Multiple sequence alignment - TraesCS7B01G447800
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
TraesCS7B01G447800
chr7B
100.000
2285
0
0
1
2285
710959532
710957248
0.000000e+00
4220
1
TraesCS7B01G447800
chr7B
95.253
969
36
6
649
1608
211695019
211695986
0.000000e+00
1526
2
TraesCS7B01G447800
chr7B
94.500
200
7
3
1416
1611
592642691
592642492
2.850000e-79
305
3
TraesCS7B01G447800
chr7A
95.846
963
33
5
652
1608
6752330
6751369
0.000000e+00
1550
4
TraesCS7B01G447800
chr7A
97.393
652
17
0
1
652
6754185
6753534
0.000000e+00
1110
5
TraesCS7B01G447800
chr7A
78.435
524
92
11
1695
2206
562004461
562004975
2.830000e-84
322
6
TraesCS7B01G447800
chr7A
73.473
524
99
21
1695
2206
679058483
679057988
6.530000e-36
161
7
TraesCS7B01G447800
chr2B
95.657
967
31
8
652
1608
798711419
798710454
0.000000e+00
1543
8
TraesCS7B01G447800
chr2B
94.792
960
43
4
649
1603
607300851
607301808
0.000000e+00
1489
9
TraesCS7B01G447800
chr2B
97.853
652
14
0
1
652
798713272
798712621
0.000000e+00
1127
10
TraesCS7B01G447800
chr2B
97.546
652
16
0
1
652
607250966
607251617
0.000000e+00
1116
11
TraesCS7B01G447800
chr2B
81.739
230
36
3
1842
2071
198274621
198274844
1.080000e-43
187
12
TraesCS7B01G447800
chr1B
95.322
962
39
4
652
1608
388170228
388169268
0.000000e+00
1522
13
TraesCS7B01G447800
chr1B
95.135
966
40
5
649
1608
394374970
394375934
0.000000e+00
1517
14
TraesCS7B01G447800
chr1B
97.853
652
14
0
1
652
388172080
388171429
0.000000e+00
1127
15
TraesCS7B01G447800
chr1B
97.090
653
18
1
1
652
656529243
656529895
0.000000e+00
1099
16
TraesCS7B01G447800
chr1B
96.779
652
21
0
1
652
394373120
394373771
0.000000e+00
1088
17
TraesCS7B01G447800
chr1B
83.598
189
25
4
2015
2202
493648173
493648356
3.020000e-39
172
18
TraesCS7B01G447800
chr1B
90.090
111
5
5
1504
1609
338604650
338604759
3.060000e-29
139
19
TraesCS7B01G447800
chr5B
95.150
969
38
6
649
1609
123020816
123021783
0.000000e+00
1520
20
TraesCS7B01G447800
chr5B
97.393
652
17
0
1
652
123018966
123019617
0.000000e+00
1110
21
TraesCS7B01G447800
chr5B
82.553
235
35
6
1842
2071
489339157
489338924
3.850000e-48
202
22
TraesCS7B01G447800
chr5B
74.463
419
76
13
1778
2184
2549039
2549438
3.930000e-33
152
23
TraesCS7B01G447800
chr6B
94.928
966
43
4
649
1609
717064740
717065704
0.000000e+00
1507
24
TraesCS7B01G447800
chr6B
96.933
652
20
0
1
652
717062892
717063543
0.000000e+00
1094
25
TraesCS7B01G447800
chr1A
94.819
965
42
5
649
1608
579648178
579649139
0.000000e+00
1498
26
TraesCS7B01G447800
chr1A
79.756
410
68
8
1689
2089
163377216
163377619
1.340000e-72
283
27
TraesCS7B01G447800
chr4B
96.933
652
20
0
1
652
630346093
630345442
0.000000e+00
1094
28
TraesCS7B01G447800
chr4A
90.339
383
24
6
1228
1608
570903318
570903689
2.030000e-140
508
29
TraesCS7B01G447800
chr4A
82.716
162
20
5
1445
1600
647120047
647120206
1.100000e-28
137
30
TraesCS7B01G447800
chr4A
82.716
162
20
6
1445
1604
734886567
734886412
1.100000e-28
137
31
TraesCS7B01G447800
chr3B
79.497
517
86
13
1698
2203
700232334
700231827
1.300000e-92
350
32
TraesCS7B01G447800
chr3B
75.442
452
85
15
1631
2071
27991946
27992382
1.790000e-46
196
33
TraesCS7B01G447800
chr2D
78.320
512
81
13
1696
2196
102304412
102304904
1.030000e-78
303
34
TraesCS7B01G447800
chr2A
78.082
511
79
10
1695
2196
475869214
475868728
2.220000e-75
292
35
TraesCS7B01G447800
chr3A
77.087
515
75
23
1646
2144
653919300
653918813
8.100000e-65
257
36
TraesCS7B01G447800
chr5D
78.147
421
68
10
1794
2203
472371823
472371416
1.750000e-61
246
37
TraesCS7B01G447800
chr1D
83.043
230
35
4
1842
2067
8462070
8461841
2.980000e-49
206
38
TraesCS7B01G447800
chr1D
76.289
388
70
12
1753
2135
341181080
341180710
1.080000e-43
187
39
TraesCS7B01G447800
chr4D
84.343
198
27
3
2003
2199
7470292
7470098
8.330000e-45
191
40
TraesCS7B01G447800
chr7D
85.294
170
12
9
1445
1608
469633047
469632885
1.820000e-36
163
41
TraesCS7B01G447800
chr5A
79.679
187
8
16
1445
1608
604749596
604749775
8.630000e-20
108
42
TraesCS7B01G447800
chr5A
78.857
175
18
11
1448
1604
9724300
9724127
1.440000e-17
100
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
TraesCS7B01G447800
chr7B
710957248
710959532
2284
True
4220.0
4220
100.0000
1
2285
1
chr7B.!!$R2
2284
1
TraesCS7B01G447800
chr7B
211695019
211695986
967
False
1526.0
1526
95.2530
649
1608
1
chr7B.!!$F1
959
2
TraesCS7B01G447800
chr7A
6751369
6754185
2816
True
1330.0
1550
96.6195
1
1608
2
chr7A.!!$R2
1607
3
TraesCS7B01G447800
chr7A
562004461
562004975
514
False
322.0
322
78.4350
1695
2206
1
chr7A.!!$F1
511
4
TraesCS7B01G447800
chr2B
607300851
607301808
957
False
1489.0
1489
94.7920
649
1603
1
chr2B.!!$F3
954
5
TraesCS7B01G447800
chr2B
798710454
798713272
2818
True
1335.0
1543
96.7550
1
1608
2
chr2B.!!$R1
1607
6
TraesCS7B01G447800
chr2B
607250966
607251617
651
False
1116.0
1116
97.5460
1
652
1
chr2B.!!$F2
651
7
TraesCS7B01G447800
chr1B
388169268
388172080
2812
True
1324.5
1522
96.5875
1
1608
2
chr1B.!!$R1
1607
8
TraesCS7B01G447800
chr1B
394373120
394375934
2814
False
1302.5
1517
95.9570
1
1608
2
chr1B.!!$F4
1607
9
TraesCS7B01G447800
chr1B
656529243
656529895
652
False
1099.0
1099
97.0900
1
652
1
chr1B.!!$F3
651
10
TraesCS7B01G447800
chr5B
123018966
123021783
2817
False
1315.0
1520
96.2715
1
1609
2
chr5B.!!$F2
1608
11
TraesCS7B01G447800
chr6B
717062892
717065704
2812
False
1300.5
1507
95.9305
1
1609
2
chr6B.!!$F1
1608
12
TraesCS7B01G447800
chr1A
579648178
579649139
961
False
1498.0
1498
94.8190
649
1608
1
chr1A.!!$F2
959
13
TraesCS7B01G447800
chr4B
630345442
630346093
651
True
1094.0
1094
96.9330
1
652
1
chr4B.!!$R1
651
14
TraesCS7B01G447800
chr3B
700231827
700232334
507
True
350.0
350
79.4970
1698
2203
1
chr3B.!!$R1
505
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
673
3079
1.301423
TCCTTCAAAACGTCAACGGG
58.699
50.0
7.53
0.0
44.95
5.28
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2244
4676
0.103026
TGCTATACTGCTGCAGACCG
59.897
55.0
34.28
19.27
35.18
4.79
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
142
144
7.882271
AGAAACTACTTCTGAGCATGAAAATCT
59.118
33.333
0.00
0.00
43.09
2.40
170
172
4.299586
TGAGGTGAATAAAGATGGTGCA
57.700
40.909
0.00
0.00
0.00
4.57
445
447
6.959639
AAGTAATGGTGAGTTTGTTGACAT
57.040
33.333
0.00
0.00
0.00
3.06
527
529
5.186996
TCAAATCAAAACTGAGCAAGTCC
57.813
39.130
0.00
0.00
38.56
3.85
573
575
1.498865
CTGGAAGCGTTTGAGTGCGT
61.499
55.000
0.00
0.00
35.87
5.24
673
3079
1.301423
TCCTTCAAAACGTCAACGGG
58.699
50.000
7.53
0.00
44.95
5.28
698
3104
5.831702
AGAAAGAGGCATCATGATGAAAC
57.168
39.130
34.65
23.43
41.20
2.78
792
3201
5.300034
TGACAATGCAGTTCTTTCATTGACT
59.700
36.000
20.75
8.32
45.87
3.41
797
3206
5.610398
TGCAGTTCTTTCATTGACTAGTCA
58.390
37.500
21.74
21.74
37.91
3.41
805
3214
8.908786
TCTTTCATTGACTAGTCACTTTGATT
57.091
30.769
25.13
2.07
39.66
2.57
881
3291
2.846206
AGTCCCTGGATGATAGCAAACA
59.154
45.455
0.00
0.00
0.00
2.83
905
3315
3.058293
CAGGAATGTTGCGCTACTTTTGA
60.058
43.478
22.01
2.48
0.00
2.69
966
3376
7.430992
TCTTCATGATTTTGTCTCAGAGTTG
57.569
36.000
0.00
0.00
0.00
3.16
1125
3535
6.147000
CCTCAGCTGAAAGAAGTTTCTCTAAC
59.853
42.308
18.85
0.00
42.39
2.34
1191
3601
3.607490
AGATTGAATGGCCTGGCTATT
57.393
42.857
27.55
27.55
42.17
1.73
1314
3725
9.477484
ACTGAAGTATTATTGTTATCGATGGAC
57.523
33.333
8.54
7.46
0.00
4.02
1600
4020
2.742372
CCTCCGAAACACAGGGCG
60.742
66.667
0.00
0.00
0.00
6.13
1623
4043
3.152865
TGGAGCGCCAGTACCAAA
58.847
55.556
4.49
0.00
39.92
3.28
1624
4044
1.682849
TGGAGCGCCAGTACCAAAT
59.317
52.632
4.49
0.00
39.92
2.32
1625
4045
0.037590
TGGAGCGCCAGTACCAAATT
59.962
50.000
4.49
0.00
39.92
1.82
1626
4046
0.451783
GGAGCGCCAGTACCAAATTG
59.548
55.000
2.29
0.00
0.00
2.32
1627
4047
1.448985
GAGCGCCAGTACCAAATTGA
58.551
50.000
2.29
0.00
0.00
2.57
1628
4048
1.398390
GAGCGCCAGTACCAAATTGAG
59.602
52.381
2.29
0.00
0.00
3.02
1629
4049
0.179163
GCGCCAGTACCAAATTGAGC
60.179
55.000
0.00
0.00
0.00
4.26
1630
4050
1.164411
CGCCAGTACCAAATTGAGCA
58.836
50.000
0.00
0.00
0.00
4.26
1631
4051
1.131126
CGCCAGTACCAAATTGAGCAG
59.869
52.381
0.00
0.00
0.00
4.24
1632
4052
1.474077
GCCAGTACCAAATTGAGCAGG
59.526
52.381
0.00
0.00
0.00
4.85
1633
4053
2.879756
GCCAGTACCAAATTGAGCAGGA
60.880
50.000
0.00
0.00
0.00
3.86
1634
4054
3.012518
CCAGTACCAAATTGAGCAGGAG
58.987
50.000
0.00
0.00
0.00
3.69
1635
4055
3.307691
CCAGTACCAAATTGAGCAGGAGA
60.308
47.826
0.00
0.00
0.00
3.71
1636
4056
4.521146
CAGTACCAAATTGAGCAGGAGAT
58.479
43.478
0.00
0.00
0.00
2.75
1637
4057
4.574013
CAGTACCAAATTGAGCAGGAGATC
59.426
45.833
0.00
0.00
0.00
2.75
1638
4058
3.010200
ACCAAATTGAGCAGGAGATCC
57.990
47.619
0.00
0.00
0.00
3.36
1639
4059
1.945394
CCAAATTGAGCAGGAGATCCG
59.055
52.381
0.00
0.00
42.08
4.18
1640
4060
1.945394
CAAATTGAGCAGGAGATCCGG
59.055
52.381
0.00
0.00
42.08
5.14
1641
4061
0.471617
AATTGAGCAGGAGATCCGGG
59.528
55.000
0.00
0.00
42.08
5.73
1642
4062
2.049627
ATTGAGCAGGAGATCCGGGC
62.050
60.000
0.00
9.67
42.08
6.13
1643
4063
4.292178
GAGCAGGAGATCCGGGCG
62.292
72.222
0.00
0.00
43.05
6.13
1644
4064
4.841617
AGCAGGAGATCCGGGCGA
62.842
66.667
0.00
0.00
43.05
5.54
1645
4065
4.292178
GCAGGAGATCCGGGCGAG
62.292
72.222
0.00
0.00
42.08
5.03
1646
4066
3.610669
CAGGAGATCCGGGCGAGG
61.611
72.222
0.00
0.00
42.08
4.63
1647
4067
4.144727
AGGAGATCCGGGCGAGGT
62.145
66.667
0.00
0.00
42.08
3.85
1648
4068
3.917760
GGAGATCCGGGCGAGGTG
61.918
72.222
0.00
0.00
0.00
4.00
1649
4069
3.148279
GAGATCCGGGCGAGGTGT
61.148
66.667
0.00
0.00
0.00
4.16
1650
4070
3.432051
GAGATCCGGGCGAGGTGTG
62.432
68.421
0.00
0.00
0.00
3.82
1671
4091
2.887568
CCTGCATCGCTGTCGGTC
60.888
66.667
0.00
0.00
36.13
4.79
1672
4092
2.182791
CTGCATCGCTGTCGGTCT
59.817
61.111
0.00
0.00
36.13
3.85
1673
4093
2.125952
TGCATCGCTGTCGGTCTG
60.126
61.111
0.00
0.00
36.13
3.51
1674
4094
3.558411
GCATCGCTGTCGGTCTGC
61.558
66.667
0.00
0.00
37.59
4.26
1679
4099
4.400109
GCTGTCGGTCTGCGTCGA
62.400
66.667
0.00
0.00
0.00
4.20
1680
4100
2.202362
CTGTCGGTCTGCGTCGAG
60.202
66.667
0.00
0.00
36.00
4.04
1681
4101
2.667199
TGTCGGTCTGCGTCGAGA
60.667
61.111
0.00
0.00
36.00
4.04
1682
4102
2.202324
GTCGGTCTGCGTCGAGAC
60.202
66.667
13.26
13.26
41.55
3.36
1683
4103
2.358369
TCGGTCTGCGTCGAGACT
60.358
61.111
18.10
0.00
41.90
3.24
1684
4104
1.964891
TCGGTCTGCGTCGAGACTT
60.965
57.895
18.10
0.00
41.90
3.01
1685
4105
1.797933
CGGTCTGCGTCGAGACTTG
60.798
63.158
18.10
11.12
41.90
3.16
1686
4106
1.286260
GGTCTGCGTCGAGACTTGT
59.714
57.895
18.10
0.00
41.90
3.16
1687
4107
0.729816
GGTCTGCGTCGAGACTTGTC
60.730
60.000
18.10
0.00
41.90
3.18
1688
4108
1.060726
GTCTGCGTCGAGACTTGTCG
61.061
60.000
13.97
5.13
39.52
4.35
1689
4109
1.797933
CTGCGTCGAGACTTGTCGG
60.798
63.158
10.69
0.00
40.49
4.79
1690
4110
2.183858
CTGCGTCGAGACTTGTCGGA
62.184
60.000
10.69
7.31
40.49
4.55
1691
4111
1.512310
GCGTCGAGACTTGTCGGAG
60.512
63.158
10.69
0.00
40.49
4.63
1692
4112
1.512310
CGTCGAGACTTGTCGGAGC
60.512
63.158
1.81
0.00
40.49
4.70
1693
4113
1.153997
GTCGAGACTTGTCGGAGCC
60.154
63.158
0.00
0.00
40.49
4.70
1711
4131
1.671901
CCGAGGAGGAAGAGGAGCAC
61.672
65.000
0.00
0.00
45.00
4.40
1714
4134
0.178891
AGGAGGAAGAGGAGCACCAA
60.179
55.000
2.07
0.00
38.94
3.67
1738
4158
3.871623
TCCGAGGGAGATGGCTAAT
57.128
52.632
0.00
0.00
0.00
1.73
1751
4171
2.832838
TGGCTAATCCAGAGAAGGACA
58.167
47.619
0.00
0.00
41.30
4.02
1755
4175
2.797177
AATCCAGAGAAGGACAAGGC
57.203
50.000
0.00
0.00
41.30
4.35
1776
4196
4.847444
GCAGCCGGAAGAGGAGCC
62.847
72.222
5.05
0.00
0.00
4.70
1814
4234
0.038166
GGGCTTCAACATGGAGGACA
59.962
55.000
0.00
0.00
0.00
4.02
1825
4245
4.131088
GAGGACACGGAGGCGGTC
62.131
72.222
0.00
0.00
0.00
4.79
1873
4302
0.625683
AGGCCATCCTGGAGTCCATT
60.626
55.000
13.56
0.00
40.96
3.16
1875
4304
0.533755
GCCATCCTGGAGTCCATTCG
60.534
60.000
13.56
0.47
40.96
3.34
1892
4321
0.398522
TCGGGATGAGGCCTATGTGT
60.399
55.000
4.42
0.00
0.00
3.72
1957
4386
3.285306
GGTTTTCGCCGAATTCGAC
57.715
52.632
28.76
17.08
43.02
4.20
1958
4387
0.513820
GGTTTTCGCCGAATTCGACA
59.486
50.000
28.76
9.19
43.02
4.35
1999
4429
2.284995
GGGGAGCAGTGGAGGAGT
60.285
66.667
0.00
0.00
0.00
3.85
2058
4488
2.690497
CACGGTGATAGTGGACATCTCT
59.310
50.000
0.74
0.00
36.06
3.10
2079
4510
5.698104
TCTGACGAGGATTAGGGTGTATAA
58.302
41.667
0.00
0.00
0.00
0.98
2084
4515
7.230108
TGACGAGGATTAGGGTGTATAAGTTAG
59.770
40.741
0.00
0.00
0.00
2.34
2094
4525
8.834004
AGGGTGTATAAGTTAGTTGATCTACA
57.166
34.615
9.96
0.00
0.00
2.74
2113
4545
7.634671
TCTACATAGTACGTGGATTTTCTCA
57.365
36.000
0.00
0.00
0.00
3.27
2146
4578
7.029563
GCTTTTGTATGGATCTAAGGTTTGTG
58.970
38.462
0.00
0.00
0.00
3.33
2164
4596
6.042781
GGTTTGTGGTATGAGGTATCCAGATA
59.957
42.308
0.00
0.00
0.00
1.98
2184
4616
5.825151
AGATACAGAGGAGCAAATTTAAGGC
59.175
40.000
0.00
0.00
0.00
4.35
2185
4617
3.766545
ACAGAGGAGCAAATTTAAGGCA
58.233
40.909
2.29
0.00
0.00
4.75
2206
4638
3.499737
CCGGTCATTGTCCGCAGC
61.500
66.667
15.60
0.00
45.71
5.25
2207
4639
3.499737
CGGTCATTGTCCGCAGCC
61.500
66.667
9.33
0.00
41.48
4.85
2208
4640
2.359850
GGTCATTGTCCGCAGCCA
60.360
61.111
0.00
0.00
0.00
4.75
2209
4641
1.971167
GGTCATTGTCCGCAGCCAA
60.971
57.895
0.00
0.00
0.00
4.52
2210
4642
1.523154
GGTCATTGTCCGCAGCCAAA
61.523
55.000
0.00
0.00
0.00
3.28
2211
4643
0.387239
GTCATTGTCCGCAGCCAAAC
60.387
55.000
0.00
0.00
0.00
2.93
2212
4644
1.442520
CATTGTCCGCAGCCAAACG
60.443
57.895
0.00
0.00
0.00
3.60
2219
4651
2.746277
GCAGCCAAACGGACGGAT
60.746
61.111
0.00
0.00
0.00
4.18
2220
4652
3.039202
GCAGCCAAACGGACGGATG
62.039
63.158
0.00
0.69
41.70
3.51
2221
4653
2.746277
AGCCAAACGGACGGATGC
60.746
61.111
0.00
0.00
0.00
3.91
2222
4654
2.746277
GCCAAACGGACGGATGCT
60.746
61.111
0.00
0.00
0.00
3.79
2223
4655
1.448893
GCCAAACGGACGGATGCTA
60.449
57.895
0.00
0.00
0.00
3.49
2224
4656
1.702491
GCCAAACGGACGGATGCTAC
61.702
60.000
0.00
0.00
0.00
3.58
2225
4657
1.418342
CCAAACGGACGGATGCTACG
61.418
60.000
0.00
0.00
37.36
3.51
2226
4658
1.153706
AAACGGACGGATGCTACGG
60.154
57.895
0.00
0.00
35.23
4.02
2227
4659
1.880819
AAACGGACGGATGCTACGGT
61.881
55.000
0.00
0.00
35.23
4.83
2228
4660
1.031571
AACGGACGGATGCTACGGTA
61.032
55.000
0.00
0.00
35.23
4.02
2229
4661
1.009222
CGGACGGATGCTACGGTAC
60.009
63.158
0.00
0.00
35.23
3.34
2243
4675
4.487412
GTACGGTGGCGACGGGAG
62.487
72.222
10.98
0.00
35.23
4.30
2261
4693
2.892305
GCGGTCTGCAGCAGTATAG
58.108
57.895
22.10
12.73
45.45
1.31
2262
4694
1.218230
GCGGTCTGCAGCAGTATAGC
61.218
60.000
22.10
17.97
45.45
2.97
2263
4695
0.103026
CGGTCTGCAGCAGTATAGCA
59.897
55.000
22.10
0.00
36.85
3.49
2264
4696
1.576356
GGTCTGCAGCAGTATAGCAC
58.424
55.000
22.10
11.35
36.85
4.40
2265
4697
1.137872
GGTCTGCAGCAGTATAGCACT
59.862
52.381
22.10
0.00
38.32
4.40
2266
4698
2.468831
GTCTGCAGCAGTATAGCACTC
58.531
52.381
22.10
0.18
34.26
3.51
2267
4699
1.410517
TCTGCAGCAGTATAGCACTCC
59.589
52.381
22.10
0.00
34.26
3.85
2268
4700
1.411977
CTGCAGCAGTATAGCACTCCT
59.588
52.381
14.90
0.00
34.26
3.69
2269
4701
1.833630
TGCAGCAGTATAGCACTCCTT
59.166
47.619
0.00
0.00
34.26
3.36
2270
4702
2.208431
GCAGCAGTATAGCACTCCTTG
58.792
52.381
0.00
0.00
34.26
3.61
2271
4703
2.159043
GCAGCAGTATAGCACTCCTTGA
60.159
50.000
0.00
0.00
34.26
3.02
2272
4704
3.679917
GCAGCAGTATAGCACTCCTTGAA
60.680
47.826
0.00
0.00
34.26
2.69
2273
4705
4.507710
CAGCAGTATAGCACTCCTTGAAA
58.492
43.478
0.00
0.00
34.26
2.69
2274
4706
4.937620
CAGCAGTATAGCACTCCTTGAAAA
59.062
41.667
0.00
0.00
34.26
2.29
2275
4707
5.064452
CAGCAGTATAGCACTCCTTGAAAAG
59.936
44.000
0.00
0.00
38.62
2.27
2276
4708
5.046304
AGCAGTATAGCACTCCTTGAAAAGA
60.046
40.000
0.00
0.00
40.58
2.52
2277
4709
5.643777
GCAGTATAGCACTCCTTGAAAAGAA
59.356
40.000
0.00
0.00
40.58
2.52
2278
4710
6.183360
GCAGTATAGCACTCCTTGAAAAGAAG
60.183
42.308
0.00
0.00
40.58
2.85
2279
4711
6.876257
CAGTATAGCACTCCTTGAAAAGAAGT
59.124
38.462
0.00
0.00
40.58
3.01
2280
4712
7.064016
CAGTATAGCACTCCTTGAAAAGAAGTC
59.936
40.741
0.00
0.00
40.58
3.01
2281
4713
7.038658
AGTATAGCACTCCTTGAAAAGAAGTCT
60.039
37.037
0.00
0.00
45.77
3.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
142
144
7.770433
CACCATCTTTATTCACCTCAACATCTA
59.230
37.037
0.00
0.00
0.00
1.98
159
161
0.963962
CCTGTGCTTGCACCATCTTT
59.036
50.000
21.01
0.00
0.00
2.52
170
172
2.603075
TTATTTGCTCCCCTGTGCTT
57.397
45.000
0.00
0.00
32.27
3.91
527
529
1.911057
ATCCATCAGATGCCAGCATG
58.089
50.000
10.41
0.00
36.70
4.06
573
575
5.930569
CACTGTTCTCATGATCTTTGAGACA
59.069
40.000
21.31
19.66
46.92
3.41
673
3079
6.446781
TTCATCATGATGCCTCTTTCTTTC
57.553
37.500
27.68
0.00
38.65
2.62
698
3104
9.865321
ACAATTGTATTTCTTCTTGATCATTGG
57.135
29.630
9.97
0.00
0.00
3.16
805
3214
9.936759
AAACACCTTTTCAAATTTCTTCAACTA
57.063
25.926
0.00
0.00
0.00
2.24
857
3267
1.688735
TGCTATCATCCAGGGACTTCG
59.311
52.381
0.00
0.00
34.60
3.79
865
3275
4.264253
TCCTGTTGTTTGCTATCATCCAG
58.736
43.478
0.00
0.00
0.00
3.86
881
3291
2.185004
AGTAGCGCAACATTCCTGTT
57.815
45.000
11.47
0.00
46.54
3.16
966
3376
3.796717
GCAAAGTTACCTGCAACACTTTC
59.203
43.478
8.51
3.23
37.36
2.62
1191
3601
5.045012
AGATATCCTTCTCAATGCAGCAA
57.955
39.130
0.00
0.00
0.00
3.91
1305
3716
5.067936
ACGAAATTAGACTGAGTCCATCGAT
59.932
40.000
21.26
0.00
32.18
3.59
1398
3809
9.840427
CAATAATAACCAAATTCGAACTGACTT
57.160
29.630
0.00
0.00
0.00
3.01
1609
4029
1.453155
CTCAATTTGGTACTGGCGCT
58.547
50.000
7.64
0.00
0.00
5.92
1610
4030
0.179163
GCTCAATTTGGTACTGGCGC
60.179
55.000
0.00
0.00
0.00
6.53
1611
4031
1.131126
CTGCTCAATTTGGTACTGGCG
59.869
52.381
0.00
0.00
0.00
5.69
1612
4032
1.474077
CCTGCTCAATTTGGTACTGGC
59.526
52.381
0.00
0.00
0.00
4.85
1613
4033
3.012518
CTCCTGCTCAATTTGGTACTGG
58.987
50.000
0.00
1.19
0.00
4.00
1614
4034
3.942829
TCTCCTGCTCAATTTGGTACTG
58.057
45.455
0.00
0.00
0.00
2.74
1615
4035
4.384647
GGATCTCCTGCTCAATTTGGTACT
60.385
45.833
0.00
0.00
0.00
2.73
1616
4036
3.879892
GGATCTCCTGCTCAATTTGGTAC
59.120
47.826
0.00
0.00
0.00
3.34
1617
4037
3.432186
CGGATCTCCTGCTCAATTTGGTA
60.432
47.826
0.00
0.00
0.00
3.25
1618
4038
2.681976
CGGATCTCCTGCTCAATTTGGT
60.682
50.000
0.00
0.00
0.00
3.67
1619
4039
1.945394
CGGATCTCCTGCTCAATTTGG
59.055
52.381
0.00
0.00
0.00
3.28
1620
4040
1.945394
CCGGATCTCCTGCTCAATTTG
59.055
52.381
0.00
0.00
0.00
2.32
1621
4041
1.133976
CCCGGATCTCCTGCTCAATTT
60.134
52.381
0.73
0.00
0.00
1.82
1622
4042
0.471617
CCCGGATCTCCTGCTCAATT
59.528
55.000
0.73
0.00
0.00
2.32
1623
4043
2.049627
GCCCGGATCTCCTGCTCAAT
62.050
60.000
0.73
0.00
0.00
2.57
1624
4044
2.735772
GCCCGGATCTCCTGCTCAA
61.736
63.158
0.73
0.00
0.00
3.02
1625
4045
3.157252
GCCCGGATCTCCTGCTCA
61.157
66.667
0.73
0.00
0.00
4.26
1626
4046
4.292178
CGCCCGGATCTCCTGCTC
62.292
72.222
0.73
0.00
31.70
4.26
1627
4047
4.841617
TCGCCCGGATCTCCTGCT
62.842
66.667
0.73
0.00
31.70
4.24
1628
4048
4.292178
CTCGCCCGGATCTCCTGC
62.292
72.222
0.73
0.00
0.00
4.85
1629
4049
3.610669
CCTCGCCCGGATCTCCTG
61.611
72.222
0.73
0.00
0.00
3.86
1630
4050
4.144727
ACCTCGCCCGGATCTCCT
62.145
66.667
0.73
0.00
0.00
3.69
1631
4051
3.917760
CACCTCGCCCGGATCTCC
61.918
72.222
0.73
0.00
0.00
3.71
1632
4052
3.148279
ACACCTCGCCCGGATCTC
61.148
66.667
0.73
0.00
0.00
2.75
1633
4053
3.461773
CACACCTCGCCCGGATCT
61.462
66.667
0.73
0.00
0.00
2.75
1654
4074
2.887568
GACCGACAGCGATGCAGG
60.888
66.667
12.61
12.61
40.82
4.85
1655
4075
2.163390
CAGACCGACAGCGATGCAG
61.163
63.158
0.00
0.00
40.82
4.41
1656
4076
2.125952
CAGACCGACAGCGATGCA
60.126
61.111
0.00
0.00
40.82
3.96
1657
4077
3.558411
GCAGACCGACAGCGATGC
61.558
66.667
0.00
0.00
40.82
3.91
1662
4082
4.400109
TCGACGCAGACCGACAGC
62.400
66.667
0.00
0.00
41.02
4.40
1663
4083
2.202362
CTCGACGCAGACCGACAG
60.202
66.667
0.00
0.00
41.02
3.51
1664
4084
2.667199
TCTCGACGCAGACCGACA
60.667
61.111
0.00
0.00
41.02
4.35
1665
4085
2.185103
AAGTCTCGACGCAGACCGAC
62.185
60.000
17.92
6.52
43.53
4.79
1666
4086
1.964891
AAGTCTCGACGCAGACCGA
60.965
57.895
17.92
0.00
43.53
4.69
1667
4087
1.797933
CAAGTCTCGACGCAGACCG
60.798
63.158
17.92
10.06
43.53
4.79
1668
4088
0.729816
GACAAGTCTCGACGCAGACC
60.730
60.000
17.92
5.37
43.53
3.85
1669
4089
1.060726
CGACAAGTCTCGACGCAGAC
61.061
60.000
15.33
15.33
42.91
3.51
1670
4090
1.206831
CGACAAGTCTCGACGCAGA
59.793
57.895
0.00
0.00
35.58
4.26
1671
4091
1.797933
CCGACAAGTCTCGACGCAG
60.798
63.158
0.00
0.00
35.58
5.18
1672
4092
2.183858
CTCCGACAAGTCTCGACGCA
62.184
60.000
0.00
0.00
35.58
5.24
1673
4093
1.512310
CTCCGACAAGTCTCGACGC
60.512
63.158
0.00
0.00
35.58
5.19
1674
4094
1.512310
GCTCCGACAAGTCTCGACG
60.512
63.158
0.00
0.00
35.58
5.12
1675
4095
1.153997
GGCTCCGACAAGTCTCGAC
60.154
63.158
0.00
0.00
35.58
4.20
1676
4096
2.687805
CGGCTCCGACAAGTCTCGA
61.688
63.158
1.35
0.00
42.83
4.04
1677
4097
2.202492
CGGCTCCGACAAGTCTCG
60.202
66.667
1.35
0.00
42.83
4.04
1678
4098
1.137825
CTCGGCTCCGACAAGTCTC
59.862
63.158
6.95
0.00
44.01
3.36
1679
4099
2.344203
CCTCGGCTCCGACAAGTCT
61.344
63.158
6.95
0.00
44.01
3.24
1680
4100
2.182030
CCTCGGCTCCGACAAGTC
59.818
66.667
6.95
0.00
44.01
3.01
1681
4101
2.282958
TCCTCGGCTCCGACAAGT
60.283
61.111
6.95
0.00
44.01
3.16
1682
4102
2.492090
CTCCTCGGCTCCGACAAG
59.508
66.667
6.95
4.10
44.01
3.16
1683
4103
3.068691
CCTCCTCGGCTCCGACAA
61.069
66.667
6.95
0.00
44.01
3.18
1684
4104
3.578968
TTCCTCCTCGGCTCCGACA
62.579
63.158
6.95
0.00
44.01
4.35
1685
4105
2.754658
TTCCTCCTCGGCTCCGAC
60.755
66.667
6.95
0.00
44.01
4.79
1686
4106
2.440430
CTTCCTCCTCGGCTCCGA
60.440
66.667
10.84
10.84
46.87
4.55
1687
4107
2.440430
TCTTCCTCCTCGGCTCCG
60.440
66.667
1.14
1.14
41.35
4.63
1688
4108
2.131067
CCTCTTCCTCCTCGGCTCC
61.131
68.421
0.00
0.00
0.00
4.70
1689
4109
1.076632
TCCTCTTCCTCCTCGGCTC
60.077
63.158
0.00
0.00
0.00
4.70
1690
4110
1.076339
CTCCTCTTCCTCCTCGGCT
60.076
63.158
0.00
0.00
0.00
5.52
1691
4111
2.791868
GCTCCTCTTCCTCCTCGGC
61.792
68.421
0.00
0.00
0.00
5.54
1692
4112
1.380515
TGCTCCTCTTCCTCCTCGG
60.381
63.158
0.00
0.00
0.00
4.63
1693
4113
1.671901
GGTGCTCCTCTTCCTCCTCG
61.672
65.000
0.00
0.00
0.00
4.63
1735
4155
2.168521
CGCCTTGTCCTTCTCTGGATTA
59.831
50.000
0.00
0.00
38.52
1.75
1738
4158
1.544825
CCGCCTTGTCCTTCTCTGGA
61.545
60.000
0.00
0.00
0.00
3.86
1741
4161
1.893919
GCTCCGCCTTGTCCTTCTCT
61.894
60.000
0.00
0.00
0.00
3.10
1745
4165
2.348998
CTGCTCCGCCTTGTCCTT
59.651
61.111
0.00
0.00
0.00
3.36
1792
4212
1.002134
CTCCATGTTGAAGCCCGGT
60.002
57.895
0.00
0.00
0.00
5.28
1826
4246
2.180017
CATGTTGGCCGCTTGAGC
59.820
61.111
0.00
0.00
37.78
4.26
1827
4247
2.879907
CCATGTTGGCCGCTTGAG
59.120
61.111
12.56
2.53
0.00
3.02
1873
4302
0.398522
ACACATAGGCCTCATCCCGA
60.399
55.000
9.68
0.00
0.00
5.14
1875
4304
1.625818
CCTACACATAGGCCTCATCCC
59.374
57.143
9.68
0.00
41.80
3.85
1892
4321
1.138266
GATGAACTGCCGGTTAGCCTA
59.862
52.381
1.90
0.00
38.41
3.93
1917
4346
4.452733
CGGTCTCCGCCTGTTCCC
62.453
72.222
0.00
0.00
41.17
3.97
1947
4376
1.200483
CATCTCCGTGTCGAATTCGG
58.800
55.000
26.47
11.89
44.76
4.30
1951
4380
0.747255
CCTCCATCTCCGTGTCGAAT
59.253
55.000
0.00
0.00
0.00
3.34
1952
4381
1.945354
GCCTCCATCTCCGTGTCGAA
61.945
60.000
0.00
0.00
0.00
3.71
1957
4386
3.144120
CTCCGCCTCCATCTCCGTG
62.144
68.421
0.00
0.00
0.00
4.94
1958
4387
2.835431
CTCCGCCTCCATCTCCGT
60.835
66.667
0.00
0.00
0.00
4.69
1983
4412
1.610673
TGACTCCTCCACTGCTCCC
60.611
63.158
0.00
0.00
0.00
4.30
1988
4417
0.531657
CAGCTCTGACTCCTCCACTG
59.468
60.000
0.00
0.00
0.00
3.66
1991
4420
2.346541
CGCAGCTCTGACTCCTCCA
61.347
63.158
0.29
0.00
0.00
3.86
1992
4421
2.493973
CGCAGCTCTGACTCCTCC
59.506
66.667
0.29
0.00
0.00
4.30
2013
4443
2.445085
TCCGGATACATGGGCGGT
60.445
61.111
0.00
0.00
0.00
5.68
2042
4472
3.886123
TCGTCAGAGATGTCCACTATCA
58.114
45.455
0.00
0.00
0.00
2.15
2058
4488
5.452255
ACTTATACACCCTAATCCTCGTCA
58.548
41.667
0.00
0.00
0.00
4.35
2079
4510
7.772292
TCCACGTACTATGTAGATCAACTAACT
59.228
37.037
0.00
0.00
32.49
2.24
2084
4515
8.644318
AAAATCCACGTACTATGTAGATCAAC
57.356
34.615
0.00
0.00
0.00
3.18
2094
4525
9.832445
ATGTAAATGAGAAAATCCACGTACTAT
57.168
29.630
0.00
0.00
0.00
2.12
2097
4528
6.687105
GCATGTAAATGAGAAAATCCACGTAC
59.313
38.462
0.00
0.00
0.00
3.67
2117
4549
6.426587
ACCTTAGATCCATACAAAAGCATGT
58.573
36.000
0.00
0.00
37.32
3.21
2146
4578
5.654650
CCTCTGTATCTGGATACCTCATACC
59.345
48.000
15.45
0.00
42.19
2.73
2164
4596
3.766545
TGCCTTAAATTTGCTCCTCTGT
58.233
40.909
0.00
0.00
0.00
3.41
2206
4638
1.418342
CGTAGCATCCGTCCGTTTGG
61.418
60.000
0.00
0.00
0.00
3.28
2207
4639
1.418342
CCGTAGCATCCGTCCGTTTG
61.418
60.000
0.00
0.00
0.00
2.93
2208
4640
1.153706
CCGTAGCATCCGTCCGTTT
60.154
57.895
0.00
0.00
0.00
3.60
2209
4641
1.031571
TACCGTAGCATCCGTCCGTT
61.032
55.000
0.00
0.00
0.00
4.44
2210
4642
1.451927
TACCGTAGCATCCGTCCGT
60.452
57.895
0.00
0.00
0.00
4.69
2211
4643
1.009222
GTACCGTAGCATCCGTCCG
60.009
63.158
0.00
0.00
0.00
4.79
2212
4644
1.009222
CGTACCGTAGCATCCGTCC
60.009
63.158
0.00
0.00
0.00
4.79
2213
4645
1.009222
CCGTACCGTAGCATCCGTC
60.009
63.158
0.00
0.00
0.00
4.79
2214
4646
1.750399
ACCGTACCGTAGCATCCGT
60.750
57.895
0.00
0.00
0.00
4.69
2215
4647
1.298863
CACCGTACCGTAGCATCCG
60.299
63.158
0.00
0.00
0.00
4.18
2216
4648
1.066918
CCACCGTACCGTAGCATCC
59.933
63.158
0.00
0.00
0.00
3.51
2217
4649
1.590792
GCCACCGTACCGTAGCATC
60.591
63.158
0.41
0.00
0.00
3.91
2218
4650
2.497770
GCCACCGTACCGTAGCAT
59.502
61.111
0.41
0.00
0.00
3.79
2219
4651
4.118995
CGCCACCGTACCGTAGCA
62.119
66.667
5.74
0.00
0.00
3.49
2220
4652
3.814268
TCGCCACCGTACCGTAGC
61.814
66.667
0.00
0.00
35.54
3.58
2221
4653
2.100991
GTCGCCACCGTACCGTAG
59.899
66.667
0.00
0.00
35.54
3.51
2222
4654
3.798650
CGTCGCCACCGTACCGTA
61.799
66.667
0.00
0.00
35.54
4.02
2226
4658
4.487412
CTCCCGTCGCCACCGTAC
62.487
72.222
0.00
0.00
35.54
3.67
2236
4668
4.803426
CTGCAGACCGCTCCCGTC
62.803
72.222
8.42
0.00
43.06
4.79
2240
4672
2.303549
ATACTGCTGCAGACCGCTCC
62.304
60.000
34.28
0.00
43.06
4.70
2241
4673
0.385751
TATACTGCTGCAGACCGCTC
59.614
55.000
34.28
0.00
43.06
5.03
2242
4674
0.387202
CTATACTGCTGCAGACCGCT
59.613
55.000
34.28
15.19
43.06
5.52
2243
4675
1.218230
GCTATACTGCTGCAGACCGC
61.218
60.000
34.28
23.99
42.89
5.68
2244
4676
0.103026
TGCTATACTGCTGCAGACCG
59.897
55.000
34.28
19.27
35.18
4.79
2245
4677
1.137872
AGTGCTATACTGCTGCAGACC
59.862
52.381
34.28
16.92
38.49
3.85
2246
4678
2.468831
GAGTGCTATACTGCTGCAGAC
58.531
52.381
34.28
20.52
40.53
3.51
2247
4679
1.410517
GGAGTGCTATACTGCTGCAGA
59.589
52.381
34.28
18.63
43.69
4.26
2248
4680
1.863267
GGAGTGCTATACTGCTGCAG
58.137
55.000
27.02
27.02
43.69
4.41
2253
4685
8.486333
ACTTCTTTTCAAGGAGTGCTATACTGC
61.486
40.741
0.00
0.00
45.68
4.40
2254
4686
6.876257
ACTTCTTTTCAAGGAGTGCTATACTG
59.124
38.462
0.00
0.00
45.68
2.74
2255
4687
7.010339
ACTTCTTTTCAAGGAGTGCTATACT
57.990
36.000
0.00
0.00
45.68
2.12
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.