Multiple sequence alignment - TraesCS5B01G017500
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
TraesCS5B01G017500
chr5B
100.000
2717
0
0
1
2717
16198571
16201287
0.000000e+00
5018.0
1
TraesCS5B01G017500
chr5B
83.616
1178
135
34
563
1717
16173359
16174501
0.000000e+00
1053.0
2
TraesCS5B01G017500
chr5B
87.380
935
84
17
863
1782
16369056
16368141
0.000000e+00
1042.0
3
TraesCS5B01G017500
chr5B
89.698
728
54
11
1077
1801
16185696
16186405
0.000000e+00
909.0
4
TraesCS5B01G017500
chr5B
89.399
566
44
4
69
629
16386498
16385944
0.000000e+00
699.0
5
TraesCS5B01G017500
chr5B
92.282
298
15
6
276
567
16172226
16172521
1.500000e-112
416.0
6
TraesCS5B01G017500
chr5B
90.000
130
11
2
1795
1923
16368091
16367963
1.670000e-37
167.0
7
TraesCS5B01G017500
chr5B
86.131
137
17
1
637
771
16370555
16370419
2.180000e-31
147.0
8
TraesCS5B01G017500
chr5B
81.022
137
21
5
1801
1935
669292583
669292716
1.330000e-18
104.0
9
TraesCS5B01G017500
chr5B
88.372
86
4
2
1715
1799
16174594
16174674
6.190000e-17
99.0
10
TraesCS5B01G017500
chr5D
92.723
907
43
7
831
1717
23011477
23010574
0.000000e+00
1288.0
11
TraesCS5B01G017500
chr5D
85.877
963
89
21
863
1806
23058229
23057295
0.000000e+00
981.0
12
TraesCS5B01G017500
chr5D
85.995
764
66
19
4
755
23059024
23058290
0.000000e+00
780.0
13
TraesCS5B01G017500
chr5D
87.478
575
48
10
1
564
23014638
23014077
2.280000e-180
641.0
14
TraesCS5B01G017500
chr5D
91.315
426
35
2
2292
2716
22965467
22965043
5.040000e-162
580.0
15
TraesCS5B01G017500
chr5D
85.377
212
15
6
559
761
23011665
23011461
3.550000e-49
206.0
16
TraesCS5B01G017500
chr5D
88.618
123
10
3
1715
1837
23010493
23010375
2.180000e-31
147.0
17
TraesCS5B01G017500
chrUn
87.343
877
77
17
921
1782
312425225
312426082
0.000000e+00
974.0
18
TraesCS5B01G017500
chrUn
90.000
130
11
2
1795
1923
312426132
312426260
1.670000e-37
167.0
19
TraesCS5B01G017500
chr5A
86.589
768
70
16
4
755
16839649
16838899
0.000000e+00
817.0
20
TraesCS5B01G017500
chr5A
91.078
538
23
3
1211
1744
16734743
16734227
0.000000e+00
704.0
21
TraesCS5B01G017500
chr5A
89.696
427
42
2
2292
2717
16730362
16729937
6.620000e-151
544.0
22
TraesCS5B01G017500
chr5A
83.574
554
57
17
1
548
16735536
16735011
3.140000e-134
488.0
23
TraesCS5B01G017500
chr5A
91.321
265
18
3
584
844
16735012
16734749
9.250000e-95
357.0
24
TraesCS5B01G017500
chr5A
82.412
199
25
6
863
1061
16838817
16838629
6.020000e-37
165.0
25
TraesCS5B01G017500
chr3B
77.666
694
112
30
840
1501
18305776
18306458
1.530000e-102
383.0
26
TraesCS5B01G017500
chr3B
77.169
657
111
26
874
1501
18484421
18485067
2.000000e-91
346.0
27
TraesCS5B01G017500
chr3D
82.759
406
58
9
1099
1501
12848511
12848907
4.300000e-93
351.0
28
TraesCS5B01G017500
chr3D
81.381
333
53
6
1171
1501
12841343
12841668
2.070000e-66
263.0
29
TraesCS5B01G017500
chr3D
78.344
157
19
9
1572
1726
12836231
12836374
1.340000e-13
87.9
30
TraesCS5B01G017500
chr7B
89.362
47
5
0
1955
2001
13651613
13651659
2.920000e-05
60.2
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
TraesCS5B01G017500
chr5B
16198571
16201287
2716
False
5018.000000
5018
100.00000
1
2717
1
chr5B.!!$F2
2716
1
TraesCS5B01G017500
chr5B
16185696
16186405
709
False
909.000000
909
89.69800
1077
1801
1
chr5B.!!$F1
724
2
TraesCS5B01G017500
chr5B
16385944
16386498
554
True
699.000000
699
89.39900
69
629
1
chr5B.!!$R1
560
3
TraesCS5B01G017500
chr5B
16172226
16174674
2448
False
522.666667
1053
88.09000
276
1799
3
chr5B.!!$F4
1523
4
TraesCS5B01G017500
chr5B
16367963
16370555
2592
True
452.000000
1042
87.83700
637
1923
3
chr5B.!!$R2
1286
5
TraesCS5B01G017500
chr5D
23057295
23059024
1729
True
880.500000
981
85.93600
4
1806
2
chr5D.!!$R3
1802
6
TraesCS5B01G017500
chr5D
23010375
23014638
4263
True
570.500000
1288
88.54900
1
1837
4
chr5D.!!$R2
1836
7
TraesCS5B01G017500
chrUn
312425225
312426260
1035
False
570.500000
974
88.67150
921
1923
2
chrUn.!!$F1
1002
8
TraesCS5B01G017500
chr5A
16729937
16735536
5599
True
523.250000
704
88.91725
1
2717
4
chr5A.!!$R1
2716
9
TraesCS5B01G017500
chr5A
16838629
16839649
1020
True
491.000000
817
84.50050
4
1061
2
chr5A.!!$R2
1057
10
TraesCS5B01G017500
chr3B
18305776
18306458
682
False
383.000000
383
77.66600
840
1501
1
chr3B.!!$F1
661
11
TraesCS5B01G017500
chr3B
18484421
18485067
646
False
346.000000
346
77.16900
874
1501
1
chr3B.!!$F2
627
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
996
4751
0.174389
TGTCTCGAAGCTGCAGATCC
59.826
55.0
20.43
0.0
0.0
3.36
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2272
9743
0.25589
TACAAAGAGGGGCAGATGGC
59.744
55.0
0.0
0.0
43.74
4.4
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
60
61
1.311859
GATTCCATTCGCATGAGGCA
58.688
50.000
0.00
0.00
45.17
4.75
64
65
2.517875
ATTCGCATGAGGCAGCCC
60.518
61.111
8.22
0.00
45.17
5.19
65
66
3.052909
ATTCGCATGAGGCAGCCCT
62.053
57.895
8.22
0.00
46.74
5.19
82
83
0.179100
CCTGCGGAAGATCATCGTGT
60.179
55.000
0.00
0.00
0.00
4.49
85
86
1.812214
GCGGAAGATCATCGTGTCGC
61.812
60.000
4.11
4.11
35.34
5.19
130
131
4.803426
CCCCTGCTCGTGCTCGTC
62.803
72.222
11.19
2.52
40.48
4.20
168
169
4.462483
AGGAAATGGTTATGTTTGATGCGT
59.538
37.500
0.00
0.00
0.00
5.24
198
199
3.010361
AGGGAGTAGGATCGAATCGGTAT
59.990
47.826
1.76
0.00
0.00
2.73
211
212
1.262417
TCGGTATGTGAGTGGCAAGA
58.738
50.000
0.00
0.00
0.00
3.02
360
382
5.106157
ACCTTTGGTCTCGATTATGCTTTTG
60.106
40.000
0.00
0.00
0.00
2.44
401
423
2.128507
GCCAAACCAAACGGACCCA
61.129
57.895
0.00
0.00
0.00
4.51
402
424
1.737201
CCAAACCAAACGGACCCAC
59.263
57.895
0.00
0.00
0.00
4.61
403
425
0.753848
CCAAACCAAACGGACCCACT
60.754
55.000
0.00
0.00
0.00
4.00
404
426
1.477195
CCAAACCAAACGGACCCACTA
60.477
52.381
0.00
0.00
0.00
2.74
471
498
6.179756
TGAACTAAAGCACATATCACCACAT
58.820
36.000
0.00
0.00
0.00
3.21
504
531
9.178427
CTTATTCAGAAGAAACAAGAGCAAAAG
57.822
33.333
0.00
0.00
37.29
2.27
593
3042
8.693504
CAACAAACTATTTTGCAAGTCACATAG
58.306
33.333
0.00
4.97
45.32
2.23
597
3046
5.939883
ACTATTTTGCAAGTCACATAGCTGA
59.060
36.000
0.00
0.00
0.00
4.26
629
3078
9.740239
AGATCGTATACGCTAATTTTTAGTGAA
57.260
29.630
20.42
0.00
39.60
3.18
630
3079
9.990888
GATCGTATACGCTAATTTTTAGTGAAG
57.009
33.333
20.42
2.46
39.60
3.02
632
3081
8.800972
TCGTATACGCTAATTTTTAGTGAAGTG
58.199
33.333
20.42
0.00
39.60
3.16
633
3082
8.800972
CGTATACGCTAATTTTTAGTGAAGTGA
58.199
33.333
13.08
0.00
0.00
3.41
634
3083
9.897349
GTATACGCTAATTTTTAGTGAAGTGAC
57.103
33.333
13.21
2.80
0.00
3.67
635
3084
6.237313
ACGCTAATTTTTAGTGAAGTGACC
57.763
37.500
13.21
0.00
0.00
4.02
689
3145
6.948353
ACACACACTTCGAATGAATATATGC
58.052
36.000
0.00
0.00
32.61
3.14
692
3148
7.374228
CACACACTTCGAATGAATATATGCAAC
59.626
37.037
0.00
0.00
32.61
4.17
750
3209
2.046314
ACTAATGCGCCGGTTGCT
60.046
55.556
19.32
5.33
38.05
3.91
845
4230
5.012664
TCAAATCTGGGTTGTAAGAGCTGTA
59.987
40.000
0.00
0.00
0.00
2.74
871
4620
8.671384
TTGGATATAATTTCCGGTTGTAGAAG
57.329
34.615
0.00
0.00
35.94
2.85
912
4661
1.006922
GTTGCTTTGTCTGCAGGCC
60.007
57.895
17.28
6.61
41.71
5.19
983
4738
0.242825
TACGTCCCTGCTTTGTCTCG
59.757
55.000
0.00
0.00
0.00
4.04
985
4740
0.319555
CGTCCCTGCTTTGTCTCGAA
60.320
55.000
0.00
0.00
0.00
3.71
996
4751
0.174389
TGTCTCGAAGCTGCAGATCC
59.826
55.000
20.43
0.00
0.00
3.36
997
4752
0.869454
GTCTCGAAGCTGCAGATCCG
60.869
60.000
20.43
12.35
0.00
4.18
1033
4808
0.592247
CGAACCAGCAAAGCACACAC
60.592
55.000
0.00
0.00
0.00
3.82
1034
4809
0.455410
GAACCAGCAAAGCACACACA
59.545
50.000
0.00
0.00
0.00
3.72
1039
4814
1.019673
AGCAAAGCACACACAGACAG
58.980
50.000
0.00
0.00
0.00
3.51
1047
4830
0.179045
ACACACAGACAGAGGGCAAC
60.179
55.000
0.00
0.00
0.00
4.17
1311
5128
1.161843
TCATAGTGTCGCTGTCGTCA
58.838
50.000
0.00
0.00
36.96
4.35
1643
5470
2.808206
GGGGTATGCCTCAGTCCCG
61.808
68.421
0.00
0.00
39.06
5.14
1697
5524
1.373497
CTTCGGAGCAGAGCACGTT
60.373
57.895
0.00
0.00
34.08
3.99
1747
5701
4.100084
TCCGTGGAGCCCTGCATG
62.100
66.667
2.41
2.41
37.62
4.06
1806
5799
2.825532
AGGCGTGGTGAATTGCTTTATT
59.174
40.909
0.00
0.00
0.00
1.40
1881
5874
1.134007
TGGAGAGCCTGCCATATGTTG
60.134
52.381
1.24
0.00
34.31
3.33
1894
5887
3.480470
CATATGTTGGATCTGTCCCACC
58.520
50.000
0.00
0.00
44.41
4.61
1899
5892
1.923395
GGATCTGTCCCACCCACCA
60.923
63.158
0.00
0.00
38.69
4.17
1905
5898
3.465832
TCTGTCCCACCCACCATAAATA
58.534
45.455
0.00
0.00
0.00
1.40
1931
5924
9.661563
ATGAAGATTTTGCAATATTGTTCATGT
57.338
25.926
24.49
13.23
0.00
3.21
1995
5988
2.831685
TGTTGTAGTGGCAACTCGAT
57.168
45.000
0.00
0.00
46.33
3.59
2006
5999
1.159285
CAACTCGATGGTGCACACAT
58.841
50.000
20.43
18.64
0.00
3.21
2036
6029
7.616103
TTTTTGCAACATAACGTCTATTGTG
57.384
32.000
0.00
0.00
0.00
3.33
2042
6035
8.079203
TGCAACATAACGTCTATTGTGAAAAAT
58.921
29.630
0.00
0.00
0.00
1.82
2043
6036
8.365210
GCAACATAACGTCTATTGTGAAAAATG
58.635
33.333
0.00
0.00
0.00
2.32
2044
6037
9.605955
CAACATAACGTCTATTGTGAAAAATGA
57.394
29.630
0.00
0.00
0.00
2.57
2134
9604
6.708949
GGAACATGACCTCTGTTACAAAACTA
59.291
38.462
0.00
0.00
37.39
2.24
2157
9628
9.841295
ACTATTTGTTTGTAGACTCCAAGTAAA
57.159
29.630
0.00
0.00
0.00
2.01
2169
9640
6.719370
AGACTCCAAGTAAATGTAAAATGCCA
59.281
34.615
0.00
0.00
0.00
4.92
2177
9648
8.546597
AGTAAATGTAAAATGCCAAATCAACC
57.453
30.769
0.00
0.00
0.00
3.77
2183
9654
6.667414
TGTAAAATGCCAAATCAACCTCCTAT
59.333
34.615
0.00
0.00
0.00
2.57
2189
9660
5.103728
TGCCAAATCAACCTCCTATCCATTA
60.104
40.000
0.00
0.00
0.00
1.90
2191
9662
6.494835
GCCAAATCAACCTCCTATCCATTATT
59.505
38.462
0.00
0.00
0.00
1.40
2197
9668
6.389869
TCAACCTCCTATCCATTATTTCCACT
59.610
38.462
0.00
0.00
0.00
4.00
2206
9677
6.573664
TCCATTATTTCCACTGAACACAAG
57.426
37.500
0.00
0.00
0.00
3.16
2225
9696
1.137872
AGCATTGAGGGACGCTAGAAG
59.862
52.381
0.00
0.00
31.60
2.85
2247
9718
3.904234
GCGAATTTTTGTACTGTTCGTCC
59.096
43.478
14.81
2.87
42.45
4.79
2255
9726
3.064207
TGTACTGTTCGTCCAAAGCATC
58.936
45.455
0.00
0.00
0.00
3.91
2256
9727
1.148310
ACTGTTCGTCCAAAGCATCG
58.852
50.000
0.00
0.00
0.00
3.84
2257
9728
1.148310
CTGTTCGTCCAAAGCATCGT
58.852
50.000
0.00
0.00
0.00
3.73
2258
9729
1.126846
CTGTTCGTCCAAAGCATCGTC
59.873
52.381
0.00
0.00
0.00
4.20
2259
9730
0.442699
GTTCGTCCAAAGCATCGTCC
59.557
55.000
0.00
0.00
0.00
4.79
2260
9731
0.034198
TTCGTCCAAAGCATCGTCCA
59.966
50.000
0.00
0.00
0.00
4.02
2261
9732
0.389817
TCGTCCAAAGCATCGTCCAG
60.390
55.000
0.00
0.00
0.00
3.86
2262
9733
1.361668
CGTCCAAAGCATCGTCCAGG
61.362
60.000
0.00
0.00
0.00
4.45
2263
9734
1.026718
GTCCAAAGCATCGTCCAGGG
61.027
60.000
0.00
0.00
0.00
4.45
2264
9735
1.002134
CCAAAGCATCGTCCAGGGT
60.002
57.895
0.00
0.00
0.00
4.34
2265
9736
1.308069
CCAAAGCATCGTCCAGGGTG
61.308
60.000
0.00
0.00
0.00
4.61
2266
9737
1.675641
AAAGCATCGTCCAGGGTGC
60.676
57.895
0.00
0.00
37.84
5.01
2267
9738
3.005539
AGCATCGTCCAGGGTGCT
61.006
61.111
1.09
1.09
42.66
4.40
2268
9739
2.045926
GCATCGTCCAGGGTGCTT
60.046
61.111
0.00
0.00
34.85
3.91
2269
9740
1.220749
GCATCGTCCAGGGTGCTTA
59.779
57.895
0.00
0.00
34.85
3.09
2270
9741
1.090052
GCATCGTCCAGGGTGCTTAC
61.090
60.000
0.00
0.00
34.85
2.34
2271
9742
0.537188
CATCGTCCAGGGTGCTTACT
59.463
55.000
0.00
0.00
0.00
2.24
2272
9743
0.537188
ATCGTCCAGGGTGCTTACTG
59.463
55.000
0.00
0.00
34.54
2.74
2273
9744
1.741770
CGTCCAGGGTGCTTACTGC
60.742
63.158
0.00
0.00
43.25
4.40
2274
9745
1.377333
GTCCAGGGTGCTTACTGCC
60.377
63.158
0.00
0.00
42.00
4.85
2275
9746
1.845664
TCCAGGGTGCTTACTGCCA
60.846
57.895
0.00
0.00
42.00
4.92
2276
9747
1.207488
TCCAGGGTGCTTACTGCCAT
61.207
55.000
0.00
0.00
42.00
4.40
2277
9748
0.749454
CCAGGGTGCTTACTGCCATC
60.749
60.000
0.00
0.00
42.00
3.51
2278
9749
0.254178
CAGGGTGCTTACTGCCATCT
59.746
55.000
0.00
0.00
42.00
2.90
2279
9750
0.254178
AGGGTGCTTACTGCCATCTG
59.746
55.000
0.00
0.00
42.00
2.90
2280
9751
1.379642
GGGTGCTTACTGCCATCTGC
61.380
60.000
0.00
0.00
42.00
4.26
2281
9752
1.379642
GGTGCTTACTGCCATCTGCC
61.380
60.000
0.00
0.00
42.00
4.85
2282
9753
1.077501
TGCTTACTGCCATCTGCCC
60.078
57.895
0.00
0.00
42.00
5.36
2283
9754
1.825622
GCTTACTGCCATCTGCCCC
60.826
63.158
0.00
0.00
40.16
5.80
2284
9755
1.918253
CTTACTGCCATCTGCCCCT
59.082
57.895
0.00
0.00
40.16
4.79
2285
9756
0.179034
CTTACTGCCATCTGCCCCTC
60.179
60.000
0.00
0.00
40.16
4.30
2286
9757
0.621571
TTACTGCCATCTGCCCCTCT
60.622
55.000
0.00
0.00
40.16
3.69
2287
9758
0.621571
TACTGCCATCTGCCCCTCTT
60.622
55.000
0.00
0.00
40.16
2.85
2288
9759
1.305623
CTGCCATCTGCCCCTCTTT
59.694
57.895
0.00
0.00
40.16
2.52
2289
9760
1.000521
TGCCATCTGCCCCTCTTTG
60.001
57.895
0.00
0.00
40.16
2.77
2290
9761
1.000396
GCCATCTGCCCCTCTTTGT
60.000
57.895
0.00
0.00
0.00
2.83
2291
9762
0.255890
GCCATCTGCCCCTCTTTGTA
59.744
55.000
0.00
0.00
0.00
2.41
2292
9763
1.133668
GCCATCTGCCCCTCTTTGTAT
60.134
52.381
0.00
0.00
0.00
2.29
2296
9767
3.634397
TCTGCCCCTCTTTGTATTCTG
57.366
47.619
0.00
0.00
0.00
3.02
2306
9777
4.406456
TCTTTGTATTCTGTTGGCACCAT
58.594
39.130
0.00
0.00
0.00
3.55
2307
9778
4.458989
TCTTTGTATTCTGTTGGCACCATC
59.541
41.667
0.00
0.00
0.00
3.51
2319
9790
1.789078
GCACCATCGATGCCACATCC
61.789
60.000
20.25
0.00
37.08
3.51
2320
9791
0.464193
CACCATCGATGCCACATCCA
60.464
55.000
20.25
0.00
0.00
3.41
2323
9794
1.475571
CCATCGATGCCACATCCAGAA
60.476
52.381
20.25
0.00
0.00
3.02
2327
9798
2.945008
TCGATGCCACATCCAGAAATTC
59.055
45.455
2.15
0.00
0.00
2.17
2342
9814
5.006649
CCAGAAATTCGCATCGATTTCTGTA
59.993
40.000
27.37
1.60
45.62
2.74
2343
9815
5.898606
CAGAAATTCGCATCGATTTCTGTAC
59.101
40.000
24.95
0.00
44.32
2.90
2344
9816
4.795970
AATTCGCATCGATTTCTGTACC
57.204
40.909
0.00
0.00
35.23
3.34
2349
9821
3.006940
GCATCGATTTCTGTACCCACAA
58.993
45.455
0.00
0.00
33.22
3.33
2363
9835
7.181305
TCTGTACCCACAAAGATAGTTTATCCA
59.819
37.037
0.00
0.00
33.13
3.41
2382
9854
5.227569
TCCATCTTTCTTAAGTGTGAGCA
57.772
39.130
1.63
0.00
32.98
4.26
2392
9864
7.658179
TCTTAAGTGTGAGCAAATAGAGTTG
57.342
36.000
1.63
0.00
0.00
3.16
2427
9899
3.077359
GCATTCACCCAGCATACCTATC
58.923
50.000
0.00
0.00
0.00
2.08
2431
9903
1.774254
CACCCAGCATACCTATCCCAA
59.226
52.381
0.00
0.00
0.00
4.12
2433
9905
3.587061
CACCCAGCATACCTATCCCAATA
59.413
47.826
0.00
0.00
0.00
1.90
2443
9915
7.659390
GCATACCTATCCCAATATAGATCTTGC
59.341
40.741
0.00
0.00
32.13
4.01
2461
9933
3.266510
TGCAGATTCCTAGCGAAATGT
57.733
42.857
0.00
0.00
33.08
2.71
2464
9936
3.797039
CAGATTCCTAGCGAAATGTCCA
58.203
45.455
0.00
0.00
33.08
4.02
2494
9966
6.040842
ACTCAACCTGAAAATGTTAGCACAAT
59.959
34.615
0.00
0.00
36.16
2.71
2505
9977
9.979578
AAAATGTTAGCACAATGATTTCAGTTA
57.020
25.926
0.00
0.00
36.16
2.24
2509
9981
7.860373
TGTTAGCACAATGATTTCAGTTAACAC
59.140
33.333
8.61
0.00
0.00
3.32
2513
9985
7.596248
AGCACAATGATTTCAGTTAACACATTC
59.404
33.333
8.61
0.00
0.00
2.67
2514
9986
7.148755
GCACAATGATTTCAGTTAACACATTCC
60.149
37.037
8.61
0.00
0.00
3.01
2521
9993
9.271828
GATTTCAGTTAACACATTCCCAAAATT
57.728
29.630
8.61
0.00
0.00
1.82
2524
9996
8.472007
TCAGTTAACACATTCCCAAAATTAGT
57.528
30.769
8.61
0.00
0.00
2.24
2558
10030
3.129113
TGGCACATGCAGCAGTAAAATAG
59.871
43.478
12.17
0.00
44.36
1.73
2561
10033
5.032863
GCACATGCAGCAGTAAAATAGAAG
58.967
41.667
0.00
0.00
41.59
2.85
2574
10046
9.307121
CAGTAAAATAGAAGATCACACACCTAG
57.693
37.037
0.00
0.00
0.00
3.02
2624
10096
1.510492
TATTCCCTGCATCAGCCTCA
58.490
50.000
0.00
0.00
41.13
3.86
2625
10097
0.183014
ATTCCCTGCATCAGCCTCAG
59.817
55.000
0.00
0.00
41.13
3.35
2657
10129
2.224426
TGCTTCGAGGGTCAGCTAAAAA
60.224
45.455
7.50
0.00
34.42
1.94
2688
10160
0.608640
ACATCACCTCTTCGTCCACC
59.391
55.000
0.00
0.00
0.00
4.61
2689
10161
0.898320
CATCACCTCTTCGTCCACCT
59.102
55.000
0.00
0.00
0.00
4.00
2690
10162
1.276421
CATCACCTCTTCGTCCACCTT
59.724
52.381
0.00
0.00
0.00
3.50
2691
10163
0.679505
TCACCTCTTCGTCCACCTTG
59.320
55.000
0.00
0.00
0.00
3.61
2700
10172
2.989639
TCCACCTTGGAGCATCGG
59.010
61.111
0.00
0.00
42.67
4.18
2705
10177
1.452108
CCTTGGAGCATCGGGGTTC
60.452
63.158
0.00
0.00
34.37
3.62
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
29
30
2.403252
ATGGAATCCTTCACGTGACC
57.597
50.000
19.90
15.47
0.00
4.02
64
65
1.203928
GACACGATGATCTTCCGCAG
58.796
55.000
3.19
0.00
0.00
5.18
65
66
0.525455
CGACACGATGATCTTCCGCA
60.525
55.000
3.19
0.00
0.00
5.69
67
68
1.209275
GGCGACACGATGATCTTCCG
61.209
60.000
3.19
2.59
0.00
4.30
73
74
2.413351
CTCCGGCGACACGATGAT
59.587
61.111
9.30
0.00
35.47
2.45
85
86
3.391665
CTTGCCACTAGCCCTCCGG
62.392
68.421
0.00
0.00
42.71
5.14
102
103
1.512735
GAGCAGGGGATAGGGTTTCT
58.487
55.000
0.00
0.00
0.00
2.52
130
131
0.709992
TTCCTCCTTTCCCCCATTGG
59.290
55.000
0.00
0.00
0.00
3.16
168
169
2.487445
CGATCCTACTCCCTGTAGCTCA
60.487
54.545
0.00
0.00
45.44
4.26
174
175
2.231529
CGATTCGATCCTACTCCCTGT
58.768
52.381
0.00
0.00
0.00
4.00
198
199
1.357137
TACCCATCTTGCCACTCACA
58.643
50.000
0.00
0.00
0.00
3.58
211
212
5.357032
CCAACTTCTAAGCGAAATTACCCAT
59.643
40.000
0.00
0.00
0.00
4.00
264
265
1.035139
CCACAGCTTTTCCACAGCTT
58.965
50.000
0.00
0.00
45.82
3.74
266
267
1.032014
TTCCACAGCTTTTCCACAGC
58.968
50.000
0.00
0.00
37.56
4.40
267
268
3.799281
TTTTCCACAGCTTTTCCACAG
57.201
42.857
0.00
0.00
0.00
3.66
268
269
3.740764
GCATTTTCCACAGCTTTTCCACA
60.741
43.478
0.00
0.00
0.00
4.17
269
270
2.802247
GCATTTTCCACAGCTTTTCCAC
59.198
45.455
0.00
0.00
0.00
4.02
270
271
2.433604
TGCATTTTCCACAGCTTTTCCA
59.566
40.909
0.00
0.00
0.00
3.53
271
272
2.802247
GTGCATTTTCCACAGCTTTTCC
59.198
45.455
0.00
0.00
33.50
3.13
272
273
3.721035
AGTGCATTTTCCACAGCTTTTC
58.279
40.909
0.00
0.00
35.69
2.29
273
274
3.825143
AGTGCATTTTCCACAGCTTTT
57.175
38.095
0.00
0.00
35.69
2.27
274
275
4.584325
TCTTAGTGCATTTTCCACAGCTTT
59.416
37.500
0.00
0.00
35.69
3.51
360
382
5.551760
TTCTAAGCTAACTTCTGCATTGC
57.448
39.130
0.46
0.46
37.33
3.56
401
423
2.151202
CAAACAGACGGGCATGTTAGT
58.849
47.619
0.00
0.00
38.66
2.24
402
424
2.151202
ACAAACAGACGGGCATGTTAG
58.849
47.619
0.00
0.00
38.66
2.34
403
425
2.264005
ACAAACAGACGGGCATGTTA
57.736
45.000
0.00
0.00
38.66
2.41
404
426
2.151202
CTACAAACAGACGGGCATGTT
58.849
47.619
0.00
0.00
41.28
2.71
471
498
9.948964
TCTTGTTTCTTCTGAATAAGATCATCA
57.051
29.630
0.00
0.00
35.48
3.07
478
505
9.178427
CTTTTGCTCTTGTTTCTTCTGAATAAG
57.822
33.333
0.00
0.00
32.65
1.73
593
3042
5.154932
AGCGTATACGATCTAATGTTCAGC
58.845
41.667
28.66
5.54
43.02
4.26
629
3078
7.639113
TTTGAAAAACAATGACTAGGTCACT
57.361
32.000
2.34
0.00
45.65
3.41
630
3079
8.871686
AATTTGAAAAACAATGACTAGGTCAC
57.128
30.769
2.34
0.00
45.65
3.67
633
3082
9.883142
TCAAAATTTGAAAAACAATGACTAGGT
57.117
25.926
5.87
0.00
38.36
3.08
689
3145
2.553086
ACAAAAGCTTGTGCATGGTTG
58.447
42.857
16.88
8.93
44.28
3.77
692
3148
3.922240
GTGATACAAAAGCTTGTGCATGG
59.078
43.478
16.88
0.00
45.53
3.66
771
3230
5.538849
TGTTCACATAGTACTCACCACAA
57.461
39.130
0.00
0.00
0.00
3.33
774
3233
6.605471
AAGATGTTCACATAGTACTCACCA
57.395
37.500
0.00
0.00
36.57
4.17
845
4230
9.284968
CTTCTACAACCGGAAATTATATCCAAT
57.715
33.333
9.46
0.00
36.74
3.16
871
4620
1.448540
CTGTCCCGATGTCACCAGC
60.449
63.158
0.00
0.00
0.00
4.85
912
4661
5.818336
TGTCTCGTCTAAGAATCCTGTCTAG
59.182
44.000
0.00
0.00
0.00
2.43
983
4738
2.032860
TAGGCCGGATCTGCAGCTTC
62.033
60.000
9.47
8.39
0.00
3.86
985
4740
0.542938
TATAGGCCGGATCTGCAGCT
60.543
55.000
9.47
0.00
0.00
4.24
996
4751
4.483311
GTTCGAGGAGTTTATATAGGCCG
58.517
47.826
0.00
0.00
0.00
6.13
997
4752
4.282703
TGGTTCGAGGAGTTTATATAGGCC
59.717
45.833
0.00
0.00
0.00
5.19
1033
4808
0.107945
GCTAGGTTGCCCTCTGTCTG
60.108
60.000
0.00
0.00
41.45
3.51
1034
4809
0.252467
AGCTAGGTTGCCCTCTGTCT
60.252
55.000
0.00
0.00
41.45
3.41
1039
4814
3.206964
GTTTATCAGCTAGGTTGCCCTC
58.793
50.000
0.00
0.00
41.45
4.30
1047
4830
3.386078
TCAGCTCCTGTTTATCAGCTAGG
59.614
47.826
0.00
0.00
42.38
3.02
1090
4904
1.734388
AAAACCACTGCGACCTTGGC
61.734
55.000
0.00
0.00
33.25
4.52
1311
5128
3.849951
CCGCCGGCATACCACTCT
61.850
66.667
28.98
0.00
34.57
3.24
1333
5150
1.675641
GGATCAACTTGCCGCACCT
60.676
57.895
0.00
0.00
0.00
4.00
1643
5470
2.167900
AGTAACGGCCCTGAGACATTAC
59.832
50.000
0.00
0.00
0.00
1.89
1881
5874
1.281925
ATGGTGGGTGGGACAGATCC
61.282
60.000
0.00
0.00
41.80
3.36
1884
5877
1.748732
TTTATGGTGGGTGGGACAGA
58.251
50.000
0.00
0.00
41.80
3.41
1886
5879
3.788708
TCATATTTATGGTGGGTGGGACA
59.211
43.478
0.00
0.00
34.50
4.02
1894
5887
8.945481
TTGCAAAATCTTCATATTTATGGTGG
57.055
30.769
0.00
0.00
34.50
4.61
1905
5898
9.661563
ACATGAACAATATTGCAAAATCTTCAT
57.338
25.926
15.48
16.11
29.57
2.57
1938
5931
6.969043
AGACACATGGATGATACCCTAAAAA
58.031
36.000
0.00
0.00
0.00
1.94
1939
5932
6.575244
AGACACATGGATGATACCCTAAAA
57.425
37.500
0.00
0.00
0.00
1.52
1940
5933
7.684317
TTAGACACATGGATGATACCCTAAA
57.316
36.000
0.00
0.00
0.00
1.85
1941
5934
7.684317
TTTAGACACATGGATGATACCCTAA
57.316
36.000
0.00
0.00
0.00
2.69
1942
5935
7.126573
TGTTTTAGACACATGGATGATACCCTA
59.873
37.037
0.00
0.00
32.00
3.53
1943
5936
6.069673
TGTTTTAGACACATGGATGATACCCT
60.070
38.462
0.00
0.00
32.00
4.34
1944
5937
6.119536
TGTTTTAGACACATGGATGATACCC
58.880
40.000
0.00
0.00
32.00
3.69
1945
5938
7.642669
CATGTTTTAGACACATGGATGATACC
58.357
38.462
0.00
0.00
45.34
2.73
1955
5948
6.899393
ACATTCCACATGTTTTAGACACAT
57.101
33.333
0.00
0.00
42.04
3.21
1956
5949
6.096141
ACAACATTCCACATGTTTTAGACACA
59.904
34.615
0.00
0.00
42.04
3.72
1957
5950
6.503524
ACAACATTCCACATGTTTTAGACAC
58.496
36.000
0.00
0.00
42.04
3.67
1958
5951
6.707440
ACAACATTCCACATGTTTTAGACA
57.293
33.333
0.00
0.00
39.94
3.41
1959
5952
7.803189
CACTACAACATTCCACATGTTTTAGAC
59.197
37.037
20.18
0.00
41.32
2.59
2031
6024
9.582431
CTTATCTTGCAGATCATTTTTCACAAT
57.418
29.630
0.00
0.00
36.20
2.71
2036
6029
9.286946
CAGAACTTATCTTGCAGATCATTTTTC
57.713
33.333
0.00
0.00
36.20
2.29
2042
6035
5.122869
GCAACAGAACTTATCTTGCAGATCA
59.877
40.000
0.00
0.00
38.46
2.92
2043
6036
5.122869
TGCAACAGAACTTATCTTGCAGATC
59.877
40.000
0.00
0.00
41.56
2.75
2044
6037
5.005740
TGCAACAGAACTTATCTTGCAGAT
58.994
37.500
0.00
4.45
41.56
2.90
2045
6038
4.388485
TGCAACAGAACTTATCTTGCAGA
58.612
39.130
0.00
0.00
41.56
4.26
2072
6065
9.209175
TGTAGCAAAAATTGTGTTGTAGTTTTT
57.791
25.926
0.00
0.00
33.63
1.94
2106
6101
5.241403
TGTAACAGAGGTCATGTTCCAAT
57.759
39.130
11.03
0.00
41.08
3.16
2107
6102
4.698201
TGTAACAGAGGTCATGTTCCAA
57.302
40.909
11.03
0.00
41.08
3.53
2110
6105
6.619801
AGTTTTGTAACAGAGGTCATGTTC
57.380
37.500
0.00
0.00
41.08
3.18
2134
9604
9.131791
ACATTTACTTGGAGTCTACAAACAAAT
57.868
29.630
0.00
4.99
0.00
2.32
2150
9621
9.810231
GTTGATTTGGCATTTTACATTTACTTG
57.190
29.630
0.00
0.00
0.00
3.16
2153
9624
8.546597
AGGTTGATTTGGCATTTTACATTTAC
57.453
30.769
0.00
0.00
0.00
2.01
2157
9628
5.484998
AGGAGGTTGATTTGGCATTTTACAT
59.515
36.000
0.00
0.00
0.00
2.29
2158
9629
4.837860
AGGAGGTTGATTTGGCATTTTACA
59.162
37.500
0.00
0.00
0.00
2.41
2164
9635
3.205056
TGGATAGGAGGTTGATTTGGCAT
59.795
43.478
0.00
0.00
0.00
4.40
2169
9640
8.288812
TGGAAATAATGGATAGGAGGTTGATTT
58.711
33.333
0.00
0.00
0.00
2.17
2177
9648
7.227512
GTGTTCAGTGGAAATAATGGATAGGAG
59.772
40.741
0.00
0.00
34.13
3.69
2183
9654
5.048083
GCTTGTGTTCAGTGGAAATAATGGA
60.048
40.000
0.00
0.00
34.13
3.41
2189
9660
4.341806
TCAATGCTTGTGTTCAGTGGAAAT
59.658
37.500
0.00
0.00
34.13
2.17
2191
9662
3.286353
TCAATGCTTGTGTTCAGTGGAA
58.714
40.909
0.00
0.00
0.00
3.53
2197
9668
2.229792
GTCCCTCAATGCTTGTGTTCA
58.770
47.619
0.00
0.00
0.00
3.18
2206
9677
1.576356
CTTCTAGCGTCCCTCAATGC
58.424
55.000
0.00
0.00
0.00
3.56
2225
9696
3.904234
GGACGAACAGTACAAAAATTCGC
59.096
43.478
13.41
8.60
44.53
4.70
2239
9710
1.144969
GACGATGCTTTGGACGAACA
58.855
50.000
0.00
0.00
0.00
3.18
2247
9718
1.926511
GCACCCTGGACGATGCTTTG
61.927
60.000
0.00
0.00
35.16
2.77
2255
9726
1.741770
GCAGTAAGCACCCTGGACG
60.742
63.158
0.00
0.00
44.79
4.79
2256
9727
4.303257
GCAGTAAGCACCCTGGAC
57.697
61.111
0.00
0.00
44.79
4.02
2272
9743
0.255890
TACAAAGAGGGGCAGATGGC
59.744
55.000
0.00
0.00
43.74
4.40
2273
9744
3.117738
AGAATACAAAGAGGGGCAGATGG
60.118
47.826
0.00
0.00
0.00
3.51
2274
9745
3.881688
CAGAATACAAAGAGGGGCAGATG
59.118
47.826
0.00
0.00
0.00
2.90
2275
9746
3.525199
ACAGAATACAAAGAGGGGCAGAT
59.475
43.478
0.00
0.00
0.00
2.90
2276
9747
2.912956
ACAGAATACAAAGAGGGGCAGA
59.087
45.455
0.00
0.00
0.00
4.26
2277
9748
3.356529
ACAGAATACAAAGAGGGGCAG
57.643
47.619
0.00
0.00
0.00
4.85
2278
9749
3.420893
CAACAGAATACAAAGAGGGGCA
58.579
45.455
0.00
0.00
0.00
5.36
2279
9750
2.755103
CCAACAGAATACAAAGAGGGGC
59.245
50.000
0.00
0.00
0.00
5.80
2280
9751
2.755103
GCCAACAGAATACAAAGAGGGG
59.245
50.000
0.00
0.00
0.00
4.79
2281
9752
3.191371
GTGCCAACAGAATACAAAGAGGG
59.809
47.826
0.00
0.00
0.00
4.30
2282
9753
3.191371
GGTGCCAACAGAATACAAAGAGG
59.809
47.826
0.00
0.00
0.00
3.69
2283
9754
3.820467
TGGTGCCAACAGAATACAAAGAG
59.180
43.478
0.00
0.00
0.00
2.85
2284
9755
3.826524
TGGTGCCAACAGAATACAAAGA
58.173
40.909
0.00
0.00
0.00
2.52
2285
9756
4.672542
CGATGGTGCCAACAGAATACAAAG
60.673
45.833
0.00
0.00
0.00
2.77
2286
9757
3.190327
CGATGGTGCCAACAGAATACAAA
59.810
43.478
0.00
0.00
0.00
2.83
2287
9758
2.746904
CGATGGTGCCAACAGAATACAA
59.253
45.455
0.00
0.00
0.00
2.41
2288
9759
2.027653
TCGATGGTGCCAACAGAATACA
60.028
45.455
0.00
0.00
0.00
2.29
2289
9760
2.627945
TCGATGGTGCCAACAGAATAC
58.372
47.619
0.00
0.00
0.00
1.89
2290
9761
3.205338
CATCGATGGTGCCAACAGAATA
58.795
45.455
17.96
0.00
0.00
1.75
2291
9762
2.019249
CATCGATGGTGCCAACAGAAT
58.981
47.619
17.96
0.00
0.00
2.40
2292
9763
1.452110
CATCGATGGTGCCAACAGAA
58.548
50.000
17.96
0.00
0.00
3.02
2306
9777
2.715749
ATTTCTGGATGTGGCATCGA
57.284
45.000
0.00
0.00
0.00
3.59
2307
9778
2.286595
CGAATTTCTGGATGTGGCATCG
60.287
50.000
0.00
0.00
0.00
3.84
2320
9791
5.006746
GGTACAGAAATCGATGCGAATTTCT
59.993
40.000
0.00
15.04
40.48
2.52
2323
9794
3.560068
GGGTACAGAAATCGATGCGAATT
59.440
43.478
0.00
0.00
39.99
2.17
2327
9798
1.593006
GTGGGTACAGAAATCGATGCG
59.407
52.381
0.00
0.00
0.00
4.73
2342
9814
7.213178
AGATGGATAAACTATCTTTGTGGGT
57.787
36.000
0.00
0.00
42.75
4.51
2363
9835
9.160496
CTCTATTTGCTCACACTTAAGAAAGAT
57.840
33.333
10.09
0.00
36.50
2.40
2382
9854
7.260603
GCAATTGGTATCTTGCAACTCTATTT
58.739
34.615
7.72
0.00
45.50
1.40
2392
9864
4.114794
GGTGAATGCAATTGGTATCTTGC
58.885
43.478
7.72
0.51
46.19
4.01
2443
9915
3.797039
TGGACATTTCGCTAGGAATCTG
58.203
45.455
0.00
0.00
33.85
2.90
2461
9933
4.705110
TTTTCAGGTTGAGTCTGATGGA
57.295
40.909
0.00
0.00
40.46
3.41
2464
9936
6.150140
GCTAACATTTTCAGGTTGAGTCTGAT
59.850
38.462
0.00
0.00
40.46
2.90
2494
9966
6.968263
TTGGGAATGTGTTAACTGAAATCA
57.032
33.333
7.22
0.00
0.00
2.57
2534
10006
1.097232
TTACTGCTGCATGTGCCATC
58.903
50.000
1.31
0.00
41.18
3.51
2545
10017
7.413438
GGTGTGTGATCTTCTATTTTACTGCTG
60.413
40.741
0.00
0.00
0.00
4.41
2549
10021
9.256228
TCTAGGTGTGTGATCTTCTATTTTACT
57.744
33.333
0.00
0.00
0.00
2.24
2558
10030
6.701145
TGATACTCTAGGTGTGTGATCTTC
57.299
41.667
0.00
0.00
0.00
2.87
2603
10075
2.224695
TGAGGCTGATGCAGGGAATATG
60.225
50.000
0.00
0.00
41.91
1.78
2624
10096
2.033550
CCTCGAAGCAGTAGATTACGCT
59.966
50.000
0.00
0.00
39.13
5.07
2625
10097
2.386249
CCTCGAAGCAGTAGATTACGC
58.614
52.381
0.00
0.00
0.00
4.42
2657
10129
6.037940
CGAAGAGGTGATGTCATCATTTGAAT
59.962
38.462
18.32
4.56
42.04
2.57
2688
10160
0.745845
CTGAACCCCGATGCTCCAAG
60.746
60.000
0.00
0.00
0.00
3.61
2689
10161
1.299648
CTGAACCCCGATGCTCCAA
59.700
57.895
0.00
0.00
0.00
3.53
2690
10162
2.989639
CTGAACCCCGATGCTCCA
59.010
61.111
0.00
0.00
0.00
3.86
2691
10163
2.514824
GCTGAACCCCGATGCTCC
60.515
66.667
0.00
0.00
0.00
4.70
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.