Multiple sequence alignment - TraesCS1A01G061000
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
TraesCS1A01G061000
chr1A
100.000
2714
0
0
1
2714
41871732
41874445
0.000000e+00
5012.0
1
TraesCS1A01G061000
chr1A
93.370
920
49
4
61
970
452048103
452047186
0.000000e+00
1351.0
2
TraesCS1A01G061000
chr1A
92.216
925
55
11
63
973
300770371
300769450
0.000000e+00
1293.0
3
TraesCS1A01G061000
chr1A
81.106
434
66
10
2290
2714
41831907
41831481
1.560000e-87
333.0
4
TraesCS1A01G061000
chr1A
81.250
112
14
5
1782
1893
41831308
41831412
1.730000e-12
84.2
5
TraesCS1A01G061000
chr1A
73.705
251
43
17
1925
2156
41830492
41830738
2.900000e-10
76.8
6
TraesCS1A01G061000
chr5B
97.919
913
17
2
61
972
406282232
406281321
0.000000e+00
1580.0
7
TraesCS1A01G061000
chr5B
90.130
385
36
2
52
434
565894150
565894534
1.450000e-137
499.0
8
TraesCS1A01G061000
chrUn
96.158
911
34
1
61
970
329813131
329814041
0.000000e+00
1487.0
9
TraesCS1A01G061000
chrUn
95.939
911
36
1
61
970
329821662
329820752
0.000000e+00
1476.0
10
TraesCS1A01G061000
chr5A
93.608
923
45
4
60
970
677745037
677745957
0.000000e+00
1365.0
11
TraesCS1A01G061000
chr4A
92.842
922
52
5
61
970
632867341
632866422
0.000000e+00
1325.0
12
TraesCS1A01G061000
chr4A
92.017
927
47
10
60
974
323531704
323532615
0.000000e+00
1277.0
13
TraesCS1A01G061000
chr3A
92.423
937
43
11
58
983
430396525
430397444
0.000000e+00
1312.0
14
TraesCS1A01G061000
chr3A
81.081
407
67
8
2315
2714
11837214
11836811
1.570000e-82
316.0
15
TraesCS1A01G061000
chr3B
91.883
924
46
11
61
971
766165283
766166190
0.000000e+00
1264.0
16
TraesCS1A01G061000
chr3B
80.000
400
66
9
2319
2711
11620750
11621142
1.590000e-72
283.0
17
TraesCS1A01G061000
chr1B
86.329
1185
117
28
1557
2714
61962722
61963888
0.000000e+00
1249.0
18
TraesCS1A01G061000
chr1B
89.667
600
43
4
971
1558
61962061
61962653
0.000000e+00
747.0
19
TraesCS1A01G061000
chr1B
81.416
113
18
2
1781
1892
62199079
62199189
3.720000e-14
89.8
20
TraesCS1A01G061000
chr1B
80.899
89
14
2
2070
2156
61954189
61954276
1.740000e-07
67.6
21
TraesCS1A01G061000
chr6D
89.936
944
59
14
61
971
445080977
445080037
0.000000e+00
1184.0
22
TraesCS1A01G061000
chr6D
83.158
380
55
9
2338
2712
412631503
412631128
3.350000e-89
339.0
23
TraesCS1A01G061000
chr7B
90.053
935
51
18
59
971
696589124
696588210
0.000000e+00
1173.0
24
TraesCS1A01G061000
chr7A
89.519
935
56
9
61
972
456680582
456681497
0.000000e+00
1146.0
25
TraesCS1A01G061000
chr1D
93.255
593
35
4
971
1558
41820804
41821396
0.000000e+00
869.0
26
TraesCS1A01G061000
chr1D
90.610
639
47
7
1557
2183
41821465
41822102
0.000000e+00
835.0
27
TraesCS1A01G061000
chr1D
82.796
93
13
2
2066
2156
41767267
41767358
2.240000e-11
80.5
28
TraesCS1A01G061000
chr5D
81.140
456
72
12
2263
2714
522762289
522762734
1.200000e-93
353.0
29
TraesCS1A01G061000
chr5D
82.955
352
49
7
2372
2714
232835940
232835591
9.440000e-80
307.0
30
TraesCS1A01G061000
chr3D
78.846
468
85
10
2253
2712
578267590
578267129
1.220000e-78
303.0
31
TraesCS1A01G061000
chr6B
84.615
312
39
7
2408
2714
64965611
64965304
4.390000e-78
302.0
32
TraesCS1A01G061000
chr4B
80.196
409
59
15
2291
2690
48636908
48637303
1.230000e-73
287.0
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
TraesCS1A01G061000
chr1A
41871732
41874445
2713
False
5012
5012
100.0000
1
2714
1
chr1A.!!$F1
2713
1
TraesCS1A01G061000
chr1A
452047186
452048103
917
True
1351
1351
93.3700
61
970
1
chr1A.!!$R3
909
2
TraesCS1A01G061000
chr1A
300769450
300770371
921
True
1293
1293
92.2160
63
973
1
chr1A.!!$R2
910
3
TraesCS1A01G061000
chr5B
406281321
406282232
911
True
1580
1580
97.9190
61
972
1
chr5B.!!$R1
911
4
TraesCS1A01G061000
chrUn
329813131
329814041
910
False
1487
1487
96.1580
61
970
1
chrUn.!!$F1
909
5
TraesCS1A01G061000
chrUn
329820752
329821662
910
True
1476
1476
95.9390
61
970
1
chrUn.!!$R1
909
6
TraesCS1A01G061000
chr5A
677745037
677745957
920
False
1365
1365
93.6080
60
970
1
chr5A.!!$F1
910
7
TraesCS1A01G061000
chr4A
632866422
632867341
919
True
1325
1325
92.8420
61
970
1
chr4A.!!$R1
909
8
TraesCS1A01G061000
chr4A
323531704
323532615
911
False
1277
1277
92.0170
60
974
1
chr4A.!!$F1
914
9
TraesCS1A01G061000
chr3A
430396525
430397444
919
False
1312
1312
92.4230
58
983
1
chr3A.!!$F1
925
10
TraesCS1A01G061000
chr3B
766165283
766166190
907
False
1264
1264
91.8830
61
971
1
chr3B.!!$F2
910
11
TraesCS1A01G061000
chr1B
61962061
61963888
1827
False
998
1249
87.9980
971
2714
2
chr1B.!!$F3
1743
12
TraesCS1A01G061000
chr6D
445080037
445080977
940
True
1184
1184
89.9360
61
971
1
chr6D.!!$R2
910
13
TraesCS1A01G061000
chr7B
696588210
696589124
914
True
1173
1173
90.0530
59
971
1
chr7B.!!$R1
912
14
TraesCS1A01G061000
chr7A
456680582
456681497
915
False
1146
1146
89.5190
61
972
1
chr7A.!!$F1
911
15
TraesCS1A01G061000
chr1D
41820804
41822102
1298
False
852
869
91.9325
971
2183
2
chr1D.!!$F2
1212
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
50
51
0.601046
CGCTGCACCATCGTCCATAT
60.601
55.0
0.00
0.0
0.0
1.78
F
1455
1554
0.983467
TTGCTAGCACTCACCATGGA
59.017
50.0
21.47
0.0
0.0
3.41
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1460
1559
0.171231
GCACCCCAGAAGCGAAATTC
59.829
55.0
0.0
0.0
0.0
2.17
R
2599
2805
0.176910
TGTGTTTCTCGTGACCAGCA
59.823
50.0
0.0
0.0
0.0
4.41
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
22
23
4.556233
CACTAAACAGTAGTAGCAGTGCA
58.444
43.478
19.20
0.00
29.78
4.57
23
24
4.988540
CACTAAACAGTAGTAGCAGTGCAA
59.011
41.667
19.20
0.00
29.78
4.08
24
25
4.989168
ACTAAACAGTAGTAGCAGTGCAAC
59.011
41.667
19.20
9.65
0.00
4.17
25
26
3.469008
AACAGTAGTAGCAGTGCAACA
57.531
42.857
19.20
0.00
41.43
3.33
26
27
2.755650
ACAGTAGTAGCAGTGCAACAC
58.244
47.619
19.20
11.87
41.43
3.32
27
28
2.365617
ACAGTAGTAGCAGTGCAACACT
59.634
45.455
19.20
18.23
46.51
3.55
28
29
3.572682
ACAGTAGTAGCAGTGCAACACTA
59.427
43.478
19.20
17.24
43.43
2.74
29
30
4.038763
ACAGTAGTAGCAGTGCAACACTAA
59.961
41.667
19.20
4.26
43.43
2.24
30
31
4.623167
CAGTAGTAGCAGTGCAACACTAAG
59.377
45.833
19.20
12.54
43.43
2.18
31
32
2.417719
AGTAGCAGTGCAACACTAAGC
58.582
47.619
19.20
1.12
43.43
3.09
32
33
1.126846
GTAGCAGTGCAACACTAAGCG
59.873
52.381
19.20
0.00
43.43
4.68
33
34
1.441016
GCAGTGCAACACTAAGCGC
60.441
57.895
11.09
0.00
43.43
5.92
34
35
4.779475
AGTGCAACACTAAGCGCT
57.221
50.000
2.64
2.64
43.46
5.92
35
36
4.826600
GTGCAACACTAAGCGCTG
57.173
55.556
12.58
0.57
38.19
5.18
36
37
1.441016
GTGCAACACTAAGCGCTGC
60.441
57.895
12.58
10.04
38.19
5.25
37
38
1.891449
TGCAACACTAAGCGCTGCA
60.891
52.632
12.58
13.10
40.54
4.41
38
39
1.441016
GCAACACTAAGCGCTGCAC
60.441
57.895
12.58
0.00
33.19
4.57
39
40
1.207593
CAACACTAAGCGCTGCACC
59.792
57.895
12.58
0.00
0.00
5.01
40
41
1.227823
AACACTAAGCGCTGCACCA
60.228
52.632
12.58
0.00
0.00
4.17
41
42
0.606401
AACACTAAGCGCTGCACCAT
60.606
50.000
12.58
0.00
0.00
3.55
42
43
1.021390
ACACTAAGCGCTGCACCATC
61.021
55.000
12.58
0.00
0.00
3.51
43
44
1.811266
ACTAAGCGCTGCACCATCG
60.811
57.895
12.58
0.00
0.00
3.84
44
45
1.811266
CTAAGCGCTGCACCATCGT
60.811
57.895
12.58
0.00
0.00
3.73
45
46
1.756375
CTAAGCGCTGCACCATCGTC
61.756
60.000
12.58
0.00
0.00
4.20
48
49
2.512286
CGCTGCACCATCGTCCAT
60.512
61.111
0.00
0.00
0.00
3.41
49
50
1.227234
CGCTGCACCATCGTCCATA
60.227
57.895
0.00
0.00
0.00
2.74
50
51
0.601046
CGCTGCACCATCGTCCATAT
60.601
55.000
0.00
0.00
0.00
1.78
51
52
1.336795
CGCTGCACCATCGTCCATATA
60.337
52.381
0.00
0.00
0.00
0.86
52
53
2.675032
CGCTGCACCATCGTCCATATAT
60.675
50.000
0.00
0.00
0.00
0.86
53
54
3.428862
CGCTGCACCATCGTCCATATATA
60.429
47.826
0.00
0.00
0.00
0.86
54
55
4.115516
GCTGCACCATCGTCCATATATAG
58.884
47.826
0.00
0.00
0.00
1.31
55
56
4.142160
GCTGCACCATCGTCCATATATAGA
60.142
45.833
0.00
0.00
0.00
1.98
56
57
5.324784
TGCACCATCGTCCATATATAGAC
57.675
43.478
1.55
1.55
0.00
2.59
78
79
8.071177
AGACCATGAAAGAATTCCTTATTTGG
57.929
34.615
0.65
6.27
35.16
3.28
236
238
4.331968
TGACAAATTTACCCCTAGCACTG
58.668
43.478
0.00
0.00
0.00
3.66
495
527
4.041444
AGCAATTAAAAATCCCAAGGCACA
59.959
37.500
0.00
0.00
0.00
4.57
1002
1092
2.354902
GCCAGGCCACATTTCAGTT
58.645
52.632
5.01
0.00
0.00
3.16
1011
1104
4.293415
GCCACATTTCAGTTGAAACAGAG
58.707
43.478
9.29
4.90
45.55
3.35
1014
1107
5.342433
CACATTTCAGTTGAAACAGAGCAA
58.658
37.500
9.29
0.00
45.55
3.91
1021
1114
3.206150
GTTGAAACAGAGCAACTCTCCA
58.794
45.455
0.00
0.00
42.90
3.86
1022
1115
3.777106
TGAAACAGAGCAACTCTCCAT
57.223
42.857
0.00
0.00
42.90
3.41
1032
1125
5.021033
AGCAACTCTCCATAAGATCAGTG
57.979
43.478
0.00
0.00
32.19
3.66
1033
1126
4.713814
AGCAACTCTCCATAAGATCAGTGA
59.286
41.667
0.00
0.00
32.19
3.41
1073
1169
1.671379
GCCTGTCTTCCGTTCCCAC
60.671
63.158
0.00
0.00
0.00
4.61
1230
1329
3.322466
CAGGCTCAAGGGTCCGGT
61.322
66.667
0.00
0.00
0.00
5.28
1232
1331
4.410400
GGCTCAAGGGTCCGGTGG
62.410
72.222
0.00
0.00
0.00
4.61
1356
1455
1.262950
CACATTGAGTTTGGCGACGAA
59.737
47.619
0.00
0.00
0.00
3.85
1380
1479
1.138859
CCGTATGTTGCATCCTCCTCA
59.861
52.381
0.00
0.00
0.00
3.86
1415
1514
7.047891
TCCATGTCCACATACTATTGAACTTC
58.952
38.462
0.00
0.00
34.26
3.01
1442
1541
2.099831
GCGCTGCTTGCTTGCTAG
59.900
61.111
0.00
0.00
40.11
3.42
1454
1553
1.376543
CTTGCTAGCACTCACCATGG
58.623
55.000
19.17
11.19
0.00
3.66
1455
1554
0.983467
TTGCTAGCACTCACCATGGA
59.017
50.000
21.47
0.00
0.00
3.41
1460
1559
3.750130
GCTAGCACTCACCATGGATATTG
59.250
47.826
21.47
11.02
0.00
1.90
1534
1639
1.885388
CACACGTCCAAGGCGAACA
60.885
57.895
9.31
0.00
0.00
3.18
1582
1757
1.618837
AGTGGCTGTCGTGTATCACTT
59.381
47.619
0.00
0.00
32.34
3.16
1640
1817
5.470777
TGTTTTAGTAGCTTGTTATGGCGTT
59.529
36.000
0.00
0.00
0.00
4.84
1666
1843
2.082231
CAGTAGAGTTCGTCCTCGGAA
58.918
52.381
0.00
0.00
36.56
4.30
1674
1851
7.052142
AGAGTTCGTCCTCGGAAATATTATT
57.948
36.000
0.00
0.00
36.56
1.40
1714
1894
5.531634
AGTTGCAGTGATTGTGGTTTATTG
58.468
37.500
0.00
0.00
0.00
1.90
1726
1906
0.388006
GTTTATTGTGCGGTGTGGCC
60.388
55.000
0.00
0.00
0.00
5.36
1729
1909
2.404566
TATTGTGCGGTGTGGCCTGT
62.405
55.000
3.32
0.00
34.25
4.00
1740
1920
1.144708
TGTGGCCTGTTCTCCATTTGA
59.855
47.619
3.32
0.00
34.47
2.69
1741
1921
1.815003
GTGGCCTGTTCTCCATTTGAG
59.185
52.381
3.32
0.00
42.90
3.02
1758
1938
4.630894
TTGAGATTGTGCTCGTTTGTTT
57.369
36.364
0.00
0.00
37.73
2.83
1770
1950
8.447833
TGTGCTCGTTTGTTTCCTAATATAAAG
58.552
33.333
0.00
0.00
0.00
1.85
1775
1955
6.500910
GTTTGTTTCCTAATATAAAGGGGCG
58.499
40.000
4.60
0.00
34.66
6.13
1780
1960
4.431378
TCCTAATATAAAGGGGCGGATCA
58.569
43.478
0.00
0.00
34.66
2.92
1784
1964
0.393077
ATAAAGGGGCGGATCACTCG
59.607
55.000
0.00
0.00
0.00
4.18
1804
1984
6.420604
CACTCGTGCAAATTCCTGTAAAAATT
59.579
34.615
0.00
0.00
0.00
1.82
1893
2076
8.551205
TGAAATCATGTAAAGAGCGATAATGAC
58.449
33.333
0.00
0.00
0.00
3.06
1902
2085
5.490139
AGAGCGATAATGACATGTTTTGG
57.510
39.130
0.00
0.00
0.00
3.28
1909
2092
1.698506
TGACATGTTTTGGGGGACAC
58.301
50.000
0.00
0.00
0.00
3.67
1921
2104
3.430453
TGGGGGACACAATTTGAATCTC
58.570
45.455
2.79
0.03
0.00
2.75
2137
2323
3.568853
AGTACTGACGAGCAACTACAAGT
59.431
43.478
0.00
0.00
0.00
3.16
2159
2347
2.975193
CACATGCATTCAACACACTTCG
59.025
45.455
0.00
0.00
0.00
3.79
2163
2351
2.147958
GCATTCAACACACTTCGGGTA
58.852
47.619
0.00
0.00
0.00
3.69
2196
2391
3.055602
TCATGACATGAGACAGTTGAGGG
60.056
47.826
14.24
0.00
33.59
4.30
2197
2392
1.002430
TGACATGAGACAGTTGAGGGC
59.998
52.381
0.00
0.00
0.00
5.19
2198
2393
1.277557
GACATGAGACAGTTGAGGGCT
59.722
52.381
0.00
0.00
0.00
5.19
2199
2394
1.277557
ACATGAGACAGTTGAGGGCTC
59.722
52.381
0.00
0.00
0.00
4.70
2200
2395
1.277273
CATGAGACAGTTGAGGGCTCA
59.723
52.381
0.00
0.00
39.61
4.26
2201
2396
1.423584
TGAGACAGTTGAGGGCTCAA
58.576
50.000
0.00
0.00
46.27
3.02
2209
2404
2.452600
TTGAGGGCTCAAACCAAAGT
57.547
45.000
0.00
0.00
45.56
2.66
2210
2405
2.452600
TGAGGGCTCAAACCAAAGTT
57.547
45.000
0.00
0.00
36.53
2.66
2211
2406
2.031120
TGAGGGCTCAAACCAAAGTTG
58.969
47.619
0.00
0.00
35.97
3.16
2224
2419
1.873591
CAAAGTTGAAGTAGCGCCAGT
59.126
47.619
2.29
0.00
0.00
4.00
2229
2424
1.725641
TGAAGTAGCGCCAGTGATTG
58.274
50.000
2.29
0.00
0.00
2.67
2242
2437
4.675510
CCAGTGATTGGTAAATGATGTGC
58.324
43.478
0.00
0.00
42.41
4.57
2243
2438
4.158209
CCAGTGATTGGTAAATGATGTGCA
59.842
41.667
0.00
0.00
42.41
4.57
2244
2439
5.337554
CAGTGATTGGTAAATGATGTGCAG
58.662
41.667
0.00
0.00
0.00
4.41
2246
2441
5.711506
AGTGATTGGTAAATGATGTGCAGAA
59.288
36.000
0.00
0.00
0.00
3.02
2250
2447
6.449635
TTGGTAAATGATGTGCAGAATACC
57.550
37.500
0.00
0.00
35.28
2.73
2261
2458
2.675844
TGCAGAATACCACGGAAATTCG
59.324
45.455
0.00
0.00
35.30
3.34
2262
2459
2.031683
GCAGAATACCACGGAAATTCGG
59.968
50.000
0.00
0.00
35.30
4.30
2285
2483
2.033602
AAGTAAGTGCGGGGGCAC
59.966
61.111
11.03
11.03
40.64
5.01
2290
2488
4.101448
AGTGCGGGGGCACTCATC
62.101
66.667
15.40
0.00
46.65
2.92
2291
2489
4.408821
GTGCGGGGGCACTCATCA
62.409
66.667
11.66
0.00
37.68
3.07
2303
2501
1.302285
CTCATCACCTGCCAAGCCT
59.698
57.895
0.00
0.00
0.00
4.58
2304
2502
0.747283
CTCATCACCTGCCAAGCCTC
60.747
60.000
0.00
0.00
0.00
4.70
2322
2520
3.508840
GCCGCCTGGTCGATTTGG
61.509
66.667
11.24
0.00
37.67
3.28
2325
2523
2.464459
CGCCTGGTCGATTTGGCTC
61.464
63.158
18.55
0.00
42.90
4.70
2327
2525
2.464459
CCTGGTCGATTTGGCTCGC
61.464
63.158
0.00
0.00
38.52
5.03
2332
2530
0.373716
GTCGATTTGGCTCGCGATTT
59.626
50.000
10.36
0.00
38.52
2.17
2333
2531
0.373370
TCGATTTGGCTCGCGATTTG
59.627
50.000
10.36
0.00
38.52
2.32
2350
2548
5.398416
GCGATTTGCGAAGTAATTTAATCCC
59.602
40.000
0.00
0.00
44.57
3.85
2351
2549
6.725246
CGATTTGCGAAGTAATTTAATCCCT
58.275
36.000
0.00
0.00
44.57
4.20
2352
2550
6.851330
CGATTTGCGAAGTAATTTAATCCCTC
59.149
38.462
0.00
0.00
44.57
4.30
2353
2551
7.466725
CGATTTGCGAAGTAATTTAATCCCTCA
60.467
37.037
0.00
0.00
44.57
3.86
2355
2553
5.492895
TGCGAAGTAATTTAATCCCTCACA
58.507
37.500
0.00
0.00
0.00
3.58
2357
2555
6.431543
TGCGAAGTAATTTAATCCCTCACAAA
59.568
34.615
0.00
0.00
0.00
2.83
2362
2560
5.405935
AATTTAATCCCTCACAAAGGCAC
57.594
39.130
0.00
0.00
44.71
5.01
2363
2561
3.517296
TTAATCCCTCACAAAGGCACA
57.483
42.857
0.00
0.00
44.71
4.57
2370
2568
3.243401
CCCTCACAAAGGCACAGTAAAAC
60.243
47.826
0.00
0.00
44.71
2.43
2373
2571
4.992688
TCACAAAGGCACAGTAAAACAAG
58.007
39.130
0.00
0.00
0.00
3.16
2374
2572
4.702612
TCACAAAGGCACAGTAAAACAAGA
59.297
37.500
0.00
0.00
0.00
3.02
2375
2573
5.184096
TCACAAAGGCACAGTAAAACAAGAA
59.816
36.000
0.00
0.00
0.00
2.52
2376
2574
5.288472
CACAAAGGCACAGTAAAACAAGAAC
59.712
40.000
0.00
0.00
0.00
3.01
2377
2575
5.047660
ACAAAGGCACAGTAAAACAAGAACA
60.048
36.000
0.00
0.00
0.00
3.18
2380
2578
4.278419
AGGCACAGTAAAACAAGAACATCC
59.722
41.667
0.00
0.00
0.00
3.51
2381
2579
4.546570
GCACAGTAAAACAAGAACATCCC
58.453
43.478
0.00
0.00
0.00
3.85
2382
2580
4.278419
GCACAGTAAAACAAGAACATCCCT
59.722
41.667
0.00
0.00
0.00
4.20
2383
2581
5.562890
GCACAGTAAAACAAGAACATCCCTC
60.563
44.000
0.00
0.00
0.00
4.30
2384
2582
4.755123
ACAGTAAAACAAGAACATCCCTCG
59.245
41.667
0.00
0.00
0.00
4.63
2385
2583
4.154195
CAGTAAAACAAGAACATCCCTCGG
59.846
45.833
0.00
0.00
0.00
4.63
2386
2584
3.502123
AAAACAAGAACATCCCTCGGA
57.498
42.857
0.00
0.00
35.55
4.55
2387
2585
3.502123
AAACAAGAACATCCCTCGGAA
57.498
42.857
0.00
0.00
34.34
4.30
2390
2588
2.637872
ACAAGAACATCCCTCGGAAAGA
59.362
45.455
0.00
0.00
34.34
2.52
2403
2601
6.206048
TCCCTCGGAAAGATTTAAGTTTCAAC
59.794
38.462
8.46
0.00
34.85
3.18
2404
2602
6.016610
CCCTCGGAAAGATTTAAGTTTCAACA
60.017
38.462
8.46
0.00
34.85
3.33
2454
2654
3.119173
TGCCCAGTTTCAACAAGTTTCAG
60.119
43.478
0.00
0.00
0.00
3.02
2457
2657
4.640201
CCCAGTTTCAACAAGTTTCAGAGA
59.360
41.667
0.00
0.00
0.00
3.10
2461
2661
8.233190
CCAGTTTCAACAAGTTTCAGAGATATC
58.767
37.037
0.00
0.00
0.00
1.63
2470
2670
9.453572
ACAAGTTTCAGAGATATCATTTAAGCA
57.546
29.630
5.32
0.00
0.00
3.91
2501
2705
6.693466
TCTGTCGGTCATAGACACAAAATAA
58.307
36.000
0.00
0.00
42.91
1.40
2618
2824
0.176910
TGCTGGTCACGAGAAACACA
59.823
50.000
0.00
0.00
0.00
3.72
2620
2826
1.873591
GCTGGTCACGAGAAACACAAT
59.126
47.619
0.00
0.00
0.00
2.71
2627
2833
6.429692
TGGTCACGAGAAACACAATTATGAAT
59.570
34.615
0.00
0.00
0.00
2.57
2631
2837
8.994170
TCACGAGAAACACAATTATGAATACAA
58.006
29.630
0.00
0.00
0.00
2.41
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
4.556233
TGCACTGCTACTACTGTTTAGTG
58.444
43.478
1.98
0.00
37.78
2.74
1
2
4.866508
TGCACTGCTACTACTGTTTAGT
57.133
40.909
1.98
0.00
40.99
2.24
2
3
4.988540
TGTTGCACTGCTACTACTGTTTAG
59.011
41.667
15.26
0.00
35.51
1.85
3
4
4.748102
GTGTTGCACTGCTACTACTGTTTA
59.252
41.667
15.26
0.00
35.51
2.01
4
5
3.560068
GTGTTGCACTGCTACTACTGTTT
59.440
43.478
15.26
0.00
35.51
2.83
5
6
3.131396
GTGTTGCACTGCTACTACTGTT
58.869
45.455
15.26
0.00
35.51
3.16
6
7
2.365617
AGTGTTGCACTGCTACTACTGT
59.634
45.455
15.26
0.00
43.63
3.55
7
8
3.032017
AGTGTTGCACTGCTACTACTG
57.968
47.619
15.26
0.00
43.63
2.74
8
9
4.810790
CTTAGTGTTGCACTGCTACTACT
58.189
43.478
15.26
16.59
45.01
2.57
9
10
3.368236
GCTTAGTGTTGCACTGCTACTAC
59.632
47.826
15.26
11.65
45.01
2.73
10
11
3.585862
GCTTAGTGTTGCACTGCTACTA
58.414
45.455
15.26
11.49
45.01
1.82
11
12
2.417719
GCTTAGTGTTGCACTGCTACT
58.582
47.619
15.26
12.31
45.01
2.57
12
13
1.126846
CGCTTAGTGTTGCACTGCTAC
59.873
52.381
11.57
8.48
45.01
3.58
13
14
1.428448
CGCTTAGTGTTGCACTGCTA
58.572
50.000
11.57
0.00
45.01
3.49
14
15
1.845809
GCGCTTAGTGTTGCACTGCT
61.846
55.000
11.57
0.00
45.01
4.24
15
16
1.441016
GCGCTTAGTGTTGCACTGC
60.441
57.895
11.57
6.75
45.01
4.40
16
17
0.110509
CAGCGCTTAGTGTTGCACTG
60.111
55.000
7.50
0.00
45.01
3.66
17
18
1.845809
GCAGCGCTTAGTGTTGCACT
61.846
55.000
25.29
6.99
46.48
4.40
18
19
1.441016
GCAGCGCTTAGTGTTGCAC
60.441
57.895
25.29
1.18
46.48
4.57
19
20
2.945984
GCAGCGCTTAGTGTTGCA
59.054
55.556
25.29
0.00
46.48
4.08
21
22
1.207593
GGTGCAGCGCTTAGTGTTG
59.792
57.895
7.50
5.27
0.00
3.33
22
23
0.606401
ATGGTGCAGCGCTTAGTGTT
60.606
50.000
7.50
0.00
0.00
3.32
23
24
1.003355
ATGGTGCAGCGCTTAGTGT
60.003
52.632
7.50
0.00
0.00
3.55
24
25
1.717937
GATGGTGCAGCGCTTAGTG
59.282
57.895
7.50
0.00
0.00
2.74
25
26
1.811266
CGATGGTGCAGCGCTTAGT
60.811
57.895
7.50
0.00
36.27
2.24
26
27
3.009140
CGATGGTGCAGCGCTTAG
58.991
61.111
7.50
0.00
36.27
2.18
35
36
4.159693
TGGTCTATATATGGACGATGGTGC
59.840
45.833
19.44
7.51
38.95
5.01
36
37
5.914898
TGGTCTATATATGGACGATGGTG
57.085
43.478
19.44
0.00
38.95
4.17
37
38
6.194967
TCATGGTCTATATATGGACGATGGT
58.805
40.000
33.49
13.90
46.59
3.55
38
39
6.715347
TCATGGTCTATATATGGACGATGG
57.285
41.667
33.49
23.00
46.59
3.51
40
41
8.595362
TCTTTCATGGTCTATATATGGACGAT
57.405
34.615
19.44
18.37
38.95
3.73
41
42
8.417273
TTCTTTCATGGTCTATATATGGACGA
57.583
34.615
19.44
17.10
38.95
4.20
42
43
9.658799
AATTCTTTCATGGTCTATATATGGACG
57.341
33.333
19.44
9.01
38.95
4.79
52
53
9.189156
CCAAATAAGGAATTCTTTCATGGTCTA
57.811
33.333
6.03
0.00
36.93
2.59
53
54
7.364144
GCCAAATAAGGAATTCTTTCATGGTCT
60.364
37.037
20.37
1.65
36.93
3.85
54
55
6.758416
GCCAAATAAGGAATTCTTTCATGGTC
59.242
38.462
20.37
13.59
36.93
4.02
55
56
6.213195
TGCCAAATAAGGAATTCTTTCATGGT
59.787
34.615
20.37
0.00
36.93
3.55
56
57
6.536224
GTGCCAAATAAGGAATTCTTTCATGG
59.464
38.462
17.52
17.52
36.93
3.66
78
79
6.822073
AGGAAACGAAATTTAAAACAGTGC
57.178
33.333
0.00
0.00
0.00
4.40
255
257
5.415701
GGTGAAGCCAATGAGAATGACTTTA
59.584
40.000
0.00
0.00
37.17
1.85
495
527
7.174772
GCCTTTGGATTTATTTTTGACCATGTT
59.825
33.333
0.00
0.00
0.00
2.71
627
681
4.489493
GCACACGCACGTATAAAACAATAC
59.511
41.667
0.00
0.00
38.36
1.89
1002
1092
3.777106
ATGGAGAGTTGCTCTGTTTCA
57.223
42.857
3.12
0.00
41.35
2.69
1011
1104
5.016051
TCACTGATCTTATGGAGAGTTGC
57.984
43.478
0.00
0.00
37.93
4.17
1014
1107
3.640967
GGCTCACTGATCTTATGGAGAGT
59.359
47.826
0.00
0.00
37.93
3.24
1021
1114
4.880696
GCTTCTTTGGCTCACTGATCTTAT
59.119
41.667
0.00
0.00
0.00
1.73
1022
1115
4.256920
GCTTCTTTGGCTCACTGATCTTA
58.743
43.478
0.00
0.00
0.00
2.10
1032
1125
1.012841
CCATCTCGCTTCTTTGGCTC
58.987
55.000
0.00
0.00
0.00
4.70
1033
1126
3.165606
CCATCTCGCTTCTTTGGCT
57.834
52.632
0.00
0.00
0.00
4.75
1059
1155
1.295746
GGAGGTGGGAACGGAAGAC
59.704
63.158
0.00
0.00
0.00
3.01
1073
1169
2.806009
GCTAGCAGCAGGAGGGAGG
61.806
68.421
10.63
0.00
41.89
4.30
1224
1323
2.266055
CTGAAGCCTCCACCGGAC
59.734
66.667
9.46
0.00
0.00
4.79
1230
1329
2.066393
CCGGATCCTGAAGCCTCCA
61.066
63.158
10.75
0.00
0.00
3.86
1232
1331
2.110006
GCCGGATCCTGAAGCCTC
59.890
66.667
5.05
0.00
0.00
4.70
1337
1436
1.263217
GTTCGTCGCCAAACTCAATGT
59.737
47.619
0.00
0.00
0.00
2.71
1341
1440
1.144969
GATGTTCGTCGCCAAACTCA
58.855
50.000
0.00
0.00
0.00
3.41
1380
1479
1.556911
GTGGACATGGATGTGAGGACT
59.443
52.381
0.00
0.00
41.95
3.85
1442
1541
5.779529
AATTCAATATCCATGGTGAGTGC
57.220
39.130
12.58
0.00
0.00
4.40
1454
1553
4.580580
ACCCCAGAAGCGAAATTCAATATC
59.419
41.667
0.00
0.00
0.00
1.63
1455
1554
4.339247
CACCCCAGAAGCGAAATTCAATAT
59.661
41.667
0.00
0.00
0.00
1.28
1460
1559
0.171231
GCACCCCAGAAGCGAAATTC
59.829
55.000
0.00
0.00
0.00
2.17
1582
1757
5.845391
AAAACAAGCTACTAAAACAGGCA
57.155
34.783
0.00
0.00
0.00
4.75
1609
1786
9.922305
CATAACAAGCTACTAAAACAGATTAGC
57.078
33.333
0.00
0.00
36.54
3.09
1640
1817
2.209064
GACGAACTCTACTGGCCGCA
62.209
60.000
0.00
0.00
0.00
5.69
1652
1829
6.812998
TCAATAATATTTCCGAGGACGAACT
58.187
36.000
0.00
0.00
42.66
3.01
1674
1851
7.493645
CACTGCAACTACTAGATGATGAATTCA
59.506
37.037
11.26
11.26
39.12
2.57
1714
1894
3.660111
GAACAGGCCACACCGCAC
61.660
66.667
5.01
0.00
46.52
5.34
1740
1920
3.214328
AGGAAACAAACGAGCACAATCT
58.786
40.909
0.00
0.00
0.00
2.40
1741
1921
3.626028
AGGAAACAAACGAGCACAATC
57.374
42.857
0.00
0.00
0.00
2.67
1750
1930
6.500910
GCCCCTTTATATTAGGAAACAAACG
58.499
40.000
5.39
0.00
34.56
3.60
1758
1938
4.224370
GTGATCCGCCCCTTTATATTAGGA
59.776
45.833
5.39
0.00
34.56
2.94
1775
1955
2.096496
CAGGAATTTGCACGAGTGATCC
59.904
50.000
7.50
6.01
0.00
3.36
1780
1960
5.508200
TTTTTACAGGAATTTGCACGAGT
57.492
34.783
0.00
0.00
0.00
4.18
1854
2034
8.755696
TTACATGATTTCACATTTGCTTTACC
57.244
30.769
0.00
0.00
0.00
2.85
1893
2076
3.767902
AATTGTGTCCCCCAAAACATG
57.232
42.857
0.00
0.00
0.00
3.21
1902
2085
4.335416
TCTGAGATTCAAATTGTGTCCCC
58.665
43.478
0.00
0.00
0.00
4.81
1909
2092
9.472361
AAACTTGACATTCTGAGATTCAAATTG
57.528
29.630
4.05
0.00
0.00
2.32
1921
2104
5.126061
CCCTCCCATAAAACTTGACATTCTG
59.874
44.000
0.00
0.00
0.00
3.02
2137
2323
3.303924
CGAAGTGTGTTGAATGCATGTGA
60.304
43.478
0.00
0.00
0.00
3.58
2159
2347
3.767673
TGTCATGAGAAGTACCACTACCC
59.232
47.826
0.00
0.00
0.00
3.69
2196
2391
4.290969
GCTACTTCAACTTTGGTTTGAGC
58.709
43.478
0.00
0.00
32.73
4.26
2197
2392
4.527564
CGCTACTTCAACTTTGGTTTGAG
58.472
43.478
0.00
0.00
32.73
3.02
2198
2393
3.242936
GCGCTACTTCAACTTTGGTTTGA
60.243
43.478
0.00
0.00
32.73
2.69
2199
2394
3.042887
GCGCTACTTCAACTTTGGTTTG
58.957
45.455
0.00
0.00
32.73
2.93
2200
2395
2.034179
GGCGCTACTTCAACTTTGGTTT
59.966
45.455
7.64
0.00
32.73
3.27
2201
2396
1.607148
GGCGCTACTTCAACTTTGGTT
59.393
47.619
7.64
0.00
35.86
3.67
2202
2397
1.235724
GGCGCTACTTCAACTTTGGT
58.764
50.000
7.64
0.00
0.00
3.67
2203
2398
1.197721
CTGGCGCTACTTCAACTTTGG
59.802
52.381
7.64
0.00
0.00
3.28
2206
2401
1.070134
TCACTGGCGCTACTTCAACTT
59.930
47.619
7.64
0.00
0.00
2.66
2207
2402
0.679505
TCACTGGCGCTACTTCAACT
59.320
50.000
7.64
0.00
0.00
3.16
2208
2403
1.726853
ATCACTGGCGCTACTTCAAC
58.273
50.000
7.64
0.00
0.00
3.18
2209
2404
2.076100
CAATCACTGGCGCTACTTCAA
58.924
47.619
7.64
0.00
0.00
2.69
2210
2405
1.675714
CCAATCACTGGCGCTACTTCA
60.676
52.381
7.64
0.00
38.76
3.02
2211
2406
1.009829
CCAATCACTGGCGCTACTTC
58.990
55.000
7.64
0.00
38.76
3.01
2224
2419
6.778834
ATTCTGCACATCATTTACCAATCA
57.221
33.333
0.00
0.00
0.00
2.57
2229
2424
5.504010
CGTGGTATTCTGCACATCATTTACC
60.504
44.000
0.00
0.00
0.00
2.85
2235
2430
1.552792
TCCGTGGTATTCTGCACATCA
59.447
47.619
0.00
0.00
0.00
3.07
2236
2431
2.309528
TCCGTGGTATTCTGCACATC
57.690
50.000
0.00
0.00
0.00
3.06
2240
2435
2.675844
CGAATTTCCGTGGTATTCTGCA
59.324
45.455
11.72
0.00
0.00
4.41
2241
2436
2.031683
CCGAATTTCCGTGGTATTCTGC
59.968
50.000
11.72
0.00
0.00
4.26
2242
2437
2.612212
CCCGAATTTCCGTGGTATTCTG
59.388
50.000
11.72
7.43
0.00
3.02
2243
2438
2.420967
CCCCGAATTTCCGTGGTATTCT
60.421
50.000
11.72
0.00
0.00
2.40
2244
2439
1.944709
CCCCGAATTTCCGTGGTATTC
59.055
52.381
0.00
6.49
0.00
1.75
2246
2441
0.181824
CCCCCGAATTTCCGTGGTAT
59.818
55.000
0.00
0.00
0.00
2.73
2250
2447
0.606944
TTGTCCCCCGAATTTCCGTG
60.607
55.000
0.00
0.00
0.00
4.94
2261
2458
1.376812
CCGCACTTACTTGTCCCCC
60.377
63.158
0.00
0.00
0.00
5.40
2262
2459
1.376812
CCCGCACTTACTTGTCCCC
60.377
63.158
0.00
0.00
0.00
4.81
2266
2464
2.033602
GCCCCCGCACTTACTTGT
59.966
61.111
0.00
0.00
34.03
3.16
2285
2483
0.747283
GAGGCTTGGCAGGTGATGAG
60.747
60.000
0.00
0.00
0.00
2.90
2289
2487
4.704833
GCGAGGCTTGGCAGGTGA
62.705
66.667
3.44
0.00
0.00
4.02
2303
2501
4.077184
AAATCGACCAGGCGGCGA
62.077
61.111
12.98
13.37
42.35
5.54
2304
2502
3.864686
CAAATCGACCAGGCGGCG
61.865
66.667
0.51
0.51
34.57
6.46
2309
2507
2.464459
GCGAGCCAAATCGACCAGG
61.464
63.158
0.00
0.00
45.56
4.45
2311
2509
2.572095
ATCGCGAGCCAAATCGACCA
62.572
55.000
16.66
0.00
45.56
4.02
2313
2511
0.373716
AAATCGCGAGCCAAATCGAC
59.626
50.000
16.66
0.00
45.56
4.20
2327
2525
6.725246
AGGGATTAAATTACTTCGCAAATCG
58.275
36.000
0.00
0.00
40.15
3.34
2332
2530
5.492895
TGTGAGGGATTAAATTACTTCGCA
58.507
37.500
0.00
0.00
0.00
5.10
2333
2531
6.431198
TTGTGAGGGATTAAATTACTTCGC
57.569
37.500
0.00
0.00
0.00
4.70
2350
2548
4.630894
TGTTTTACTGTGCCTTTGTGAG
57.369
40.909
0.00
0.00
0.00
3.51
2351
2549
4.702612
TCTTGTTTTACTGTGCCTTTGTGA
59.297
37.500
0.00
0.00
0.00
3.58
2352
2550
4.992688
TCTTGTTTTACTGTGCCTTTGTG
58.007
39.130
0.00
0.00
0.00
3.33
2353
2551
5.047660
TGTTCTTGTTTTACTGTGCCTTTGT
60.048
36.000
0.00
0.00
0.00
2.83
2355
2553
5.652994
TGTTCTTGTTTTACTGTGCCTTT
57.347
34.783
0.00
0.00
0.00
3.11
2357
2555
4.278419
GGATGTTCTTGTTTTACTGTGCCT
59.722
41.667
0.00
0.00
0.00
4.75
2362
2560
4.154195
CCGAGGGATGTTCTTGTTTTACTG
59.846
45.833
0.00
0.00
0.00
2.74
2363
2561
4.041198
TCCGAGGGATGTTCTTGTTTTACT
59.959
41.667
0.00
0.00
0.00
2.24
2370
2568
3.334583
TCTTTCCGAGGGATGTTCTTG
57.665
47.619
0.00
0.00
0.00
3.02
2373
2571
5.880887
ACTTAAATCTTTCCGAGGGATGTTC
59.119
40.000
0.00
0.00
0.00
3.18
2374
2572
5.816682
ACTTAAATCTTTCCGAGGGATGTT
58.183
37.500
0.00
0.00
0.00
2.71
2375
2573
5.437191
ACTTAAATCTTTCCGAGGGATGT
57.563
39.130
0.00
0.00
0.00
3.06
2376
2574
6.374333
TGAAACTTAAATCTTTCCGAGGGATG
59.626
38.462
0.00
0.00
0.00
3.51
2377
2575
6.481643
TGAAACTTAAATCTTTCCGAGGGAT
58.518
36.000
0.00
0.00
0.00
3.85
2380
2578
6.966021
TGTTGAAACTTAAATCTTTCCGAGG
58.034
36.000
0.00
0.00
0.00
4.63
2427
2625
5.606348
ACTTGTTGAAACTGGGCATTTAA
57.394
34.783
0.00
0.00
0.00
1.52
2478
2678
6.961359
TTATTTTGTGTCTATGACCGACAG
57.039
37.500
0.00
0.00
41.62
3.51
2482
2682
9.787532
AAATCAATTATTTTGTGTCTATGACCG
57.212
29.630
0.00
0.00
33.91
4.79
2501
2705
4.253685
ACGAGTGACCGATCAAAATCAAT
58.746
39.130
0.00
0.00
36.31
2.57
2510
2714
4.612932
AACTTAGTACGAGTGACCGATC
57.387
45.455
5.83
0.00
0.00
3.69
2515
2719
7.168637
TCAATGTTGAAACTTAGTACGAGTGAC
59.831
37.037
5.83
4.68
33.55
3.67
2517
2721
7.402811
TCAATGTTGAAACTTAGTACGAGTG
57.597
36.000
5.83
0.00
33.55
3.51
2598
2804
0.582005
GTGTTTCTCGTGACCAGCAC
59.418
55.000
0.00
0.00
44.21
4.40
2599
2805
0.176910
TGTGTTTCTCGTGACCAGCA
59.823
50.000
0.00
0.00
0.00
4.41
2601
2807
5.408299
TCATAATTGTGTTTCTCGTGACCAG
59.592
40.000
1.86
0.00
0.00
4.00
2657
2863
7.383102
TCCAATTTGCAAAGTTCTAGATCTC
57.617
36.000
18.19
0.00
0.00
2.75
2658
2864
7.576477
GCTTCCAATTTGCAAAGTTCTAGATCT
60.576
37.037
18.19
0.00
0.00
2.75
2662
2868
4.925646
GGCTTCCAATTTGCAAAGTTCTAG
59.074
41.667
18.19
11.61
0.00
2.43
2673
2879
6.862608
GGCTTTTAATTTTGGCTTCCAATTTG
59.137
34.615
0.00
0.00
43.55
2.32
2678
2884
3.556004
CCGGCTTTTAATTTTGGCTTCCA
60.556
43.478
0.00
0.00
0.00
3.53
2691
2897
0.891904
GTCCCTTGTGCCGGCTTTTA
60.892
55.000
29.70
3.37
0.00
1.52
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.