Multiple sequence alignment - TraesCS5D01G191700

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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 TraesCS5D01G191700 chr5D 100.000 2213 0 0 1 2213 294588153 294590365 0.000000e+00 4087.0
1 TraesCS5D01G191700 chr5D 98.407 1067 16 1 1 1067 420607449 420608514 0.000000e+00 1875.0
2 TraesCS5D01G191700 chr3B 94.545 1210 61 4 260 1466 803621293 803620086 0.000000e+00 1864.0
3 TraesCS5D01G191700 chr2B 94.563 1214 53 3 256 1468 98131710 98132911 0.000000e+00 1864.0
4 TraesCS5D01G191700 chr2B 93.909 1215 61 3 256 1469 4914535 4913333 0.000000e+00 1821.0
5 TraesCS5D01G191700 chr6A 94.408 1216 55 4 256 1470 565055785 565056988 0.000000e+00 1857.0
6 TraesCS5D01G191700 chr7A 93.909 1215 61 3 256 1469 736100039 736098837 0.000000e+00 1821.0
7 TraesCS5D01G191700 chr7A 93.822 1214 62 3 256 1468 191846472 191847673 0.000000e+00 1814.0
8 TraesCS5D01G191700 chr7A 89.597 471 40 7 72 535 267987592 267988060 6.810000e-165 590.0
9 TraesCS5D01G191700 chr6B 93.740 1214 63 3 256 1468 558920531 558921732 0.000000e+00 1808.0
10 TraesCS5D01G191700 chr6B 93.932 824 36 4 646 1468 149020339 149019529 0.000000e+00 1232.0
11 TraesCS5D01G191700 chr5A 95.582 747 29 3 1468 2213 387893271 387894014 0.000000e+00 1194.0
12 TraesCS5D01G191700 chr6D 89.053 950 75 10 543 1468 390609118 390610062 0.000000e+00 1151.0
13 TraesCS5D01G191700 chr5B 95.918 637 15 8 1580 2213 336135604 336136232 0.000000e+00 1022.0
14 TraesCS5D01G191700 chr5B 95.041 121 5 1 1468 1588 336135367 336135486 2.900000e-44 189.0
15 TraesCS5D01G191700 chr3A 86.111 72 9 1 1839 1910 61212963 61212893 2.360000e-10 76.8


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 TraesCS5D01G191700 chr5D 294588153 294590365 2212 False 4087.0 4087 100.0000 1 2213 1 chr5D.!!$F1 2212
1 TraesCS5D01G191700 chr5D 420607449 420608514 1065 False 1875.0 1875 98.4070 1 1067 1 chr5D.!!$F2 1066
2 TraesCS5D01G191700 chr3B 803620086 803621293 1207 True 1864.0 1864 94.5450 260 1466 1 chr3B.!!$R1 1206
3 TraesCS5D01G191700 chr2B 98131710 98132911 1201 False 1864.0 1864 94.5630 256 1468 1 chr2B.!!$F1 1212
4 TraesCS5D01G191700 chr2B 4913333 4914535 1202 True 1821.0 1821 93.9090 256 1469 1 chr2B.!!$R1 1213
5 TraesCS5D01G191700 chr6A 565055785 565056988 1203 False 1857.0 1857 94.4080 256 1470 1 chr6A.!!$F1 1214
6 TraesCS5D01G191700 chr7A 736098837 736100039 1202 True 1821.0 1821 93.9090 256 1469 1 chr7A.!!$R1 1213
7 TraesCS5D01G191700 chr7A 191846472 191847673 1201 False 1814.0 1814 93.8220 256 1468 1 chr7A.!!$F1 1212
8 TraesCS5D01G191700 chr6B 558920531 558921732 1201 False 1808.0 1808 93.7400 256 1468 1 chr6B.!!$F1 1212
9 TraesCS5D01G191700 chr6B 149019529 149020339 810 True 1232.0 1232 93.9320 646 1468 1 chr6B.!!$R1 822
10 TraesCS5D01G191700 chr5A 387893271 387894014 743 False 1194.0 1194 95.5820 1468 2213 1 chr5A.!!$F1 745
11 TraesCS5D01G191700 chr6D 390609118 390610062 944 False 1151.0 1151 89.0530 543 1468 1 chr6D.!!$F1 925
12 TraesCS5D01G191700 chr5B 336135367 336136232 865 False 605.5 1022 95.4795 1468 2213 2 chr5B.!!$F1 745

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
144 145 4.497516 AGCCACCTAAGATCATCCTGTAT 58.502 43.478 0.0 0.0 0.0 2.29 F
663 665 4.985409 GGGCTACATTACTCTTCTCATTCG 59.015 45.833 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1098 1.068588 GCCCTTTTGTCAACACCCTTC 59.931 52.381 0.0 0.0 0.0 3.46 R
2040 2197 3.514309 ACAAAGAGACTAGGCGGTGTTAT 59.486 43.478 0.0 0.0 0.0 1.89 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
144 145 4.497516 AGCCACCTAAGATCATCCTGTAT 58.502 43.478 0.00 0.0 0.00 2.29
151 152 7.121315 CACCTAAGATCATCCTGTATCGTATGA 59.879 40.741 0.00 0.0 33.20 2.15
231 232 8.489489 TGCAGAAAGAAATATCTTCCTGTATCT 58.511 33.333 6.67 0.0 46.50 1.98
249 250 5.710099 TGTATCTGTTGGATGTTTTTCCCTC 59.290 40.000 0.00 0.0 35.98 4.30
254 255 5.450453 TGTTGGATGTTTTTCCCTCTGTTA 58.550 37.500 0.00 0.0 34.67 2.41
287 288 8.376270 AGCACTAGGTTCTCTTAAAACACTATT 58.624 33.333 0.00 0.0 0.00 1.73
614 616 7.233348 TCAAAGGCAAGAAAATCCATCTAAAGT 59.767 33.333 0.00 0.0 0.00 2.66
663 665 4.985409 GGGCTACATTACTCTTCTCATTCG 59.015 45.833 0.00 0.0 0.00 3.34
1071 1098 2.574322 GCTGTCACAACACGCTTTATG 58.426 47.619 0.00 0.0 31.16 1.90
1084 1111 2.811431 CGCTTTATGAAGGGTGTTGACA 59.189 45.455 6.17 0.0 40.04 3.58
1140 1168 0.684535 TCCGTCAGGCACAGATGAAA 59.315 50.000 0.00 0.0 32.26 2.69
1321 1349 7.313731 TCTTATGTAATCCCCTAAGACCATCT 58.686 38.462 0.00 0.0 0.00 2.90
1370 1398 6.127338 TGCTGCTTAGACTGATGTGTAGTATT 60.127 38.462 0.00 0.0 0.00 1.89
1549 1577 2.549754 CACAGAACATGCTTTCCTCGTT 59.450 45.455 0.00 0.0 0.00 3.85
1551 1579 3.070018 CAGAACATGCTTTCCTCGTTCT 58.930 45.455 0.00 0.0 45.34 3.01
1556 1584 0.319555 TGCTTTCCTCGTTCTCACCG 60.320 55.000 0.00 0.0 0.00 4.94
1593 1747 7.864108 AGTTTATGCTGAGCAATTGTATGTA 57.136 32.000 12.69 0.0 43.62 2.29
1885 2041 9.822727 TGTTTGATCAGGACCTATGATACTATA 57.177 33.333 0.00 0.0 37.52 1.31
2075 2232 7.757624 CCTAGTCTCTTTGTCATCTTAGTTGTC 59.242 40.741 0.00 0.0 0.00 3.18
2119 2276 3.719268 TGATCCCTGTATTGCAGTTGT 57.281 42.857 0.98 0.0 43.55 3.32
2125 2282 3.696051 CCCTGTATTGCAGTTGTAGCATT 59.304 43.478 0.98 0.0 43.55 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 5.121611 CAGCAAACAACCAATAGTCATACGA 59.878 40.000 0.00 0.00 0.00 3.43
151 152 5.240844 GTCTTACCAGCAAACAACCAATAGT 59.759 40.000 0.00 0.00 0.00 2.12
231 232 3.909732 ACAGAGGGAAAAACATCCAACA 58.090 40.909 0.00 0.00 41.55 3.33
249 250 4.727507 ACCTAGTGCTGATCTGTAACAG 57.272 45.455 1.27 0.00 37.22 3.16
254 255 3.707316 AGAGAACCTAGTGCTGATCTGT 58.293 45.455 1.27 0.00 0.00 3.41
287 288 8.792830 AGCAAATAGAAACTTAGTGCTGATAA 57.207 30.769 0.00 0.00 0.00 1.75
614 616 4.536090 ACCATGGAGAATGTACTTTCCAGA 59.464 41.667 21.47 3.06 42.54 3.86
663 665 3.802685 AGTAGTTGTTGCGAGAGTTGTTC 59.197 43.478 0.00 0.00 0.00 3.18
1071 1098 1.068588 GCCCTTTTGTCAACACCCTTC 59.931 52.381 0.00 0.00 0.00 3.46
1084 1111 2.990740 TTAGTGATGGTGGCCCTTTT 57.009 45.000 0.00 0.00 0.00 2.27
1321 1349 7.486551 GCAAATTACCGATAGTTAAATGCACAA 59.513 33.333 0.00 0.00 0.00 3.33
1370 1398 6.942005 TCTTTTATCATGGCTGTCTCAAAAGA 59.058 34.615 0.00 0.00 38.02 2.52
1551 1579 8.658609 GCATAAACTACTTAAATTACACGGTGA 58.341 33.333 16.29 0.00 0.00 4.02
1556 1584 9.704098 GCTCAGCATAAACTACTTAAATTACAC 57.296 33.333 0.00 0.00 0.00 2.90
1885 2041 7.372260 ACAGTAGAGCAATATGGAAGAAGAT 57.628 36.000 0.00 0.00 0.00 2.40
2040 2197 3.514309 ACAAAGAGACTAGGCGGTGTTAT 59.486 43.478 0.00 0.00 0.00 1.89
2110 2267 9.138062 CATTTGTAATAAATGCTACAACTGCAA 57.862 29.630 0.00 0.00 44.01 4.08
2112 2269 7.222611 CCCATTTGTAATAAATGCTACAACTGC 59.777 37.037 6.81 0.00 37.36 4.40
2119 2276 9.349713 CTACTTCCCCATTTGTAATAAATGCTA 57.650 33.333 6.81 0.00 36.56 3.49
2125 2282 9.184523 CATGAACTACTTCCCCATTTGTAATAA 57.815 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.