Multiple sequence alignment - TraesCS3B01G442500

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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 TraesCS3B01G442500 chr3B 100.000 2450 0 0 1 2450 682015432 682012983 0.000000e+00 4525
1 TraesCS3B01G442500 chr3B 91.304 138 10 2 2314 2450 321733783 321733647 1.160000e-43 187
2 TraesCS3B01G442500 chr3B 90.580 138 11 2 2314 2450 393195360 393195496 5.380000e-42 182
3 TraesCS3B01G442500 chr2B 93.040 2457 152 13 1 2450 550079267 550076823 0.000000e+00 3572
4 TraesCS3B01G442500 chr1B 92.342 2455 146 32 2 2440 346594896 346597324 0.000000e+00 3454
5 TraesCS3B01G442500 chr1B 93.475 2314 129 15 1 2303 106887645 106889947 0.000000e+00 3417
6 TraesCS3B01G442500 chr4B 91.182 2495 165 35 1 2450 78829610 78827126 0.000000e+00 3338
7 TraesCS3B01G442500 chr4A 91.203 2478 164 36 2 2440 721639036 721641498 0.000000e+00 3319
8 TraesCS3B01G442500 chr4A 90.024 2456 223 14 2 2450 500274898 500272458 0.000000e+00 3158
9 TraesCS3B01G442500 chr6D 91.046 2457 198 12 1 2450 283635549 283633108 0.000000e+00 3299
10 TraesCS3B01G442500 chr5B 90.854 2471 183 26 1 2440 547746192 547748650 0.000000e+00 3271
11 TraesCS3B01G442500 chr5B 90.692 2471 187 26 1 2440 547767243 547769701 0.000000e+00 3249
12 TraesCS3B01G442500 chr5B 88.128 219 16 7 2241 2450 4634660 4634443 4.040000e-63 252
13 TraesCS3B01G442500 chr7B 89.855 138 12 2 2314 2450 368858040 368858176 2.500000e-40 176


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 TraesCS3B01G442500 chr3B 682012983 682015432 2449 True 4525 4525 100.000 1 2450 1 chr3B.!!$R2 2449
1 TraesCS3B01G442500 chr2B 550076823 550079267 2444 True 3572 3572 93.040 1 2450 1 chr2B.!!$R1 2449
2 TraesCS3B01G442500 chr1B 346594896 346597324 2428 False 3454 3454 92.342 2 2440 1 chr1B.!!$F2 2438
3 TraesCS3B01G442500 chr1B 106887645 106889947 2302 False 3417 3417 93.475 1 2303 1 chr1B.!!$F1 2302
4 TraesCS3B01G442500 chr4B 78827126 78829610 2484 True 3338 3338 91.182 1 2450 1 chr4B.!!$R1 2449
5 TraesCS3B01G442500 chr4A 721639036 721641498 2462 False 3319 3319 91.203 2 2440 1 chr4A.!!$F1 2438
6 TraesCS3B01G442500 chr4A 500272458 500274898 2440 True 3158 3158 90.024 2 2450 1 chr4A.!!$R1 2448
7 TraesCS3B01G442500 chr6D 283633108 283635549 2441 True 3299 3299 91.046 1 2450 1 chr6D.!!$R1 2449
8 TraesCS3B01G442500 chr5B 547746192 547748650 2458 False 3271 3271 90.854 1 2440 1 chr5B.!!$F1 2439
9 TraesCS3B01G442500 chr5B 547767243 547769701 2458 False 3249 3249 90.692 1 2440 1 chr5B.!!$F2 2439

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
427 431 3.307762 GGTGGTTGCCTCTATCTCAGTTT 60.308 47.826 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2116 2.161609 CCAAGCTAACCCGATTTCACAC 59.838 50.0 0.0 0.0 0.0 3.82 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
271 275 6.887013 ACTCTGATTGATGCTAAGTTGAGAT 58.113 36.000 0.00 0.00 0.00 2.75
368 372 5.992829 CCCACACTTGTGTTACAACTGTATA 59.007 40.000 8.52 0.00 44.21 1.47
427 431 3.307762 GGTGGTTGCCTCTATCTCAGTTT 60.308 47.826 0.00 0.00 0.00 2.66
490 494 5.395657 CCAACTCCTGCACATACATCTAAGA 60.396 44.000 0.00 0.00 0.00 2.10
578 582 5.218959 TCAATATCCTGAGAAGATCCCACA 58.781 41.667 0.00 0.00 0.00 4.17
630 634 6.992123 AGTCATCAGTGTCATTGTTGAAACTA 59.008 34.615 9.85 0.00 46.69 2.24
779 783 5.706447 TGGTAGTAGCACCATAGAAGATCT 58.294 41.667 0.00 0.00 43.76 2.75
812 816 8.090214 AGAGAGATCTCAACTTGAAGAAGAAAG 58.910 37.037 24.39 0.00 45.21 2.62
817 821 6.878317 TCTCAACTTGAAGAAGAAAGACTCA 58.122 36.000 0.00 0.00 32.98 3.41
1124 1128 6.597672 CCTGTTAGTGGCATTACTCACATTAA 59.402 38.462 0.00 0.00 35.10 1.40
1206 1210 8.478066 TCTTATGCTAGTCTTGAGCTTAATGAA 58.522 33.333 0.00 0.00 38.28 2.57
1224 1228 9.297586 CTTAATGAAAAATGTCATCCTCATGTG 57.702 33.333 0.00 0.00 37.25 3.21
1247 1251 5.645067 TGAGTATTGACCTTGCTGATTTCTG 59.355 40.000 0.00 0.00 0.00 3.02
1260 1264 5.098211 GCTGATTTCTGCCATTCTAAACAC 58.902 41.667 0.00 0.00 35.17 3.32
1272 1276 6.183360 GCCATTCTAAACACGTGCTTTATAGT 60.183 38.462 17.22 6.79 0.00 2.12
1282 1286 9.537192 AACACGTGCTTTATAGTTATGCTTATA 57.463 29.630 17.22 0.00 0.00 0.98
1365 1369 3.206150 TGTTGAGTGCTCTTTCAGGTTC 58.794 45.455 0.68 0.00 0.00 3.62
1495 1504 0.394080 GAGAAGCTGGAGCAGGCATT 60.394 55.000 0.65 0.00 45.16 3.56
1592 1605 2.170166 GCTGTTTCATGACCCATTCCA 58.830 47.619 0.00 0.00 0.00 3.53
1716 1736 6.426980 TGCTTGATGTGAATATGTGAACTC 57.573 37.500 0.00 0.00 0.00 3.01
1718 1738 6.430616 TGCTTGATGTGAATATGTGAACTCAA 59.569 34.615 0.00 0.00 0.00 3.02
1720 1740 7.642978 GCTTGATGTGAATATGTGAACTCAATC 59.357 37.037 0.00 0.00 0.00 2.67
1721 1741 7.237920 TGATGTGAATATGTGAACTCAATCG 57.762 36.000 0.00 0.00 0.00 3.34
1953 1973 2.487805 GCATGCTATGTTCCCTGGATCA 60.488 50.000 11.37 0.00 0.00 2.92
2012 2032 5.182190 TCCTATTTTTGTGCTTATGCGTTGA 59.818 36.000 0.00 0.00 43.34 3.18
2089 2116 3.781307 TTCCTGGGATCGGTGGCG 61.781 66.667 0.00 0.00 0.00 5.69
2394 2482 0.171007 AACCTTTGGCGCAATCATCG 59.829 50.000 10.83 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 275 9.739276 ACAAGTGAATTTCTCCATATCTTGTTA 57.261 29.630 0.00 0.0 39.48 2.41
317 321 2.423577 GTGCCACGACTAAATTCCACT 58.576 47.619 0.00 0.0 0.00 4.00
368 372 8.827832 TGATTTCTTCTTGACAAATATCCCAT 57.172 30.769 0.00 0.0 0.00 4.00
630 634 1.911357 TCCTCATCACCATCACTGCTT 59.089 47.619 0.00 0.0 0.00 3.91
779 783 6.726379 TCAAGTTGAGATCTCTCTTCCTCTA 58.274 40.000 22.95 0.0 43.25 2.43
812 816 3.978687 TCTTGTTCCTCGTCTTTGAGTC 58.021 45.455 0.00 0.0 34.04 3.36
817 821 4.020218 TGGATCATCTTGTTCCTCGTCTTT 60.020 41.667 0.00 0.0 37.20 2.52
1124 1128 6.045318 CGAGGAAAGTAACTGTGATCATCAT 58.955 40.000 0.00 0.0 0.00 2.45
1183 1187 9.448438 TTTTTCATTAAGCTCAAGACTAGCATA 57.552 29.630 0.22 0.0 42.62 3.14
1206 1210 7.830697 TCAATACTCACATGAGGATGACATTTT 59.169 33.333 7.39 0.0 44.69 1.82
1224 1228 5.448360 GCAGAAATCAGCAAGGTCAATACTC 60.448 44.000 0.00 0.0 0.00 2.59
1247 1251 2.989422 AAGCACGTGTTTAGAATGGC 57.011 45.000 16.52 0.0 0.00 4.40
1495 1504 8.367660 TCTTCTCTTTTTGCTTCTCTATCCTA 57.632 34.615 0.00 0.0 0.00 2.94
1592 1605 7.924947 CAGCATGTATCGATGGATGATATACTT 59.075 37.037 17.98 0.0 34.00 2.24
1716 1736 5.046910 AGTTTACAAGGCATTCACGATTG 57.953 39.130 0.00 0.0 0.00 2.67
1718 1738 5.351465 CACTAGTTTACAAGGCATTCACGAT 59.649 40.000 0.00 0.0 0.00 3.73
1720 1740 4.688879 TCACTAGTTTACAAGGCATTCACG 59.311 41.667 0.00 0.0 0.00 4.35
1721 1741 6.595716 AGATCACTAGTTTACAAGGCATTCAC 59.404 38.462 0.00 0.0 0.00 3.18
1827 1847 9.159364 GGTGTATCGAGGTAAAAGTAGAAAATT 57.841 33.333 0.00 0.0 0.00 1.82
1835 1855 6.832384 TGATCTAGGTGTATCGAGGTAAAAGT 59.168 38.462 0.00 0.0 0.00 2.66
1953 1973 3.603532 CATGTCTGGTTCACATGCTACT 58.396 45.455 0.00 0.0 43.48 2.57
2047 2073 3.626217 TGACATGCTACTGTAGGTAGTCG 59.374 47.826 16.09 0.0 46.99 4.18
2089 2116 2.161609 CCAAGCTAACCCGATTTCACAC 59.838 50.000 0.00 0.0 0.00 3.82
2394 2482 8.871686 ATAAAAGTGGATCAACAAGTTCAAAC 57.128 30.769 2.34 0.0 0.00 2.93


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

AutoCloner maintained by Alex Coulton.