Multiple sequence alignment - TraesCS1B01G026900

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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 TraesCS1B01G026900 chr1B 100.000 2243 0 0 1 2243 13013085 13015327 0.000000e+00 4143
1 TraesCS1B01G026900 chr1B 97.968 2018 41 0 1 2018 13500496 13502513 0.000000e+00 3500
2 TraesCS1B01G026900 chr1B 90.855 1509 117 7 1 1493 12499563 12501066 0.000000e+00 2002
3 TraesCS1B01G026900 chr1B 90.855 1509 117 7 1 1493 12569754 12571257 0.000000e+00 2002
4 TraesCS1B01G026900 chr1B 89.049 1251 105 18 174 1405 12374541 12373304 0.000000e+00 1522
5 TraesCS1B01G026900 chr1B 92.265 181 8 3 2064 2243 13502516 13502691 3.700000e-63 252
6 TraesCS1B01G026900 chr1B 86.500 200 15 2 1295 1482 12572405 12572604 2.260000e-50 209
7 TraesCS1B01G026900 chr1A 89.378 1158 96 12 368 1505 10708868 10710018 0.000000e+00 1432
8 TraesCS1B01G026900 chr1A 86.118 389 38 6 1515 1893 10710219 10710601 2.680000e-109 405
9 TraesCS1B01G026900 chr1A 92.830 265 18 1 1 265 10708612 10708875 1.260000e-102 383
10 TraesCS1B01G026900 chr1A 86.170 282 11 13 1962 2243 10712652 10712905 1.700000e-71 279
11 TraesCS1B01G026900 chr1D 86.436 752 70 14 710 1449 9418008 9418739 0.000000e+00 795
12 TraesCS1B01G026900 chr1D 88.268 537 34 9 1736 2243 9431917 9432453 1.140000e-172 616
13 TraesCS1B01G026900 chr1D 84.921 126 11 2 715 840 9485850 9485967 1.090000e-23 121
14 TraesCS1B01G026900 chr5D 85.465 172 25 0 1463 1634 555355220 555355049 1.770000e-41 180


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 TraesCS1B01G026900 chr1B 13013085 13015327 2242 False 4143.00 4143 100.0000 1 2243 1 chr1B.!!$F2 2242
1 TraesCS1B01G026900 chr1B 12499563 12501066 1503 False 2002.00 2002 90.8550 1 1493 1 chr1B.!!$F1 1492
2 TraesCS1B01G026900 chr1B 13500496 13502691 2195 False 1876.00 3500 95.1165 1 2243 2 chr1B.!!$F4 2242
3 TraesCS1B01G026900 chr1B 12373304 12374541 1237 True 1522.00 1522 89.0490 174 1405 1 chr1B.!!$R1 1231
4 TraesCS1B01G026900 chr1B 12569754 12572604 2850 False 1105.50 2002 88.6775 1 1493 2 chr1B.!!$F3 1492
5 TraesCS1B01G026900 chr1A 10708612 10712905 4293 False 624.75 1432 88.6240 1 2243 4 chr1A.!!$F1 2242
6 TraesCS1B01G026900 chr1D 9418008 9418739 731 False 795.00 795 86.4360 710 1449 1 chr1D.!!$F1 739
7 TraesCS1B01G026900 chr1D 9431917 9432453 536 False 616.00 616 88.2680 1736 2243 1 chr1D.!!$F2 507

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
869 884 1.370414 GCGCGATGCACACTTGTTT 60.37 52.632 12.1 0.0 45.45 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2865 0.253044 ACCTGACCATGCGCAGTAAT 59.747 50.0 18.32 0.14 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
59 60 2.695666 CTGGTGTAGAAGATCGGACCAT 59.304 50.000 0.00 0.00 33.13 3.55
139 140 1.402984 GGAGAACGACGCTCATGAACT 60.403 52.381 0.00 0.00 34.07 3.01
418 420 2.262637 TCAACCTTACCTACCCACCAG 58.737 52.381 0.00 0.00 0.00 4.00
551 557 7.727181 AGCTATTGGTATCACCTGTTACTAAG 58.273 38.462 0.00 0.00 39.58 2.18
691 701 3.390135 GCAGCAGCCTTACATACGAATA 58.610 45.455 0.00 0.00 33.58 1.75
869 884 1.370414 GCGCGATGCACACTTGTTT 60.370 52.632 12.10 0.00 45.45 2.83
1104 1119 2.037136 GCAGAGAGCGGCAACACAT 61.037 57.895 1.45 0.00 35.17 3.21
1151 1166 4.142790 TCGGTCACCCTGATCTATTCTAC 58.857 47.826 0.00 0.00 0.00 2.59
1152 1167 4.141228 TCGGTCACCCTGATCTATTCTACT 60.141 45.833 0.00 0.00 0.00 2.57
1299 1314 2.871182 CTCCATGCAGAGCGTAGTTA 57.129 50.000 0.00 0.00 0.00 2.24
1540 1761 4.546829 AGGATAGAGAGTAGCTAGTCCG 57.453 50.000 22.41 0.00 0.00 4.79
1585 1806 3.953612 CAGAGAAGGTGAGATGCTAGACT 59.046 47.826 0.00 0.00 0.00 3.24
1598 1819 0.109458 CTAGACTGCCGTGCGTTACA 60.109 55.000 0.00 0.00 0.00 2.41
1636 1857 1.302511 GATGGTGGTGTGAAGCCGT 60.303 57.895 0.00 0.00 0.00 5.68
1823 2849 3.181516 GCTGCATGTGAGTTGTTAGCTAC 60.182 47.826 0.00 0.00 0.00 3.58
1839 2865 7.561251 TGTTAGCTACCTTAATGCATGAGTTA 58.439 34.615 0.00 0.00 0.00 2.24
1909 4968 3.683340 GGTGCACTTAGCCAGTAAAGTAC 59.317 47.826 17.98 0.00 44.83 2.73
2018 5078 6.633634 GCGTGAGTCTATGTAAGAGATGTAAC 59.366 42.308 0.00 0.00 33.88 2.50
2023 5083 8.728337 AGTCTATGTAAGAGATGTAACGTGTA 57.272 34.615 0.00 0.00 33.88 2.90
2126 5186 1.475751 CCACTGTTCCTGTGTGAGCTT 60.476 52.381 0.00 0.00 33.95 3.74
2211 5272 8.709646 GCTAACTATGTTACATAATAGTGTGGC 58.290 37.037 18.09 11.47 39.11 5.01
2215 5276 8.482943 ACTATGTTACATAATAGTGTGGCAAGA 58.517 33.333 6.52 0.00 38.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 3.517296 TTGGCTAGTGGTGAAAATCCA 57.483 42.857 0.00 0.00 0.00 3.41
154 155 3.823330 ATGCTCGACGGTCCCGAC 61.823 66.667 13.54 5.34 42.83 4.79
386 388 4.354087 AGGTAAGGTTGATTCTTTGGGTCT 59.646 41.667 0.00 0.00 0.00 3.85
869 884 1.272037 TGGAGTGAAGCATGGCATGAA 60.272 47.619 30.69 9.83 0.00 2.57
1299 1314 2.706350 AGTATGATACCAGGTGGGCAT 58.294 47.619 0.76 5.67 42.05 4.40
1540 1761 1.177401 GTCTTGGTTGATGCTTCCCC 58.823 55.000 0.00 0.00 0.00 4.81
1598 1819 0.390860 GGCATCTCACCATACTCGCT 59.609 55.000 0.00 0.00 0.00 4.93
1733 1955 1.539157 TCATCTGCAGTCTCAGACGT 58.461 50.000 14.67 0.00 44.88 4.34
1823 2849 6.365839 CGCAGTAATAACTCATGCATTAAGG 58.634 40.000 0.00 0.00 31.97 2.69
1839 2865 0.253044 ACCTGACCATGCGCAGTAAT 59.747 50.000 18.32 0.14 0.00 1.89
2018 5078 6.466308 TTCTCTTGTCATCAACAATACACG 57.534 37.500 0.00 0.00 46.53 4.49
2023 5083 9.775854 CTCCTATATTCTCTTGTCATCAACAAT 57.224 33.333 0.00 0.00 46.53 2.71
2044 5104 2.972713 ACACAGCAGACCTTTTCTCCTA 59.027 45.455 0.00 0.00 28.96 2.94
2126 5186 9.581289 CTTCTTCCTCCTCTAACTATCTATCAA 57.419 37.037 0.00 0.00 0.00 2.57
2207 5268 3.069443 TCCAGAAAACCAATTCTTGCCAC 59.931 43.478 0.00 0.00 37.56 5.01
2211 5272 6.572519 TCACTTTCCAGAAAACCAATTCTTG 58.427 36.000 0.00 0.00 37.56 3.02
2215 5276 5.359756 GCTTCACTTTCCAGAAAACCAATT 58.640 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.