.246 57 1 0 2913 2969 94702819 94702875 1.950000e-17 100.0
30 TraesCS7D01G195600 chr1B 96.000 50 1 1 139 187 480973021 480972972 2.540000e-11 80.5


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 TraesCS7D01G195600 chr7D 151938568 151941640 3072 True 5675.000000 5675 100.000000 1 3073 1 chr7D.!!$R1 3072
1 TraesCS7D01G195600 chr7D 151854516 151857616 3100 True 2622.000000 2680 97.341500 1 3073 2 chr7D.!!$R4 3072
2 TraesCS7D01G195600 chr7D 152120440 152121565 1125 False 887.000000 887 81.427000 970 2100 1 chr7D.!!$F1 1130
3 TraesCS7D01G195600 chr7D 152097717 152101412 3695 True 870.500000 1609 95.173000 1 2237 4 chr7D.!!$R5 2236
4 TraesCS7D01G195600 chr7B 113770024 113772983 2959 False 1069.333333 2383 86.919333 511 2861 3 chr7B.!!$F5 2350
5 TraesCS7D01G195600 chr7B 114178288 114179655 1367 False 955.000000 955 79.915000 731 2100 1 chr7B.!!$F2 1369
6 TraesCS7D01G195600 chrUn 85641157 85642119 962 True 1230.000000 1230 90.072000 1 952 1 chrUn.!!$R1 951
7 TraesCS7D01G195600 chr7A 152540367 152541493 1126 False 952.000000 952 82.293000 970 2114 1 chr7A.!!$F1 1144

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
865 2322 1.32474 ACTAGTGCGTGGCCCGATTA 61.325 55.0 16.53 5.32 39.56 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 3796 4.084013 GGAATTCAAATAGACGGCCATACG 60.084 45.833 7.93 0.0 40.31 3.06 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
105 111 4.586421 CACCTCAGCTCATATCCTTAGTGA 59.414 45.833 0.00 0.00 0.00 3.41
293 572 3.243367 TGTCCGTTTGCTTTGAGATTTGG 60.243 43.478 0.00 0.00 0.00 3.28
459 739 2.863740 TCCAATATGAACTAAGTGCGCG 59.136 45.455 0.00 0.00 0.00 6.86
767 2217 5.183904 AGTTGTGATCATTAAGCAAAGACCC 59.816 40.000 0.00 0.00 0.00 4.46
768 2218 3.689161 TGTGATCATTAAGCAAAGACCCG 59.311 43.478 0.00 0.00 0.00 5.28
769 2219 3.938963 GTGATCATTAAGCAAAGACCCGA 59.061 43.478 0.00 0.00 0.00 5.14
770 2220 3.938963 TGATCATTAAGCAAAGACCCGAC 59.061 43.478 0.00 0.00 0.00 4.79
771 2221 2.706890 TCATTAAGCAAAGACCCGACC 58.293 47.619 0.00 0.00 0.00 4.79
865 2322 1.324740 ACTAGTGCGTGGCCCGATTA 61.325 55.000 16.53 5.32 39.56 1.75
1176 2673 1.546029 CGTCTCACCATGGACAAGAGA 59.454 52.381 21.47 20.17 33.30 3.10
1207 2704 1.009389 GTTCTGCTCCAAGTCGACGG 61.009 60.000 10.46 6.53 0.00 4.79
1212 2709 1.890894 CTCCAAGTCGACGGATGGT 59.109 57.895 26.48 2.90 34.50 3.55
1218 2715 4.137872 TCGACGGATGGTTCGGGC 62.138 66.667 0.00 0.00 0.00 6.13
1375 2885 0.524414 GTGCATGCAGCTGATGTCAA 59.476 50.000 23.41 6.15 45.94 3.18
2131 3724 3.054287 TGGTTTATTTATGCACGGGAGGA 60.054 43.478 0.00 0.00 0.00 3.71
2132 3725 3.564225 GGTTTATTTATGCACGGGAGGAG 59.436 47.826 0.00 0.00 0.00 3.69
2140 3733 2.110967 CACGGGAGGAGCAAGCATG 61.111 63.158 0.00 0.00 0.00 4.06
2243 3836 5.296780 TGAATTCCAAGCCGACTGATTTATC 59.703 40.000 2.27 0.00 0.00 1.75
2316 3933 7.090173 GCAATTCCACACTCTTGCTTTATTAA 58.910 34.615 0.00 0.00 40.55 1.40
2475 4369 4.437682 TTCTGAGGTTGTCTTTGACCAT 57.562 40.909 0.00 0.00 38.42 3.55
2572 4466 7.388224 TGTTGCAAAACTATACGGTCTAATTCA 59.612 33.333 0.00 0.00 0.00 2.57
2573 4467 7.298507 TGCAAAACTATACGGTCTAATTCAC 57.701 36.000 0.00 0.00 0.00 3.18
2786 4682 2.032290 CGTTCTTGGAAAAGGTTCGACC 60.032 50.000 0.00 0.00 38.99 4.79
3021 4927 6.383415 GTGCCACCTTCATCGTTATTTTAAA 58.617 36.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
293 572 5.351189 ACTTGTGAAACTCAAACAATTTGCC 59.649 36.000 0.00 0.00 36.11 4.52
709 2142 3.334691 CTTCGTGGTTTGCTAATCCAGA 58.665 45.455 3.32 0.00 31.54 3.86
767 2217 1.741770 CTTCTTCGGCTTGGGGTCG 60.742 63.158 0.00 0.00 45.40 4.79
768 2218 0.673956 GTCTTCTTCGGCTTGGGGTC 60.674 60.000 0.00 0.00 0.00 4.46
769 2219 1.375326 GTCTTCTTCGGCTTGGGGT 59.625 57.895 0.00 0.00 0.00 4.95
770 2220 0.035056 ATGTCTTCTTCGGCTTGGGG 60.035 55.000 0.00 0.00 0.00 4.96
771 2221 1.373570 GATGTCTTCTTCGGCTTGGG 58.626 55.000 0.00 0.00 0.00 4.12
865 2322 1.676006 CTTCTCCACCACGCAAAACTT 59.324 47.619 0.00 0.00 0.00 2.66
902 2362 7.148390 ACACGTTAGATCATCGATTCGATCTAT 60.148 37.037 24.86 14.32 45.83 1.98
1207 2704 2.781911 GGAAGAAGCCCGAACCATC 58.218 57.895 0.00 0.00 0.00 3.51
1218 2715 0.250234 TGACCCTCATGCGGAAGAAG 59.750 55.000 2.42 0.00 0.00 2.85
1375 2885 1.827969 GTCACTGCTCTGAGGTGGTAT 59.172 52.381 6.83 0.00 0.00 2.73
2131 3724 5.361571 TGAACATCCATTAATCATGCTTGCT 59.638 36.000 4.45 0.00 0.00 3.91
2132 3725 5.461078 GTGAACATCCATTAATCATGCTTGC 59.539 40.000 4.45 0.00 0.00 4.01
2203 3796 4.084013 GGAATTCAAATAGACGGCCATACG 60.084 45.833 7.93 0.00 40.31 3.06
2243 3836 5.404946 CCATGGTGCTTCTCAAAGTAAATG 58.595 41.667 2.57 0.00 34.79 2.32
2316 3933 6.292150 ACTAAAAAGAAACTAGTGAGCTGCT 58.708 36.000 0.00 0.00 0.00 4.24
2359 4253 8.157159 ACATCATCTTTAATTTTTGTAACGCG 57.843 30.769 3.53 3.53 0.00 6.01
2572 4466 6.174720 TCACTAGAAACTCCTTTGACATGT 57.825 37.500 0.00 0.00 0.00 3.21
2573 4467 8.954950 ATATCACTAGAAACTCCTTTGACATG 57.045 34.615 0.00 0.00 0.00 3.21
2786 4682 6.209391 CCAAGGGGTTAATTATAGATTGGCTG 59.791 42.308 0.00 0.00 0.00 4.85
2943 4849 5.025986 TCGTTTCACTCGAATTTAAAGGC 57.974 39.130 0.00 0.00 34.36 4.35


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

AutoCloner maintained by Alex Coulton.