Multiple sequence alignment - TraesCS4B01G319500
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
TraesCS4B01G319500
chr4B
100.000
2420
0
0
1
2420
610245482
610243063
0.000000e+00
4470
1
TraesCS4B01G319500
chr4B
79.910
1105
131
45
845
1902
610098354
610097294
0.000000e+00
726
2
TraesCS4B01G319500
chr4B
92.105
76
6
0
2050
2125
610092181
610092106
9.150000e-20
108
3
TraesCS4B01G319500
chr5A
92.950
1546
88
8
891
2420
661666550
661668090
0.000000e+00
2231
4
TraesCS4B01G319500
chr5A
92.583
782
37
14
1
762
661665370
661666150
0.000000e+00
1103
5
TraesCS4B01G319500
chr5A
80.205
293
48
4
1023
1314
662052980
662052697
6.780000e-51
211
6
TraesCS4B01G319500
chr5A
89.189
148
12
4
1082
1228
435475897
435476041
5.310000e-42
182
7
TraesCS4B01G319500
chr3D
84.549
466
53
13
161
608
534166390
534165926
6.140000e-121
444
8
TraesCS4B01G319500
chr7A
84.615
390
41
8
164
535
717277685
717277297
1.060000e-98
370
9
TraesCS4B01G319500
chr7A
93.750
128
6
2
34
159
717277890
717277763
8.830000e-45
191
10
TraesCS4B01G319500
chr5B
91.304
138
10
2
1082
1218
390524026
390524162
1.140000e-43
187
11
TraesCS4B01G319500
chr5B
90.580
138
11
2
1082
1218
390403161
390403297
5.310000e-42
182
12
TraesCS4B01G319500
chrUn
81.735
219
35
3
986
1203
171662448
171662234
6.880000e-41
178
13
TraesCS4B01G319500
chrUn
81.364
220
33
6
986
1201
60909868
60910083
3.200000e-39
172
14
TraesCS4B01G319500
chr5D
81.277
235
31
9
1082
1311
333979031
333979257
6.880000e-41
178
15
TraesCS4B01G319500
chr4A
83.158
190
27
5
1021
1208
684061174
684060988
4.140000e-38
169
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
TraesCS4B01G319500
chr4B
610243063
610245482
2419
True
4470.0
4470
100.0000
1
2420
1
chr4B.!!$R3
2419
1
TraesCS4B01G319500
chr4B
610097294
610098354
1060
True
726.0
726
79.9100
845
1902
1
chr4B.!!$R2
1057
2
TraesCS4B01G319500
chr5A
661665370
661668090
2720
False
1667.0
2231
92.7665
1
2420
2
chr5A.!!$F2
2419
3
TraesCS4B01G319500
chr7A
717277297
717277890
593
True
280.5
370
89.1825
34
535
2
chr7A.!!$R1
501
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
865
1259
0.033504
ACACGTGACTCCGCTGAATT
59.966
50.0
25.01
0.0
0.0
2.17
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1668
2101
0.041576
AAACTTCGCGCCTTTCGAAC
60.042
50.0
0.0
0.0
40.49
3.95
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
25
26
0.310854
GGAAAACGGCAGGTGTGAAG
59.689
55.000
0.00
0.00
0.00
3.02
68
70
6.026947
ACTCGTATTTCAGTTTCAGTAGCT
57.973
37.500
0.00
0.00
0.00
3.32
78
80
4.574013
CAGTTTCAGTAGCTGATCCATTCC
59.426
45.833
0.00
0.00
40.39
3.01
324
416
0.329596
GGATGAGCCAGAACCAACCT
59.670
55.000
0.00
0.00
36.34
3.50
327
419
0.823356
TGAGCCAGAACCAACCTTGC
60.823
55.000
0.00
0.00
0.00
4.01
384
477
2.216898
GCCGGAGATGAGAAAATCCTG
58.783
52.381
5.05
0.00
0.00
3.86
447
540
3.472726
GGATCGGCACCGGGGTTA
61.473
66.667
5.12
0.00
40.25
2.85
518
618
4.018409
GGGACTTGCATTCCCCAC
57.982
61.111
19.36
0.00
46.57
4.61
519
619
1.076549
GGGACTTGCATTCCCCACA
59.923
57.895
19.36
0.00
46.57
4.17
755
858
3.492353
CTGGCCCCGACATCCCAT
61.492
66.667
0.00
0.00
0.00
4.00
761
864
1.478654
GCCCCGACATCCCATATGTTT
60.479
52.381
1.24
0.00
31.52
2.83
762
865
2.224670
GCCCCGACATCCCATATGTTTA
60.225
50.000
1.24
0.00
31.52
2.01
763
866
3.749310
GCCCCGACATCCCATATGTTTAA
60.749
47.826
1.24
0.00
31.52
1.52
764
867
4.072131
CCCCGACATCCCATATGTTTAAG
58.928
47.826
1.24
0.00
31.52
1.85
775
878
4.876107
CCATATGTTTAAGTGCTCTTCCGT
59.124
41.667
3.91
0.00
35.36
4.69
776
879
5.354234
CCATATGTTTAAGTGCTCTTCCGTT
59.646
40.000
3.91
0.00
35.36
4.44
777
880
4.749245
ATGTTTAAGTGCTCTTCCGTTG
57.251
40.909
3.91
0.00
35.36
4.10
778
881
2.289547
TGTTTAAGTGCTCTTCCGTTGC
59.710
45.455
3.91
0.00
35.36
4.17
779
882
1.519408
TTAAGTGCTCTTCCGTTGCC
58.481
50.000
3.91
0.00
35.36
4.52
780
883
0.394938
TAAGTGCTCTTCCGTTGCCA
59.605
50.000
3.91
0.00
35.36
4.92
781
884
1.166531
AAGTGCTCTTCCGTTGCCAC
61.167
55.000
0.00
0.00
0.00
5.01
782
885
1.891919
GTGCTCTTCCGTTGCCACA
60.892
57.895
0.00
0.00
0.00
4.17
783
886
1.597854
TGCTCTTCCGTTGCCACAG
60.598
57.895
0.00
0.00
0.00
3.66
784
887
2.328099
GCTCTTCCGTTGCCACAGG
61.328
63.158
0.00
0.00
0.00
4.00
818
921
0.969894
CAAATTAACGCCCAACCCCA
59.030
50.000
0.00
0.00
0.00
4.96
864
1258
0.667487
CACACGTGACTCCGCTGAAT
60.667
55.000
25.01
0.00
0.00
2.57
865
1259
0.033504
ACACGTGACTCCGCTGAATT
59.966
50.000
25.01
0.00
0.00
2.17
921
1323
6.183360
CCGTGTATTTAATCCTTTGCTTAGCA
60.183
38.462
1.39
1.39
36.47
3.49
953
1355
3.254470
TCTGGTCGACTCTCTACTCTG
57.746
52.381
16.46
0.33
0.00
3.35
954
1356
1.668751
CTGGTCGACTCTCTACTCTGC
59.331
57.143
16.46
0.00
0.00
4.26
955
1357
1.018910
GGTCGACTCTCTACTCTGCC
58.981
60.000
16.46
0.00
0.00
4.85
956
1358
1.018910
GTCGACTCTCTACTCTGCCC
58.981
60.000
8.70
0.00
0.00
5.36
1052
1462
0.771755
AACCTTGAACTCACCCTCCC
59.228
55.000
0.00
0.00
0.00
4.30
1099
1509
3.858989
GCTTCTTCCTCTGCGCGC
61.859
66.667
27.26
27.26
0.00
6.86
1238
1648
4.742201
CGGTGCGCCTACTGCAGT
62.742
66.667
25.12
25.12
44.21
4.40
1240
1650
3.121030
GTGCGCCTACTGCAGTGG
61.121
66.667
29.57
25.88
44.21
4.00
1258
1668
2.765807
AGGATGAGGGCCAGACGG
60.766
66.667
6.18
0.00
0.00
4.79
1317
1727
0.253327
ATGGAAAGGCGAGAAGGACC
59.747
55.000
0.00
0.00
0.00
4.46
1332
1742
2.915659
ACCGAGCCGTGGAAGTCA
60.916
61.111
0.00
0.00
0.00
3.41
1344
1763
2.281761
AAGTCAGCCGCTGTTGGG
60.282
61.111
19.77
0.00
32.61
4.12
1439
1867
3.131755
TGATCGATCTGCTCATGTGTTCT
59.868
43.478
25.02
0.00
0.00
3.01
1445
1873
4.276058
TCTGCTCATGTGTTCTTGATCA
57.724
40.909
0.00
0.00
0.00
2.92
1456
1884
0.036388
TCTTGATCACGGCCCAGTTC
60.036
55.000
0.00
0.00
0.00
3.01
1485
1914
2.289382
TGATTTGCTAGTTGACCTCGCA
60.289
45.455
0.00
0.00
39.86
5.10
1593
2026
3.000041
TCTGCGTGTGTTGGATTCATAC
59.000
45.455
0.00
0.00
0.00
2.39
1660
2093
7.283807
ACCAGAAAGAACGTTTGGTAATTTACT
59.716
33.333
17.80
0.00
40.21
2.24
1663
2096
9.726232
AGAAAGAACGTTTGGTAATTTACTTTC
57.274
29.630
17.28
17.28
39.40
2.62
1668
2101
8.496872
AACGTTTGGTAATTTACTTTCATTCG
57.503
30.769
0.00
6.74
0.00
3.34
1680
2113
0.165079
TTCATTCGTTCGAAAGGCGC
59.835
50.000
11.22
0.00
40.61
6.53
1916
2368
2.455032
CACGAGATCGAGTGTTGATCC
58.545
52.381
9.58
0.00
42.57
3.36
1942
2394
3.368843
GGAGAAGCTAGCATCTTGTGTGA
60.369
47.826
22.42
0.00
0.00
3.58
1943
2395
3.594134
AGAAGCTAGCATCTTGTGTGAC
58.406
45.455
16.53
0.00
0.00
3.67
1954
2406
2.880268
TCTTGTGTGACTGATTTGGCTG
59.120
45.455
0.00
0.00
0.00
4.85
1956
2408
0.242017
GTGTGACTGATTTGGCTGGC
59.758
55.000
0.00
0.00
0.00
4.85
1966
2418
1.778017
TTTGGCTGGCAGGAGCACTA
61.778
55.000
17.64
0.00
44.61
2.74
2021
2473
5.630680
CCTCTGAAATTTCCACATTTGAACG
59.369
40.000
15.48
0.00
0.00
3.95
2022
2474
6.384258
TCTGAAATTTCCACATTTGAACGA
57.616
33.333
15.48
0.00
0.00
3.85
2025
2477
7.925483
TCTGAAATTTCCACATTTGAACGAAAT
59.075
29.630
15.48
0.00
35.27
2.17
2129
2582
6.398918
AGAGATTATGGTTAGTGTGTGTCAC
58.601
40.000
0.00
0.00
46.46
3.67
2131
2584
6.711277
AGATTATGGTTAGTGTGTGTCACAT
58.289
36.000
9.31
0.00
46.32
3.21
2132
2585
6.595326
AGATTATGGTTAGTGTGTGTCACATG
59.405
38.462
9.31
0.00
46.32
3.21
2172
2625
3.140814
GGTGGCCCTCGCAAATCC
61.141
66.667
0.00
0.00
36.38
3.01
2191
2644
6.737720
AATCCAAGTGCATCATCTCTAGTA
57.262
37.500
0.00
0.00
0.00
1.82
2192
2645
5.781210
TCCAAGTGCATCATCTCTAGTAG
57.219
43.478
0.00
0.00
0.00
2.57
2206
2659
4.820716
TCTCTAGTAGGTTGAGTATTCGCC
59.179
45.833
0.00
0.00
0.00
5.54
2219
2672
2.368655
ATTCGCCAGACATTTTTGCC
57.631
45.000
0.00
0.00
0.00
4.52
2221
2674
0.881118
TCGCCAGACATTTTTGCCTC
59.119
50.000
0.00
0.00
0.00
4.70
2236
2689
3.627395
TGCCTCCTAATTACACCACTG
57.373
47.619
0.00
0.00
0.00
3.66
2238
2691
3.585289
TGCCTCCTAATTACACCACTGAA
59.415
43.478
0.00
0.00
0.00
3.02
2239
2692
3.939592
GCCTCCTAATTACACCACTGAAC
59.060
47.826
0.00
0.00
0.00
3.18
2252
2705
3.003275
ACCACTGAACGCAAAATACACAG
59.997
43.478
0.00
0.00
0.00
3.66
2278
2731
9.646427
GTATTTGTGCCTTGGACATTTATTTTA
57.354
29.630
0.00
0.00
33.22
1.52
2340
2793
1.948104
TGAACAAACTGACAGGGTCG
58.052
50.000
7.51
0.00
34.95
4.79
2373
2826
5.607477
TCTCTCAGTAAACAACAATTCGGT
58.393
37.500
0.00
0.00
0.00
4.69
2379
2832
4.641094
AGTAAACAACAATTCGGTGTGGAA
59.359
37.500
0.28
0.00
0.00
3.53
2398
2851
4.586421
TGGAATTGTGAGCACACCAATAAA
59.414
37.500
11.92
0.00
45.40
1.40
2408
2861
3.247411
GCACACCAATAAAACAAACCTGC
59.753
43.478
0.00
0.00
0.00
4.85
2413
2866
6.259829
ACACCAATAAAACAAACCTGCATTTC
59.740
34.615
0.00
0.00
0.00
2.17
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
13
14
3.034030
GTGCACTTCACACCTGCC
58.966
61.111
10.32
0.00
44.98
4.85
25
26
5.961843
CGAGTTATTGAAATGATCTGTGCAC
59.038
40.000
10.75
10.75
0.00
4.57
68
70
8.328758
AGAACTATTTGTTACTGGAATGGATCA
58.671
33.333
0.00
0.00
39.30
2.92
280
372
3.309410
CCTTGATTTCTCCCTGGTCCATT
60.309
47.826
0.00
0.00
0.00
3.16
324
416
1.300542
TCGCCATCGATATGCGCAA
60.301
52.632
27.31
14.67
40.21
4.85
495
595
1.885871
GAATGCAAGTCCCACAGGC
59.114
57.895
0.00
0.00
0.00
4.85
551
654
2.100631
CGGGTCAATCTCCACGCAC
61.101
63.158
0.00
0.00
0.00
5.34
744
847
4.024048
GCACTTAAACATATGGGATGTCGG
60.024
45.833
7.80
0.00
0.00
4.79
754
857
5.163754
GCAACGGAAGAGCACTTAAACATAT
60.164
40.000
0.00
0.00
36.39
1.78
755
858
4.153475
GCAACGGAAGAGCACTTAAACATA
59.847
41.667
0.00
0.00
36.39
2.29
761
864
0.394938
TGGCAACGGAAGAGCACTTA
59.605
50.000
0.00
0.00
42.51
2.24
762
865
1.148273
TGGCAACGGAAGAGCACTT
59.852
52.632
0.00
0.00
42.51
3.16
763
866
1.598130
GTGGCAACGGAAGAGCACT
60.598
57.895
0.00
0.00
42.51
4.40
764
867
1.845809
CTGTGGCAACGGAAGAGCAC
61.846
60.000
0.00
0.00
42.51
4.40
784
887
1.595093
ATTTGCTAACGGCTGTGGGC
61.595
55.000
14.01
14.01
42.39
5.36
785
888
0.887933
AATTTGCTAACGGCTGTGGG
59.112
50.000
0.00
0.00
42.39
4.61
786
889
3.498082
GTTAATTTGCTAACGGCTGTGG
58.502
45.455
0.00
0.00
42.39
4.17
787
890
3.160545
CGTTAATTTGCTAACGGCTGTG
58.839
45.455
0.00
0.00
46.58
3.66
788
891
3.465122
CGTTAATTTGCTAACGGCTGT
57.535
42.857
7.81
0.00
46.58
4.40
794
897
3.247442
GGTTGGGCGTTAATTTGCTAAC
58.753
45.455
0.00
0.00
0.00
2.34
795
898
2.231721
GGGTTGGGCGTTAATTTGCTAA
59.768
45.455
0.00
0.00
0.00
3.09
796
899
1.819903
GGGTTGGGCGTTAATTTGCTA
59.180
47.619
0.00
0.00
0.00
3.49
797
900
0.606096
GGGTTGGGCGTTAATTTGCT
59.394
50.000
0.00
0.00
0.00
3.91
798
901
0.390603
GGGGTTGGGCGTTAATTTGC
60.391
55.000
0.00
0.00
0.00
3.68
864
1258
1.400142
CAGAGAACGGTTGTTGCACAA
59.600
47.619
0.00
0.00
38.78
3.33
865
1259
1.013596
CAGAGAACGGTTGTTGCACA
58.986
50.000
0.00
0.00
38.78
4.57
921
1323
5.419471
AGAGTCGACCAGAACTTATTAGCTT
59.581
40.000
13.01
0.00
0.00
3.74
953
1355
1.224870
GGCTGAAAGGTAGAGGGGC
59.775
63.158
0.00
0.00
0.00
5.80
954
1356
0.833949
GAGGCTGAAAGGTAGAGGGG
59.166
60.000
0.00
0.00
0.00
4.79
955
1357
1.573108
TGAGGCTGAAAGGTAGAGGG
58.427
55.000
0.00
0.00
0.00
4.30
956
1358
3.323403
CCTATGAGGCTGAAAGGTAGAGG
59.677
52.174
0.00
0.00
0.00
3.69
1099
1509
1.342082
CGGAACTTACGGTCGCAGTG
61.342
60.000
0.00
0.00
0.00
3.66
1238
1648
1.690633
GTCTGGCCCTCATCCTCCA
60.691
63.158
0.00
0.00
0.00
3.86
1240
1650
2.801631
CCGTCTGGCCCTCATCCTC
61.802
68.421
0.00
0.00
0.00
3.71
1258
1668
4.937431
GCCTCTGCCGCCATACCC
62.937
72.222
0.00
0.00
0.00
3.69
1289
1699
2.115291
GCCTTTCCATCCGCAGACC
61.115
63.158
0.00
0.00
0.00
3.85
1317
1727
2.811317
GCTGACTTCCACGGCTCG
60.811
66.667
0.00
0.00
36.79
5.03
1389
1817
1.078759
GAGCCAAGTCCACATCGTCG
61.079
60.000
0.00
0.00
0.00
5.12
1439
1867
1.002624
GGAACTGGGCCGTGATCAA
60.003
57.895
0.00
0.00
0.00
2.57
1456
1884
0.625849
ACTAGCAAATCAGGGTGGGG
59.374
55.000
0.00
0.00
0.00
4.96
1660
2093
1.399215
GCGCCTTTCGAACGAATGAAA
60.399
47.619
19.19
0.00
41.67
2.69
1663
2096
1.577616
CGCGCCTTTCGAACGAATG
60.578
57.895
10.44
12.03
41.67
2.67
1668
2101
0.041576
AAACTTCGCGCCTTTCGAAC
60.042
50.000
0.00
0.00
40.49
3.95
1703
2136
7.856145
AGCAAAGATAGAACAATAGAACTGG
57.144
36.000
0.00
0.00
0.00
4.00
1784
2223
9.561069
GTAACACAATAGACATTAATCAGGGAT
57.439
33.333
0.00
0.00
0.00
3.85
1916
2368
3.640967
ACAAGATGCTAGCTTCTCCTAGG
59.359
47.826
27.76
18.31
36.23
3.02
1942
2394
0.323178
CTCCTGCCAGCCAAATCAGT
60.323
55.000
0.00
0.00
0.00
3.41
1943
2395
1.664321
GCTCCTGCCAGCCAAATCAG
61.664
60.000
0.00
0.00
32.76
2.90
1954
2406
0.955919
GGTGTTGTAGTGCTCCTGCC
60.956
60.000
0.00
0.00
38.71
4.85
1956
2408
0.396435
TGGGTGTTGTAGTGCTCCTG
59.604
55.000
0.00
0.00
0.00
3.86
1966
2418
3.305720
TGTCTCTCTAAGTGGGTGTTGT
58.694
45.455
0.00
0.00
0.00
3.32
2045
2497
9.926158
ATGTGCATGTTTTACATTCATTTTCTA
57.074
25.926
0.00
0.00
36.53
2.10
2172
2625
5.528043
ACCTACTAGAGATGATGCACTTG
57.472
43.478
0.00
0.00
0.00
3.16
2191
2644
1.899814
TGTCTGGCGAATACTCAACCT
59.100
47.619
0.00
0.00
0.00
3.50
2192
2645
2.380084
TGTCTGGCGAATACTCAACC
57.620
50.000
0.00
0.00
0.00
3.77
2206
2659
7.029563
GTGTAATTAGGAGGCAAAAATGTCTG
58.970
38.462
0.00
0.00
0.00
3.51
2219
2672
3.617263
GCGTTCAGTGGTGTAATTAGGAG
59.383
47.826
0.00
0.00
0.00
3.69
2221
2674
3.331150
TGCGTTCAGTGGTGTAATTAGG
58.669
45.455
0.00
0.00
0.00
2.69
2252
2705
8.546597
AAAATAAATGTCCAAGGCACAAATAC
57.453
30.769
0.00
0.00
0.00
1.89
2313
2766
7.458397
ACCCTGTCAGTTTGTTCATAGATAAA
58.542
34.615
0.00
0.00
0.00
1.40
2316
2769
5.491982
GACCCTGTCAGTTTGTTCATAGAT
58.508
41.667
0.00
0.00
32.09
1.98
2321
2774
1.483004
TCGACCCTGTCAGTTTGTTCA
59.517
47.619
0.00
0.00
32.09
3.18
2326
2779
3.771577
AAGAATCGACCCTGTCAGTTT
57.228
42.857
0.00
0.00
32.09
2.66
2373
2826
1.317613
GGTGTGCTCACAATTCCACA
58.682
50.000
19.67
0.00
45.45
4.17
2379
2832
5.528043
TGTTTTATTGGTGTGCTCACAAT
57.472
34.783
19.67
17.27
45.45
2.71
2382
2835
4.506288
GGTTTGTTTTATTGGTGTGCTCAC
59.494
41.667
10.44
10.44
43.19
3.51
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.