Multiple sequence alignment - TraesCS4B01G306500
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
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
TraesCS4B01G306500
chr4B
100.000
2777
0
0
1
2777
595709940
595707164
0.000000e+00
5129
1
TraesCS4B01G306500
chr4D
93.308
2839
84
51
9
2777
473163742
473160940
0.000000e+00
4093
2
TraesCS4B01G306500
chr4A
87.500
2344
128
73
21
2268
680048179
680045905
0.000000e+00
2553
3
TraesCS4B01G306500
chr4A
87.664
535
34
15
2268
2777
680045871
680045344
6.620000e-166
593
BLAST Results - HSPs grouped
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
TraesCS4B01G306500
chr4B
595707164
595709940
2776
True
5129
5129
100.000
1
2777
1
chr4B.!!$R1
2776
1
TraesCS4B01G306500
chr4D
473160940
473163742
2802
True
4093
4093
93.308
9
2777
1
chr4D.!!$R1
2768
2
TraesCS4B01G306500
chr4A
680045344
680048179
2835
True
1573
2553
87.582
21
2777
2
chr4A.!!$R1
2756
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
498
523
0.315625
CATCACGCGCATGCAGTAAG
60.316
55.0
19.57
6.42
42.97
2.34
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1905
2004
0.177836
CGGCTACATGGATGGTCACA
59.822
55.0
0.0
0.0
0.0
3.58
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
306
314
6.603940
ATGCAAAGCTAGGTTTTTAATCCA
57.396
33.333
17.04
8.20
0.00
3.41
314
322
3.751518
AGGTTTTTAATCCAGACAGCGT
58.248
40.909
0.00
0.00
0.00
5.07
336
344
4.567385
GCAGAGAGGCGCGAGAGG
62.567
72.222
12.10
0.00
0.00
3.69
397
405
2.094675
GTGTAACTGCAGATGCCCATT
58.905
47.619
23.35
4.57
41.18
3.16
498
523
0.315625
CATCACGCGCATGCAGTAAG
60.316
55.000
19.57
6.42
42.97
2.34
591
628
4.759782
CAGGGTAGAAATCAATCGAGTGT
58.240
43.478
13.18
0.00
0.00
3.55
971
1017
2.032528
CCGAGGGAGCAAGTGCAA
59.967
61.111
6.00
0.00
45.16
4.08
972
1018
2.328099
CCGAGGGAGCAAGTGCAAC
61.328
63.158
6.00
0.00
45.16
4.17
973
1019
2.671177
CGAGGGAGCAAGTGCAACG
61.671
63.158
6.00
0.41
45.86
4.10
974
1020
2.281761
AGGGAGCAAGTGCAACGG
60.282
61.111
6.00
0.00
45.86
4.44
975
1021
4.043200
GGGAGCAAGTGCAACGGC
62.043
66.667
6.00
0.00
45.86
5.68
976
1022
4.389576
GGAGCAAGTGCAACGGCG
62.390
66.667
4.80
4.80
44.78
6.46
1137
1183
1.755008
CGAGGTGGAGGAGGAGGAC
60.755
68.421
0.00
0.00
0.00
3.85
1138
1184
1.755008
GAGGTGGAGGAGGAGGACG
60.755
68.421
0.00
0.00
0.00
4.79
1139
1185
2.212794
GAGGTGGAGGAGGAGGACGA
62.213
65.000
0.00
0.00
0.00
4.20
1149
1201
2.122167
GGAGGACGAGGAGCACGAT
61.122
63.158
0.00
0.00
34.70
3.73
1222
1274
1.446792
CTCGACATCAAGGTGCGCT
60.447
57.895
9.73
0.00
0.00
5.92
1253
1310
1.536922
CCTACTGCTGTACTCCATGCG
60.537
57.143
0.00
0.00
0.00
4.73
1258
1315
1.878522
CTGTACTCCATGCGGCGAC
60.879
63.158
12.98
2.02
0.00
5.19
1284
1341
2.577059
GATCGTCCGTCCCTGCAA
59.423
61.111
0.00
0.00
0.00
4.08
1398
1461
1.609794
GAGGACGTCCAAGGACCCT
60.610
63.158
35.00
13.05
41.76
4.34
1788
1852
1.170442
GGGACTAGCTCGCTCCTATC
58.830
60.000
0.00
0.00
0.00
2.08
1852
1927
1.409064
GATCGTCTCATGGTGCACCTA
59.591
52.381
34.75
21.96
36.82
3.08
1905
2004
6.594159
GCACCACAAGTAATGTTGTACTCTAT
59.406
38.462
0.00
0.00
41.46
1.98
1992
2105
8.094798
ACAAAATATCGTTGTTCACATGTACT
57.905
30.769
0.00
0.00
35.70
2.73
1993
2106
9.210329
ACAAAATATCGTTGTTCACATGTACTA
57.790
29.630
0.00
0.00
35.70
1.82
1994
2107
9.472995
CAAAATATCGTTGTTCACATGTACTAC
57.527
33.333
0.00
0.41
0.00
2.73
1995
2108
7.445900
AATATCGTTGTTCACATGTACTACG
57.554
36.000
21.81
21.81
42.24
3.51
2020
2133
4.076394
CTCTATTAGAGTCCGGCTTAGCT
58.924
47.826
11.86
0.00
37.57
3.32
2021
2134
5.238624
TCTATTAGAGTCCGGCTTAGCTA
57.761
43.478
3.59
0.00
0.00
3.32
2029
2156
4.449131
AGTCCGGCTTAGCTATTTAAACC
58.551
43.478
3.59
0.00
0.00
3.27
2064
2191
5.805751
GCAGTGATCATGGGGCTAATCTAAT
60.806
44.000
0.00
0.00
0.00
1.73
2065
2192
5.646793
CAGTGATCATGGGGCTAATCTAATG
59.353
44.000
0.00
0.00
0.00
1.90
2066
2193
4.397417
GTGATCATGGGGCTAATCTAATGC
59.603
45.833
0.00
0.00
0.00
3.56
2067
2194
4.290459
TGATCATGGGGCTAATCTAATGCT
59.710
41.667
0.00
0.00
0.00
3.79
2068
2195
4.292186
TCATGGGGCTAATCTAATGCTC
57.708
45.455
0.00
0.00
0.00
4.26
2071
2198
2.906389
TGGGGCTAATCTAATGCTCGAT
59.094
45.455
0.00
0.00
0.00
3.59
2090
2217
5.056480
TCGATCGGTGCTATGAATTGAATT
58.944
37.500
16.41
0.00
0.00
2.17
2100
2227
9.309516
GTGCTATGAATTGAATTGAATGAATGT
57.690
29.630
0.00
0.00
0.00
2.71
2266
2404
2.386661
AGTGGCGACTACAATCCTTG
57.613
50.000
0.00
0.00
0.00
3.61
2345
2520
0.820891
GCACCCCGGAGATACGTAGA
60.821
60.000
0.73
0.00
0.00
2.59
2379
2554
3.504863
CAGACGAATTTTCCATGCAAGG
58.495
45.455
0.19
0.19
0.00
3.61
2468
2663
1.836999
TTGCCGCCTGGACTACACAT
61.837
55.000
0.00
0.00
37.49
3.21
2470
2665
0.249489
GCCGCCTGGACTACACATAG
60.249
60.000
0.00
0.00
37.49
2.23
2485
2682
1.275666
CATAGATATCCGGTGGCCCA
58.724
55.000
0.00
0.00
0.00
5.36
2513
2710
3.578282
TCAGAACAGAAGTGGTGCTATCA
59.422
43.478
0.00
0.00
0.00
2.15
2560
2761
1.335810
GCGTCCGGATGTGTGTAGATA
59.664
52.381
24.33
0.00
0.00
1.98
2592
2793
2.668457
GTGTCGTGAGCTAATGTGGAAG
59.332
50.000
0.00
0.00
0.00
3.46
2618
2823
0.759436
GGCCGGGTGAGAGGAGATTA
60.759
60.000
2.18
0.00
0.00
1.75
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
3.589881
GCCATCGCCATGCCAGTC
61.590
66.667
0.00
0.00
0.00
3.51
1
2
3.726558
ATGCCATCGCCATGCCAGT
62.727
57.895
0.00
0.00
0.00
4.00
2
3
2.495409
AATGCCATCGCCATGCCAG
61.495
57.895
0.00
0.00
0.00
4.85
3
4
2.442458
AATGCCATCGCCATGCCA
60.442
55.556
0.00
0.00
0.00
4.92
4
5
2.028484
CAATGCCATCGCCATGCC
59.972
61.111
0.00
0.00
0.00
4.40
5
6
2.660552
GCAATGCCATCGCCATGC
60.661
61.111
0.00
0.00
38.08
4.06
52
53
6.183360
CGAAATGGATAGGGATTAATCATGCC
60.183
42.308
17.07
9.14
44.01
4.40
332
340
3.247162
GGCATTAATCCTCTCTCCCTCT
58.753
50.000
0.00
0.00
0.00
3.69
335
343
2.039613
CAGGGCATTAATCCTCTCTCCC
59.960
54.545
0.00
0.00
0.00
4.30
336
344
2.975489
TCAGGGCATTAATCCTCTCTCC
59.025
50.000
0.00
0.00
0.00
3.71
340
348
3.803186
CCATCAGGGCATTAATCCTCT
57.197
47.619
0.00
0.00
0.00
3.69
520
553
3.003173
CTCCCAGAGACCGGCCAA
61.003
66.667
0.00
0.00
0.00
4.52
591
628
0.930310
GCGCAGTTCAATATCTCGCA
59.070
50.000
0.30
0.00
40.63
5.10
959
1005
4.389576
CGCCGTTGCACTTGCTCC
62.390
66.667
2.33
0.00
42.66
4.70
960
1006
4.389576
CCGCCGTTGCACTTGCTC
62.390
66.667
2.33
0.00
42.66
4.26
994
1040
1.376466
GCAGGGACACCATGTCTGT
59.624
57.895
8.75
0.00
46.19
3.41
1137
1183
1.006805
GATCCCATCGTGCTCCTCG
60.007
63.158
0.00
0.00
0.00
4.63
1149
1201
1.480545
TCGAAATTGAGCTCGATCCCA
59.519
47.619
17.02
0.00
39.07
4.37
1222
1274
2.892640
CAGTAGGCTAGGCACGCA
59.107
61.111
19.70
0.00
0.00
5.24
1232
1284
1.808133
GCATGGAGTACAGCAGTAGGC
60.808
57.143
0.00
0.00
45.30
3.93
1241
1298
2.183300
GTCGCCGCATGGAGTACA
59.817
61.111
0.00
0.00
37.49
2.90
1244
1301
3.774959
GATCGTCGCCGCATGGAGT
62.775
63.158
0.00
0.00
37.49
3.85
1245
1302
3.032609
GATCGTCGCCGCATGGAG
61.033
66.667
0.00
0.00
37.49
3.86
1330
1387
2.203139
CCCCGACTGCACAACACA
60.203
61.111
0.00
0.00
0.00
3.72
1499
1562
1.739338
CTCCTTGACGGGCGAGCTAT
61.739
60.000
0.00
0.00
0.00
2.97
1503
1566
3.764466
AGCTCCTTGACGGGCGAG
61.764
66.667
0.00
0.00
35.07
5.03
1593
1656
4.241555
ATCTCCATGCCGCCGGAC
62.242
66.667
7.68
0.00
0.00
4.79
1852
1927
2.563179
ACAGTCCTCGTTGCACTTATCT
59.437
45.455
0.00
0.00
0.00
1.98
1905
2004
0.177836
CGGCTACATGGATGGTCACA
59.822
55.000
0.00
0.00
0.00
3.58
1969
2082
8.377681
CGTAGTACATGTGAACAACGATATTTT
58.622
33.333
9.11
0.00
0.00
1.82
2008
2121
4.272748
CAGGTTTAAATAGCTAAGCCGGAC
59.727
45.833
5.05
0.00
37.27
4.79
2009
2122
4.162698
TCAGGTTTAAATAGCTAAGCCGGA
59.837
41.667
5.05
0.00
37.27
5.14
2010
2123
4.448210
TCAGGTTTAAATAGCTAAGCCGG
58.552
43.478
0.00
0.00
37.27
6.13
2011
2124
4.511826
CCTCAGGTTTAAATAGCTAAGCCG
59.488
45.833
0.00
0.00
37.27
5.52
2013
2126
6.350103
ACTCCTCAGGTTTAAATAGCTAAGC
58.650
40.000
0.00
0.00
0.00
3.09
2020
2133
5.222048
ACTGCCAACTCCTCAGGTTTAAATA
60.222
40.000
0.00
0.00
32.42
1.40
2021
2134
4.082125
CTGCCAACTCCTCAGGTTTAAAT
58.918
43.478
0.00
0.00
0.00
1.40
2029
2156
1.277273
TGATCACTGCCAACTCCTCAG
59.723
52.381
0.00
0.00
0.00
3.35
2064
2191
0.744281
TTCATAGCACCGATCGAGCA
59.256
50.000
26.49
16.42
0.00
4.26
2065
2192
2.071688
ATTCATAGCACCGATCGAGC
57.928
50.000
18.66
19.64
0.00
5.03
2066
2193
3.642705
TCAATTCATAGCACCGATCGAG
58.357
45.455
18.66
9.99
0.00
4.04
2067
2194
3.726291
TCAATTCATAGCACCGATCGA
57.274
42.857
18.66
0.00
0.00
3.59
2068
2195
4.997905
ATTCAATTCATAGCACCGATCG
57.002
40.909
8.51
8.51
0.00
3.69
2071
2198
6.318396
TCATTCAATTCAATTCATAGCACCGA
59.682
34.615
0.00
0.00
0.00
4.69
2191
2329
3.001127
CCAACCAACTTTCAAACATTGCG
59.999
43.478
0.00
0.00
0.00
4.85
2259
2397
4.370917
GAAAATGTGTGTGTGCAAGGATT
58.629
39.130
0.00
0.00
0.00
3.01
2261
2399
2.100584
GGAAAATGTGTGTGTGCAAGGA
59.899
45.455
0.00
0.00
0.00
3.36
2262
2400
2.101249
AGGAAAATGTGTGTGTGCAAGG
59.899
45.455
0.00
0.00
0.00
3.61
2263
2401
3.441496
AGGAAAATGTGTGTGTGCAAG
57.559
42.857
0.00
0.00
0.00
4.01
2265
2403
3.446873
AGAAAGGAAAATGTGTGTGTGCA
59.553
39.130
0.00
0.00
0.00
4.57
2266
2404
4.045636
AGAAAGGAAAATGTGTGTGTGC
57.954
40.909
0.00
0.00
0.00
4.57
2345
2520
1.587350
CGTCTGCGATCGATGCACT
60.587
57.895
21.57
0.00
41.33
4.40
2386
2561
1.340088
TGCATGCATGTTCCTGGTTT
58.660
45.000
26.79
0.00
0.00
3.27
2414
2591
3.612371
AAGCTGGCTCGTCGTCGTC
62.612
63.158
1.33
0.00
38.33
4.20
2425
2602
0.610687
ACTCCACTAGTGAAGCTGGC
59.389
55.000
24.68
0.00
36.93
4.85
2468
2663
1.906574
GAATGGGCCACCGGATATCTA
59.093
52.381
9.28
0.00
40.75
1.98
2470
2665
0.322546
GGAATGGGCCACCGGATATC
60.323
60.000
9.28
0.00
40.75
1.63
2485
2682
2.368875
ACCACTTCTGTTCTGACGGAAT
59.631
45.455
0.00
0.00
46.98
3.01
2513
2710
4.144297
TGCACCTTTCAGCTAACTTGATT
58.856
39.130
0.00
0.00
0.00
2.57
2538
2739
1.945354
CTACACACATCCGGACGCCT
61.945
60.000
6.12
0.00
0.00
5.52
2560
2761
2.621055
GCTCACGACACTCCATCTATCT
59.379
50.000
0.00
0.00
0.00
1.98
2618
2823
3.758554
AGTAAATGAGCCGCATTCAAACT
59.241
39.130
0.00
0.00
46.25
2.66
2721
2930
2.613026
TTGCCGTGACAAGAGAAAGA
57.387
45.000
0.00
0.00
0.00
2.52
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.