Multiple sequence alignment - TraesCS5B01G101800

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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 TraesCS5B01G101800 chr5B 100.000 4573 0 0 1 4573 134921827 134926399 0.000000e+00 8445
1 TraesCS5B01G101800 chr5B 91.346 104 8 1 1545 1648 402737637 402737535 1.720000e-29 141
2 TraesCS5B01G101800 chr5D 98.021 3083 40 5 1499 4573 122203871 122206940 0.000000e+00 5336
3 TraesCS5B01G101800 chr5D 97.245 1488 38 1 2 1489 122202331 122203815 0.000000e+00 2518
4 TraesCS5B01G101800 chr5D 94.231 104 5 1 2261 2363 299972438 299972541 1.700000e-34 158
5 TraesCS5B01G101800 chr5D 94.231 104 5 1 2261 2363 503339510 503339407 1.700000e-34 158
6 TraesCS5B01G101800 chr5D 96.703 91 3 0 1555 1645 310705351 310705261 7.920000e-33 152
7 TraesCS5B01G101800 chr5A 94.652 1608 63 8 5 1593 134089857 134091460 0.000000e+00 2471
8 TraesCS5B01G101800 chr5A 91.446 1321 69 5 2401 3704 134092166 134093459 0.000000e+00 1773
9 TraesCS5B01G101800 chr5A 95.007 701 32 2 1627 2327 134091465 134092162 0.000000e+00 1098
10 TraesCS5B01G101800 chr5A 81.994 622 68 20 3909 4492 134094865 134095480 5.320000e-134 488
11 TraesCS5B01G101800 chr1A 98.958 96 1 0 1547 1642 530756566 530756661 6.080000e-39 172
12 TraesCS5B01G101800 chrUn 94.231 104 5 1 2261 2363 445188177 445188074 1.700000e-34 158
13 TraesCS5B01G101800 chr7D 94.231 104 5 1 2261 2363 231587957 231588060 1.700000e-34 158
14 TraesCS5B01G101800 chr6D 94.231 104 5 1 2261 2363 429811843 429811946 1.700000e-34 158
15 TraesCS5B01G101800 chr6D 94.059 101 3 3 1542 1642 199210423 199210326 2.850000e-32 150
16 TraesCS5B01G101800 chr6A 94.231 104 5 1 2261 2363 53820661 53820558 1.700000e-34 158
17 TraesCS5B01G101800 chr1D 94.231 104 5 1 2261 2363 254459478 254459375 1.700000e-34 158
18 TraesCS5B01G101800 chr1B 94.231 104 5 1 2261 2363 347446031 347446134 1.700000e-34 158
19 TraesCS5B01G101800 chr2D 96.809 94 1 2 1555 1646 534925550 534925457 6.130000e-34 156
20 TraesCS5B01G101800 chr4D 94.792 96 3 2 1555 1648 252173789 252173694 1.030000e-31 148
21 TraesCS5B01G101800 chr3A 93.069 101 7 0 1543 1643 99426172 99426272 1.030000e-31 148
22 TraesCS5B01G101800 chr2A 93.878 98 4 2 1556 1653 39327505 39327410 3.690000e-31 147


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 TraesCS5B01G101800 chr5B 134921827 134926399 4572 False 8445.0 8445 100.00000 1 4573 1 chr5B.!!$F1 4572
1 TraesCS5B01G101800 chr5D 122202331 122206940 4609 False 3927.0 5336 97.63300 2 4573 2 chr5D.!!$F2 4571
2 TraesCS5B01G101800 chr5A 134089857 134095480 5623 False 1457.5 2471 90.77475 5 4492 4 chr5A.!!$F1 4487

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
730 731 0.250553 AGAGATCTCCTACGCTCGGG 60.251 60.0 19.3 0.0 32.80 5.14 F
1328 1329 0.680061 GTCCGGTTCTGGAGACACTT 59.320 55.0 0.0 0.0 39.14 3.16 F
3296 3365 0.394488 TTGAACCTGTCCCGTTTGCA 60.394 50.0 0.0 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1827 2.578714 CCTATCCGCCCTCCTGCTC 61.579 68.421 0.00 0.0 0.00 4.26 R
3305 3374 1.478510 GCTCCCACGAAATCTCTCAGA 59.521 52.381 0.00 0.0 0.00 3.27 R
4336 5720 1.321474 TCCAAGGTTGCTCTTGCTTG 58.679 50.000 8.73 0.0 41.89 4.01 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
38 39 3.944650 TGATGTTACATTGACATTCCCCG 59.055 43.478 0.00 0.00 37.83 5.73
95 96 5.570205 TCCTAAAATATGTGCCCCGAATA 57.430 39.130 0.00 0.00 0.00 1.75
152 153 6.533012 CCTACATTCAGATCACACTACACTTG 59.467 42.308 0.00 0.00 0.00 3.16
730 731 0.250553 AGAGATCTCCTACGCTCGGG 60.251 60.000 19.30 0.00 32.80 5.14
1272 1273 3.700970 TTCGAGTCCATGGGCGCA 61.701 61.111 20.52 5.70 0.00 6.09
1321 1322 0.685097 CTTCAAGGTCCGGTTCTGGA 59.315 55.000 0.00 0.05 35.04 3.86
1326 1327 1.186267 AGGTCCGGTTCTGGAGACAC 61.186 60.000 0.00 0.00 39.14 3.67
1327 1328 1.186267 GGTCCGGTTCTGGAGACACT 61.186 60.000 0.00 0.00 39.14 3.55
1328 1329 0.680061 GTCCGGTTCTGGAGACACTT 59.320 55.000 0.00 0.00 39.14 3.16
1618 1684 8.305317 ACTAAAGTAGTGATCTAAACGCTCTTT 58.695 33.333 0.00 0.00 37.69 2.52
1623 1689 9.654663 AGTAGTGATCTAAACGCTCTTTTATTT 57.345 29.630 0.00 0.00 0.00 1.40
2123 2189 3.820467 CGAGCTCTCTAAGGAGATCACAT 59.180 47.826 12.85 0.00 45.63 3.21
2236 2302 4.389077 CGGATTGAGGTTAGTGAACTCAAC 59.611 45.833 16.86 10.93 36.46 3.18
2237 2303 5.552178 GGATTGAGGTTAGTGAACTCAACT 58.448 41.667 16.86 7.30 36.46 3.16
2238 2304 5.998363 GGATTGAGGTTAGTGAACTCAACTT 59.002 40.000 16.86 3.17 36.46 2.66
2280 2349 8.808240 ACTAATTCCTAGAATGGGGTGTTATA 57.192 34.615 0.00 0.00 37.33 0.98
2394 2463 4.260784 CGCTGGAGGTAGCAATATCAAAAC 60.261 45.833 0.00 0.00 43.87 2.43
2969 3038 6.126507 TGTGCCTGGAGAGGATGAATATAAAA 60.127 38.462 0.00 0.00 42.93 1.52
3296 3365 0.394488 TTGAACCTGTCCCGTTTGCA 60.394 50.000 0.00 0.00 0.00 4.08
3305 3374 0.678366 TCCCGTTTGCAATATGCCGT 60.678 50.000 0.00 0.00 44.23 5.68
3379 3448 1.303317 ACGATTTCCCGCTGCCTTT 60.303 52.632 0.00 0.00 0.00 3.11
3436 3505 2.281761 AGCGGAACACAAGCCTGG 60.282 61.111 0.00 0.00 0.00 4.45
3682 3768 8.571336 GGAATAAAATCTATCATGGTTGAGGTG 58.429 37.037 0.00 0.00 34.73 4.00
3688 3774 3.744940 ATCATGGTTGAGGTGGAATGT 57.255 42.857 0.00 0.00 34.73 2.71
3709 3795 4.886489 TGTCATGTGGTTTGAATCTGTTCA 59.114 37.500 0.00 0.00 42.41 3.18
3802 3889 0.955919 CCCTTTCTTGAGGCGTCCAC 60.956 60.000 3.56 0.00 35.37 4.02
3844 4742 5.238583 TCTAAGCTTACCAAACTTCTGAGC 58.761 41.667 0.86 0.00 0.00 4.26
4206 5566 1.768870 ACACCAAGAACAGTAGCACCT 59.231 47.619 0.00 0.00 0.00 4.00
4209 5569 3.997021 CACCAAGAACAGTAGCACCTAAG 59.003 47.826 0.00 0.00 0.00 2.18
4292 5676 7.771927 ATCAGGAAAGAGAAACATGACAAAT 57.228 32.000 0.00 0.00 0.00 2.32
4336 5720 2.749621 CCTGGCACTATCCACTGTTTTC 59.250 50.000 0.00 0.00 31.74 2.29
4523 5908 0.389166 ACTCGAGAGAAAGCAAGGCG 60.389 55.000 21.68 0.00 41.32 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.601613 GGGGAATGTCAATGTAACATCAGTTA 59.398 38.462 0.00 0.00 36.35 2.24
38 39 0.445436 CGCAATGTGAGAAGCTGGAC 59.555 55.000 0.00 0.00 0.00 4.02
82 83 2.491693 CAAACTTGTATTCGGGGCACAT 59.508 45.455 0.00 0.00 0.00 3.21
95 96 1.780309 TGGTGGGGAGATCAAACTTGT 59.220 47.619 0.00 0.00 0.00 3.16
170 171 1.946768 TGCCTGTTAGTTGTGCACTTC 59.053 47.619 19.41 10.84 36.88 3.01
428 429 6.458342 GGTGAGACACTTGTGAAGTTAAAAGG 60.458 42.308 7.83 0.00 40.46 3.11
959 960 1.550327 CTCTTTTGCTTTCCCCTCCC 58.450 55.000 0.00 0.00 0.00 4.30
1321 1322 9.561069 AGTAAGAAATGTAATCAACAAGTGTCT 57.439 29.630 0.00 0.00 42.70 3.41
1423 1424 9.110502 ACCATTAGCAGTAAATTAGCTAGAAAC 57.889 33.333 0.00 0.00 41.38 2.78
1482 1483 3.487372 ACAAGAAAGGGCTCCAGTTTAC 58.513 45.455 0.00 0.00 0.00 2.01
1623 1689 6.989155 TCAAAAGTACTCCCTCTGTAAAGA 57.011 37.500 0.00 0.00 0.00 2.52
1761 1827 2.578714 CCTATCCGCCCTCCTGCTC 61.579 68.421 0.00 0.00 0.00 4.26
2251 2320 7.746703 ACACCCCATTCTAGGAATTAGTAATC 58.253 38.462 0.00 0.00 0.00 1.75
2394 2463 6.128956 GCAAATCTTTCCGAATCTATCTCTCG 60.129 42.308 0.00 0.00 0.00 4.04
2969 3038 3.449737 TCGTATCCATTTTCTCTTCCGGT 59.550 43.478 0.00 0.00 0.00 5.28
3296 3365 4.202161 ACGAAATCTCTCAGACGGCATATT 60.202 41.667 0.00 0.00 0.00 1.28
3305 3374 1.478510 GCTCCCACGAAATCTCTCAGA 59.521 52.381 0.00 0.00 0.00 3.27
3359 3428 2.435938 GGCAGCGGGAAATCGTCA 60.436 61.111 0.00 0.00 0.00 4.35
3622 3708 0.643820 GGTTCTGCGTCGTTTATCCG 59.356 55.000 0.00 0.00 0.00 4.18
3682 3768 5.047802 ACAGATTCAAACCACATGACATTCC 60.048 40.000 0.00 0.00 0.00 3.01
3688 3774 4.886489 TGTGAACAGATTCAAACCACATGA 59.114 37.500 0.00 0.00 46.40 3.07
3709 3795 1.909700 CTGGGTAACATGGCAGTTGT 58.090 50.000 11.08 0.70 39.74 3.32
4142 5491 4.124970 GGAATTTTAGCTCGGGATTACGT 58.875 43.478 0.00 0.00 34.94 3.57
4206 5566 9.045223 CATCCAATGTTGATTTCGATCTACTTA 57.955 33.333 3.03 0.00 0.00 2.24
4209 5569 7.011389 TCACATCCAATGTTGATTTCGATCTAC 59.989 37.037 0.00 0.00 42.70 2.59
4292 5676 7.390440 CAGGTGGAAATGTTCTGTTTCTGTATA 59.610 37.037 0.00 0.00 36.18 1.47
4336 5720 1.321474 TCCAAGGTTGCTCTTGCTTG 58.679 50.000 8.73 0.00 41.89 4.01
4523 5908 3.068024 TGTCCAGACCAGTTGCATTTTTC 59.932 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.