Multiple sequence alignment - TraesCS2B01G146700

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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 TraesCS2B01G146700 chr2B 100.000 2284 0 0 1 2284 112841002 112843285 0.000000e+00 4218
1 TraesCS2B01G146700 chr2B 100.000 151 0 0 2444 2594 112843445 112843595 1.970000e-71 279
2 TraesCS2B01G146700 chr2B 98.675 151 2 0 2444 2594 391163252 391163402 4.250000e-68 268
3 TraesCS2B01G146700 chr5A 98.688 2286 28 2 1 2284 19248878 19246593 0.000000e+00 4054
4 TraesCS2B01G146700 chr7D 98.600 2285 31 1 1 2284 381923967 381926251 0.000000e+00 4041
5 TraesCS2B01G146700 chr7D 98.513 2286 32 2 1 2284 382050044 382052329 0.000000e+00 4032
6 TraesCS2B01G146700 chr7D 98.512 2285 33 1 1 2284 203499965 203502249 0.000000e+00 4030
7 TraesCS2B01G146700 chr7D 98.512 2285 30 2 1 2284 381973801 381971520 0.000000e+00 4028
8 TraesCS2B01G146700 chr7B 98.511 2284 34 0 1 2284 716878814 716876531 0.000000e+00 4030
9 TraesCS2B01G146700 chr7B 98.292 2284 39 0 1 2284 742989412 742991695 0.000000e+00 4002
10 TraesCS2B01G146700 chr7B 98.675 151 2 0 2444 2594 716876538 716876388 4.250000e-68 268
11 TraesCS2B01G146700 chr7B 98.026 152 2 1 2444 2594 742991688 742991839 1.980000e-66 263
12 TraesCS2B01G146700 chr6D 98.425 2285 35 1 1 2284 124517488 124519772 0.000000e+00 4019
13 TraesCS2B01G146700 chr1A 98.425 2285 35 1 1 2284 498691261 498688977 0.000000e+00 4019
14 TraesCS2B01G146700 chr1A 98.013 151 3 0 2444 2594 498688984 498688834 1.980000e-66 263
15 TraesCS2B01G146700 chrUn 100.000 151 0 0 2444 2594 186206178 186206028 1.970000e-71 279
16 TraesCS2B01G146700 chr7A 100.000 151 0 0 2444 2594 60281556 60281706 1.970000e-71 279
17 TraesCS2B01G146700 chr5B 98.675 151 2 0 2444 2594 701110409 701110259 4.250000e-68 268
18 TraesCS2B01G146700 chr4B 98.013 151 2 1 2444 2594 209301907 209302056 7.120000e-66 261
19 TraesCS2B01G146700 chr3B 97.368 152 3 1 2444 2594 797590694 797590543 9.210000e-65 257


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 TraesCS2B01G146700 chr2B 112841002 112843595 2593 False 2248.5 4218 100.000 1 2594 2 chr2B.!!$F2 2593
1 TraesCS2B01G146700 chr5A 19246593 19248878 2285 True 4054.0 4054 98.688 1 2284 1 chr5A.!!$R1 2283
2 TraesCS2B01G146700 chr7D 381923967 381926251 2284 False 4041.0 4041 98.600 1 2284 1 chr7D.!!$F2 2283
3 TraesCS2B01G146700 chr7D 382050044 382052329 2285 False 4032.0 4032 98.513 1 2284 1 chr7D.!!$F3 2283
4 TraesCS2B01G146700 chr7D 203499965 203502249 2284 False 4030.0 4030 98.512 1 2284 1 chr7D.!!$F1 2283
5 TraesCS2B01G146700 chr7D 381971520 381973801 2281 True 4028.0 4028 98.512 1 2284 1 chr7D.!!$R1 2283
6 TraesCS2B01G146700 chr7B 716876388 716878814 2426 True 2149.0 4030 98.593 1 2594 2 chr7B.!!$R1 2593
7 TraesCS2B01G146700 chr7B 742989412 742991839 2427 False 2132.5 4002 98.159 1 2594 2 chr7B.!!$F1 2593
8 TraesCS2B01G146700 chr6D 124517488 124519772 2284 False 4019.0 4019 98.425 1 2284 1 chr6D.!!$F1 2283
9 TraesCS2B01G146700 chr1A 498688834 498691261 2427 True 2141.0 4019 98.219 1 2594 2 chr1A.!!$R1 2593

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
981 987 1.13345 CCCTCTCCCTCGGACTCAATA 60.133 57.143 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2453 0.169009 GGGCTAAGCGCAGTTCTTTG 59.831 55.0 11.47 0.0 41.23 2.77 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
43 44 2.270850 CCGAAGCCCCGAATGGAA 59.729 61.111 0.00 0.00 37.49 3.53
363 365 1.216990 AGGACCCCTCCAATCATGTC 58.783 55.000 0.00 0.00 39.39 3.06
448 450 2.439507 AGGTGCATATCCCTTACCACTG 59.560 50.000 0.00 0.00 33.88 3.66
546 549 3.703001 TCATCGAAAAGGAAGAAGGCT 57.297 42.857 0.00 0.00 0.00 4.58
608 611 5.878669 ACGTTCTAATAAAGAATTCCGGCTT 59.121 36.000 0.65 0.00 45.84 4.35
719 722 7.684529 ACTACAAAAGAGAGAATCCACTTCAT 58.315 34.615 0.00 0.00 36.24 2.57
900 903 2.703007 CCCTTTTGTGTGAATTCCCCAA 59.297 45.455 2.27 0.45 0.00 4.12
981 987 1.133450 CCCTCTCCCTCGGACTCAATA 60.133 57.143 0.00 0.00 0.00 1.90
1558 1564 2.447443 CAGTGGGAGTAGTGACTAGCA 58.553 52.381 0.00 0.00 35.45 3.49
1609 1615 3.200165 GCCATAAGTAAGGTTGGGAGACT 59.800 47.826 0.00 0.00 0.00 3.24
1794 1800 3.589735 TGAATGGAAGTTGGCCTTAGGTA 59.410 43.478 3.32 0.00 32.03 3.08
1858 1864 1.302993 CCCCGTCGGTTGTTGGAAT 60.303 57.895 11.06 0.00 0.00 3.01
2001 2007 0.464013 TTCGTTGGGAAAGAACGGCA 60.464 50.000 0.00 0.00 44.96 5.69
2115 2121 2.530151 TGTGGGGGAGAAGCAGCT 60.530 61.111 0.00 0.00 0.00 4.24
2138 2144 1.139058 GCTCATTCCCTTCGCTTCCTA 59.861 52.381 0.00 0.00 0.00 2.94
2204 2210 5.072741 GGGGCTGATTGCAAAAGATATCTA 58.927 41.667 14.83 0.00 45.15 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.012673 GCAGAAGCAGAAACGATCCAT 58.987 47.619 0.00 0.00 41.58 3.41
258 259 2.879372 TGCTTTCCTGTGTTGCACA 58.121 47.368 1.88 1.88 42.45 4.57
363 365 0.179073 CCGGGTGAACATAGGCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
448 450 1.351153 CTTCGTCGAGCCTTTCCTTC 58.649 55.000 0.00 0.00 0.00 3.46
546 549 1.056700 GGAAGGCTGCTATCCCCTCA 61.057 60.000 11.57 0.00 0.00 3.86
719 722 2.621998 GCCTAGCAGAGACGTGGTTATA 59.378 50.000 0.00 0.00 0.00 0.98
789 792 2.953648 TGTTCACGTAACTCCACTCTCA 59.046 45.455 0.00 0.00 38.99 3.27
900 903 2.031508 CCACAAGTTGTTAATTCGCCGT 60.032 45.455 5.57 0.00 0.00 5.68
981 987 8.317679 GCCCACATATATAGAGTCAAAAGAGAT 58.682 37.037 0.00 0.00 0.00 2.75
1592 1598 3.328050 CCTTCAGTCTCCCAACCTTACTT 59.672 47.826 0.00 0.00 0.00 2.24
1609 1615 0.749818 TGCACGGAAAACTGCCTTCA 60.750 50.000 0.00 0.00 31.97 3.02
1636 1642 3.259064 GCAACTGATTCGGTAAGCTACA 58.741 45.455 13.04 0.00 0.00 2.74
1794 1800 4.281182 CGCAGTAACTGGGAGTCCTATTAT 59.719 45.833 9.58 0.00 45.41 1.28
1874 1880 2.879103 TTTGAAAGGAATCGAGGCCT 57.121 45.000 3.86 3.86 35.61 5.19
1968 1974 2.823154 CCAACGAAAATGGAAAGGGCTA 59.177 45.455 0.00 0.00 40.56 3.93
2001 2007 0.618981 GGAGGGTTCGGATGGACTTT 59.381 55.000 0.00 0.00 0.00 2.66
2115 2121 0.615331 AAGCGAAGGGAATGAGCTCA 59.385 50.000 20.79 20.79 37.15 4.26
2443 2449 3.420828 GCTAAGCGCAGTTCTTTGAATC 58.579 45.455 11.47 0.00 38.92 2.52
2444 2450 2.162408 GGCTAAGCGCAGTTCTTTGAAT 59.838 45.455 11.47 0.00 41.67 2.57
2445 2451 1.535462 GGCTAAGCGCAGTTCTTTGAA 59.465 47.619 11.47 0.00 41.67 2.69
2446 2452 1.156736 GGCTAAGCGCAGTTCTTTGA 58.843 50.000 11.47 0.00 41.67 2.69
2447 2453 0.169009 GGGCTAAGCGCAGTTCTTTG 59.831 55.000 11.47 0.00 41.23 2.77
2448 2454 0.960861 GGGGCTAAGCGCAGTTCTTT 60.961 55.000 11.47 0.00 43.41 2.52
2449 2455 1.377333 GGGGCTAAGCGCAGTTCTT 60.377 57.895 11.47 0.00 43.41 2.52
2450 2456 2.269241 GGGGCTAAGCGCAGTTCT 59.731 61.111 11.47 0.00 43.41 3.01


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

AutoCloner maintained by Alex Coulton.