Multiple sequence alignment - TraesCS1D01G438300

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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 TraesCS1D01G438300 chr1D 100.000 2509 0 0 1 2509 485327308 485324800 0.000000e+00 4634.0
1 TraesCS1D01G438300 chr1A 95.840 1779 64 7 736 2509 582510031 582508258 0.000000e+00 2867.0
2 TraesCS1D01G438300 chr1A 96.388 1135 27 4 773 1903 582560789 582559665 0.000000e+00 1857.0
3 TraesCS1D01G438300 chr1A 95.408 392 15 3 1 391 582561590 582561201 2.740000e-174 621.0
4 TraesCS1D01G438300 chr1A 95.846 337 14 0 384 720 582510355 582510019 1.700000e-151 545.0
5 TraesCS1D01G438300 chr1A 97.170 318 8 1 387 704 582561100 582560784 1.020000e-148 536.0
6 TraesCS1D01G438300 chr1A 83.922 566 44 20 1514 2072 582638475 582637950 4.820000e-137 497.0
7 TraesCS1D01G438300 chr1B 95.811 1122 38 2 382 1503 675656221 675655109 0.000000e+00 1803.0
8 TraesCS1D01G438300 chr1B 86.168 535 40 9 1539 2043 675653352 675652822 4.720000e-152 547.0
9 TraesCS1D01G438300 chr1B 83.519 449 57 10 2074 2509 675652820 675652376 1.080000e-108 403.0
10 TraesCS1D01G438300 chr1B 82.723 191 11 7 222 391 675656506 675656317 1.550000e-32 150.0
11 TraesCS1D01G438300 chr1B 83.929 112 18 0 2394 2505 307153778 307153889 9.490000e-20 108.0
12 TraesCS1D01G438300 chr1B 91.139 79 5 2 1 78 675656561 675656484 3.410000e-19 106.0
13 TraesCS1D01G438300 chr7D 83.444 302 46 4 386 686 252550837 252550539 6.840000e-71 278.0
14 TraesCS1D01G438300 chr7D 100.000 31 0 0 278 308 523544169 523544199 9.690000e-05 58.4
15 TraesCS1D01G438300 chr7A 82.828 297 48 3 389 683 27948208 27947913 1.910000e-66 263.0
16 TraesCS1D01G438300 chr7A 82.492 297 49 3 389 683 527993715 527994010 8.900000e-65 257.0
17 TraesCS1D01G438300 chr7A 82.155 297 50 3 389 683 735503312 735503607 4.140000e-63 252.0
18 TraesCS1D01G438300 chr3D 82.155 297 50 3 389 683 127298506 127298801 4.140000e-63 252.0
19 TraesCS1D01G438300 chr3D 81.145 297 53 3 389 683 14532738 14533033 4.170000e-58 235.0
20 TraesCS1D01G438300 chr2B 84.252 127 16 4 2381 2505 736402933 736402809 1.220000e-23 121.0
21 TraesCS1D01G438300 chr2B 83.465 127 17 4 2381 2504 35036431 35036306 5.670000e-22 115.0
22 TraesCS1D01G438300 chr2B 82.677 127 18 3 2382 2505 50414325 50414450 2.640000e-20 110.0
23 TraesCS1D01G438300 chr2B 82.677 127 17 5 2381 2505 785955703 785955580 9.490000e-20 108.0
24 TraesCS1D01G438300 chrUn 83.333 126 19 2 2381 2505 38942991 38942867 5.670000e-22 115.0
25 TraesCS1D01G438300 chr7B 83.465 127 17 4 2381 2505 175894831 175894955 5.670000e-22 115.0
26 TraesCS1D01G438300 chr6B 81.395 129 19 5 2381 2505 679385566 679385693 1.590000e-17 100.0


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 TraesCS1D01G438300 chr1D 485324800 485327308 2508 True 4634.000000 4634 100.000 1 2509 1 chr1D.!!$R1 2508
1 TraesCS1D01G438300 chr1A 582508258 582510355 2097 True 1706.000000 2867 95.843 384 2509 2 chr1A.!!$R2 2125
2 TraesCS1D01G438300 chr1A 582559665 582561590 1925 True 1004.666667 1857 96.322 1 1903 3 chr1A.!!$R3 1902
3 TraesCS1D01G438300 chr1A 582637950 582638475 525 True 497.000000 497 83.922 1514 2072 1 chr1A.!!$R1 558
4 TraesCS1D01G438300 chr1B 675652376 675656561 4185 True 601.800000 1803 87.872 1 2509 5 chr1B.!!$R1 2508

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
489 615 5.621193 TCGTATATGAGTGGAGAGATGTCA 58.379 41.667 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 4304 0.036875 AAAGGCAGGAGGGTTTCTCG 59.963 55.0 0.0 0.0 43.34 4.04 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
240 241 7.762615 CCATGAACTTTATTCAGATGTGCAAAT 59.237 33.333 0.00 0.00 0.00 2.32
489 615 5.621193 TCGTATATGAGTGGAGAGATGTCA 58.379 41.667 0.00 0.00 0.00 3.58
729 855 6.183360 ACCAACTGGAAATACAAGGTTCAAAG 60.183 38.462 1.86 0.00 38.94 2.77
863 990 8.487176 GTGATTAATTTGGCGCCATATTTTTAG 58.513 33.333 38.25 0.00 31.83 1.85
948 1075 9.558133 TTTCATATCTTCTCCATCTCATCCTAT 57.442 33.333 0.00 0.00 0.00 2.57
966 1093 7.619698 TCATCCTATAATCGGGACAACTATCAT 59.380 37.037 0.00 0.00 34.16 2.45
1058 1185 7.672897 CGTTTCTCGTGCTACCATCAGGTAT 62.673 48.000 0.00 0.00 40.97 2.73
1122 1249 7.094291 CCATCAAATTTTGCCAATAACAATGGT 60.094 33.333 4.19 0.00 40.23 3.55
1222 1349 2.416836 GGTACAGCGTGTGATAGAAGCA 60.417 50.000 0.00 0.00 0.00 3.91
1359 1486 3.004419 GTGATGATCACAGCCATCCATTG 59.996 47.826 19.96 0.00 46.22 2.82
1366 1493 3.530260 GCCATCCATTGGGGCACG 61.530 66.667 15.76 0.00 46.55 5.34
1571 3419 1.613925 CCTTCCAGACGTGTCTCAAGA 59.386 52.381 15.30 5.29 37.98 3.02
1651 3508 0.172127 ATCGATGGATGGATCGCTCG 59.828 55.000 0.00 0.00 44.04 5.03
1743 3600 1.472201 GCTTGACCTCGATGATGCTCA 60.472 52.381 0.00 0.00 0.00 4.26
1940 3818 7.062605 GGTGCATTAATGATTTGTCTTCACAAG 59.937 37.037 19.73 0.00 43.54 3.16
1987 3865 5.892119 AGGGACGATTACTTGTATTCTCAGA 59.108 40.000 0.00 0.00 0.00 3.27
2086 3970 1.372872 GTGCGGCCACAATGGTTTC 60.373 57.895 2.24 0.00 40.46 2.78
2093 3977 1.547675 GCCACAATGGTTTCCAGAGGA 60.548 52.381 0.00 0.00 40.46 3.71
2218 4109 2.430465 GACTCTACGGTCTACACCACA 58.570 52.381 0.00 0.00 44.02 4.17
2256 4147 2.160417 CGCTCTCCCTTTGTTCACATTC 59.840 50.000 0.00 0.00 0.00 2.67
2288 4179 7.178628 TGGCTTGGCTTAATCTATACCTACTAG 59.821 40.741 0.00 0.00 0.00 2.57
2368 4259 7.454694 ACCCCTTGCTTTTTCTATGAATTAACT 59.545 33.333 0.00 0.00 0.00 2.24
2370 4261 7.976175 CCCTTGCTTTTTCTATGAATTAACTCC 59.024 37.037 0.00 0.00 0.00 3.85
2371 4262 8.743714 CCTTGCTTTTTCTATGAATTAACTCCT 58.256 33.333 0.00 0.00 0.00 3.69
2413 4304 2.939756 ACAAACCGGGTTTTGCATTTTC 59.060 40.909 22.13 0.00 39.67 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.824534 AATTTGAAAAATGTTCACAAAGTTGAC 57.175 25.926 0.00 0.00 34.73 3.18
209 210 9.512435 CACATCTGAATAAAGTTCATGGATTTC 57.488 33.333 0.00 0.00 0.00 2.17
322 344 5.175491 GCGCATTGAAGAAAGAAAACAATGA 59.825 36.000 18.09 0.00 45.70 2.57
523 649 0.321298 GGCACAAGGAAGCCGTTCTA 60.321 55.000 0.00 0.00 41.70 2.10
744 870 2.170397 AGCCAACGGATCACATGATGTA 59.830 45.455 0.00 0.00 34.37 2.29
863 990 8.637986 TCCAATATGTTAATTTAGGAATGCCAC 58.362 33.333 0.00 0.00 36.29 5.01
948 1075 4.343814 TGCTGATGATAGTTGTCCCGATTA 59.656 41.667 0.00 0.00 0.00 1.75
951 1078 2.107366 TGCTGATGATAGTTGTCCCGA 58.893 47.619 0.00 0.00 0.00 5.14
1222 1349 6.357367 AGTTCTTACATTTGTCCTCACACTT 58.643 36.000 0.00 0.00 29.76 3.16
1255 1382 7.394816 ACACAAGTAGAATGCTGGTAATAGTT 58.605 34.615 0.00 0.00 30.05 2.24
1359 1486 1.947456 GATCAGTTTATTCCGTGCCCC 59.053 52.381 0.00 0.00 0.00 5.80
1798 3655 1.295792 TTGTGCTTGTGTCTCCGTTC 58.704 50.000 0.00 0.00 0.00 3.95
1940 3818 3.308438 TCGTTACCAGAACTACTTGGC 57.692 47.619 0.00 0.00 0.00 4.52
2086 3970 0.398664 ACGGTTAGGGGATCCTCTGG 60.399 60.000 25.43 12.72 43.66 3.86
2093 3977 2.249309 AGTTCAGACGGTTAGGGGAT 57.751 50.000 0.00 0.00 0.00 3.85
2164 4052 4.520492 ACTCTGCCAGGTTGAATACAAAAG 59.480 41.667 0.00 0.00 37.77 2.27
2218 4109 3.896888 AGAGCGAGAGAGGAATCAATCAT 59.103 43.478 0.00 0.00 0.00 2.45
2256 4147 1.394266 ATTAAGCCAAGCCATGCCCG 61.394 55.000 0.00 0.00 0.00 6.13
2304 4195 1.135721 GACGGACGGGTATAAGCACTT 59.864 52.381 0.00 0.00 0.00 3.16
2312 4203 2.381911 ACTTATGTGACGGACGGGTAT 58.618 47.619 0.00 0.00 0.00 2.73
2368 4259 7.047891 GTCCATGACTTAAATGTGTGATAGGA 58.952 38.462 0.00 0.00 0.00 2.94
2370 4261 7.848223 TGTCCATGACTTAAATGTGTGATAG 57.152 36.000 0.00 0.00 33.15 2.08
2371 4262 8.511321 GTTTGTCCATGACTTAAATGTGTGATA 58.489 33.333 0.00 0.00 33.15 2.15
2413 4304 0.036875 AAAGGCAGGAGGGTTTCTCG 59.963 55.000 0.00 0.00 43.34 4.04


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

AutoCloner maintained by Alex Coulton.