Multiple sequence alignment - TraesCS2B01G498600
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
TraesCS2B01G498600
chr2B
100.000
4710
0
0
1
4710
695105864
695110573
0.000000e+00
8698.0
1
TraesCS2B01G498600
chr2B
86.905
1512
145
28
988
2482
695379990
695378515
0.000000e+00
1646.0
2
TraesCS2B01G498600
chr2B
84.211
1615
194
34
3086
4665
695170414
695168826
0.000000e+00
1513.0
3
TraesCS2B01G498600
chr2B
84.343
1354
156
24
996
2317
695172117
695170788
0.000000e+00
1275.0
4
TraesCS2B01G498600
chr2B
81.420
1394
199
29
996
2341
695508139
695509520
0.000000e+00
1085.0
5
TraesCS2B01G498600
chr2B
80.000
1440
215
41
988
2378
695439916
695438501
0.000000e+00
996.0
6
TraesCS2B01G498600
chr2B
88.762
614
45
10
2579
3170
695378393
695377782
0.000000e+00
730.0
7
TraesCS2B01G498600
chr2B
81.156
865
139
13
988
1833
695414334
695413475
0.000000e+00
673.0
8
TraesCS2B01G498600
chr2B
80.714
700
77
27
3073
3728
695410486
695409801
4.230000e-135
492.0
9
TraesCS2B01G498600
chr2B
86.375
389
35
4
3174
3550
695377747
695377365
4.390000e-110
409.0
10
TraesCS2B01G498600
chr2B
83.333
150
14
5
2579
2721
695411640
695411495
1.380000e-25
128.0
11
TraesCS2B01G498600
chr2B
91.566
83
5
2
2501
2583
695378524
695378444
3.850000e-21
113.0
12
TraesCS2B01G498600
chr2D
92.854
2421
112
24
12
2414
577582880
577580503
0.000000e+00
3456.0
13
TraesCS2B01G498600
chr2D
89.805
2668
177
53
1150
3785
577440816
577443420
0.000000e+00
3332.0
14
TraesCS2B01G498600
chr2D
91.139
2178
116
30
2526
4664
577580507
577578368
0.000000e+00
2881.0
15
TraesCS2B01G498600
chr2D
84.693
1581
181
31
3118
4665
577537952
577539504
0.000000e+00
1522.0
16
TraesCS2B01G498600
chr2D
86.169
1381
133
31
988
2337
577802853
577801500
0.000000e+00
1439.0
17
TraesCS2B01G498600
chr2D
85.417
1344
148
19
996
2314
577536221
577537541
0.000000e+00
1352.0
18
TraesCS2B01G498600
chr2D
84.846
1267
109
34
2486
3705
577801390
577800160
0.000000e+00
1199.0
19
TraesCS2B01G498600
chr2D
78.014
705
89
31
3118
3791
578325205
578325874
2.660000e-102
383.0
20
TraesCS2B01G498600
chr2D
81.186
489
51
14
3290
3747
577827648
577827170
5.800000e-94
355.0
21
TraesCS2B01G498600
chr2D
81.443
291
36
12
2439
2724
578308833
578309110
6.130000e-54
222.0
22
TraesCS2B01G498600
chr2D
85.922
206
10
10
943
1134
577440655
577440855
7.990000e-48
202.0
23
TraesCS2B01G498600
chr2A
85.154
3085
251
92
781
3785
715951423
715948466
0.000000e+00
2968.0
24
TraesCS2B01G498600
chr2A
92.380
2021
121
10
1
2015
715879657
715881650
0.000000e+00
2848.0
25
TraesCS2B01G498600
chr2A
88.962
1667
123
24
3017
4664
715890391
715892015
0.000000e+00
2002.0
26
TraesCS2B01G498600
chr2A
96.373
965
29
3
2056
3019
715887434
715888393
0.000000e+00
1583.0
27
TraesCS2B01G498600
chr2A
84.383
1620
185
38
3086
4664
715916302
715914710
0.000000e+00
1528.0
28
TraesCS2B01G498600
chr2A
85.210
1359
139
25
996
2317
715917977
715916644
0.000000e+00
1339.0
29
TraesCS2B01G498600
chr2A
96.029
680
19
3
2056
2735
715881656
715882327
0.000000e+00
1099.0
30
TraesCS2B01G498600
chrUn
83.333
150
14
5
2579
2721
476501721
476501866
1.380000e-25
128.0
31
TraesCS2B01G498600
chrUn
94.000
50
2
1
2392
2441
26664185
26664137
1.820000e-09
75.0
32
TraesCS2B01G498600
chr3D
97.727
44
1
0
2397
2440
542823564
542823521
5.050000e-10
76.8
33
TraesCS2B01G498600
chr1D
97.674
43
1
0
2397
2439
435345183
435345141
1.820000e-09
75.0
34
TraesCS2B01G498600
chr6A
90.741
54
4
1
2388
2441
539230010
539229958
2.350000e-08
71.3
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
TraesCS2B01G498600
chr2B
695105864
695110573
4709
False
8698.0
8698
100.000000
1
4710
1
chr2B.!!$F1
4709
1
TraesCS2B01G498600
chr2B
695168826
695172117
3291
True
1394.0
1513
84.277000
996
4665
2
chr2B.!!$R2
3669
2
TraesCS2B01G498600
chr2B
695508139
695509520
1381
False
1085.0
1085
81.420000
996
2341
1
chr2B.!!$F2
1345
3
TraesCS2B01G498600
chr2B
695438501
695439916
1415
True
996.0
996
80.000000
988
2378
1
chr2B.!!$R1
1390
4
TraesCS2B01G498600
chr2B
695377365
695379990
2625
True
724.5
1646
88.402000
988
3550
4
chr2B.!!$R3
2562
5
TraesCS2B01G498600
chr2B
695409801
695414334
4533
True
431.0
673
81.734333
988
3728
3
chr2B.!!$R4
2740
6
TraesCS2B01G498600
chr2D
577578368
577582880
4512
True
3168.5
3456
91.996500
12
4664
2
chr2D.!!$R2
4652
7
TraesCS2B01G498600
chr2D
577440655
577443420
2765
False
1767.0
3332
87.863500
943
3785
2
chr2D.!!$F3
2842
8
TraesCS2B01G498600
chr2D
577536221
577539504
3283
False
1437.0
1522
85.055000
996
4665
2
chr2D.!!$F4
3669
9
TraesCS2B01G498600
chr2D
577800160
577802853
2693
True
1319.0
1439
85.507500
988
3705
2
chr2D.!!$R3
2717
10
TraesCS2B01G498600
chr2D
578325205
578325874
669
False
383.0
383
78.014000
3118
3791
1
chr2D.!!$F2
673
11
TraesCS2B01G498600
chr2A
715948466
715951423
2957
True
2968.0
2968
85.154000
781
3785
1
chr2A.!!$R1
3004
12
TraesCS2B01G498600
chr2A
715879657
715882327
2670
False
1973.5
2848
94.204500
1
2735
2
chr2A.!!$F1
2734
13
TraesCS2B01G498600
chr2A
715887434
715892015
4581
False
1792.5
2002
92.667500
2056
4664
2
chr2A.!!$F2
2608
14
TraesCS2B01G498600
chr2A
715914710
715917977
3267
True
1433.5
1528
84.796500
996
4664
2
chr2A.!!$R2
3668
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
260
261
0.107017
CATCTTGTCGGGCCTCCATT
60.107
55.000
0.84
0.0
0.00
3.16
F
962
1014
0.108424
CCTCACTCCTCTTCCAAGCG
60.108
60.000
0.00
0.0
0.00
4.68
F
964
1016
0.318441
TCACTCCTCTTCCAAGCGTG
59.682
55.000
0.00
0.0
0.00
5.34
F
1408
1535
1.079612
GGAGTTCGGTACAACCCCG
60.080
63.158
0.00
0.0
46.83
5.73
F
1690
1817
1.523154
TTGGCAAACCGAGTCCATGC
61.523
55.000
0.00
0.0
39.70
4.06
F
2445
3774
2.889678
GGGACCGAGGTTGTATAGTAGG
59.110
54.545
0.00
0.0
0.00
3.18
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2053
3318
0.328258
CCACTCCGGGGATTTGAAGT
59.672
55.000
9.33
0.0
0.00
3.01
R
2445
3774
2.863401
AAACGGAAAGTTGAGGTTGC
57.137
45.000
0.00
0.0
43.37
4.17
R
2923
4597
3.890756
GTGCCATTGGGATAATCATGTGA
59.109
43.478
4.53
0.0
35.59
3.58
R
3186
7132
2.218603
ACACCACTGCCTTCTAAAACG
58.781
47.619
0.00
0.0
0.00
3.60
R
3361
7314
3.408634
ACCAACATTTCCAGTAACCTCG
58.591
45.455
0.00
0.0
0.00
4.63
R
4099
8135
0.399454
AGATGGCCGAAGCATAGCAT
59.601
50.000
0.00
0.0
42.56
3.79
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
30
31
1.675310
CACCCAGAAGCGGCATTCA
60.675
57.895
1.45
0.00
0.00
2.57
92
93
1.843206
ACAACAAAGGGCCACCAAATT
59.157
42.857
6.18
0.00
40.13
1.82
128
129
1.300620
CGGCGAACACCTCTCACAA
60.301
57.895
0.00
0.00
0.00
3.33
141
142
1.021202
CTCACAACGGAAACCTGCAA
58.979
50.000
0.00
0.00
0.00
4.08
143
144
0.453793
CACAACGGAAACCTGCAACA
59.546
50.000
0.00
0.00
0.00
3.33
214
215
3.593328
TGGATCAAGAAAGGGGAACTCAT
59.407
43.478
0.00
0.00
0.00
2.90
217
218
5.131142
GGATCAAGAAAGGGGAACTCATCTA
59.869
44.000
0.00
0.00
0.00
1.98
228
229
5.010933
GGGAACTCATCTATCGACTGGATA
58.989
45.833
0.00
0.00
36.55
2.59
256
257
1.153349
GTCCATCTTGTCGGGCCTC
60.153
63.158
0.84
0.00
0.00
4.70
260
261
0.107017
CATCTTGTCGGGCCTCCATT
60.107
55.000
0.84
0.00
0.00
3.16
266
267
3.781307
CGGGCCTCCATTCCGTCA
61.781
66.667
0.84
0.00
39.04
4.35
319
320
2.580867
CTTCTTCGCCTCGCCTCG
60.581
66.667
0.00
0.00
0.00
4.63
320
321
3.343788
CTTCTTCGCCTCGCCTCGT
62.344
63.158
0.00
0.00
0.00
4.18
363
364
2.742372
GACGCACGAAGCCCACAT
60.742
61.111
0.00
0.00
41.38
3.21
388
389
1.802337
CGAGACGTCCTGGTCCACAA
61.802
60.000
13.01
0.00
37.66
3.33
401
402
3.006752
TGGTCCACAATTCAGGAAAATGC
59.993
43.478
0.00
0.00
35.29
3.56
406
407
2.264813
CAATTCAGGAAAATGCTGCGG
58.735
47.619
0.00
0.00
35.65
5.69
420
421
1.985447
CTGCGGCGACCTACTAACGA
61.985
60.000
12.98
0.00
0.00
3.85
452
454
1.745087
CGCATATGAATATGGCCCACC
59.255
52.381
6.97
0.00
40.31
4.61
493
497
1.933853
GGTCATGGACGCACTGTATTC
59.066
52.381
0.00
0.00
32.65
1.75
497
501
3.195610
TCATGGACGCACTGTATTCTCTT
59.804
43.478
0.00
0.00
0.00
2.85
537
541
0.529992
TATCGAGCTCTGACGCGAGA
60.530
55.000
15.93
4.96
44.87
4.04
538
542
1.771073
ATCGAGCTCTGACGCGAGAG
61.771
60.000
15.93
17.19
44.87
3.20
539
543
2.745785
CGAGCTCTGACGCGAGAGT
61.746
63.158
21.63
11.45
41.50
3.24
543
547
1.719117
CTCTGACGCGAGAGTCCTC
59.281
63.158
15.93
0.00
40.26
3.71
546
550
0.523966
CTGACGCGAGAGTCCTCTTT
59.476
55.000
15.93
0.00
40.61
2.52
547
551
0.959553
TGACGCGAGAGTCCTCTTTT
59.040
50.000
15.93
0.00
40.61
2.27
548
552
1.068472
TGACGCGAGAGTCCTCTTTTC
60.068
52.381
15.93
0.00
40.61
2.29
549
553
1.200484
GACGCGAGAGTCCTCTTTTCT
59.800
52.381
15.93
0.00
40.61
2.52
577
581
2.070783
CAAAGCAACAATGGATGCACC
58.929
47.619
14.09
0.00
44.50
5.01
596
600
2.455674
CGGATTTCGGGCTCATATCA
57.544
50.000
0.00
0.00
34.75
2.15
732
742
6.985117
AGCAATCAGATTTGAACAAGCTTAA
58.015
32.000
0.00
0.00
36.78
1.85
955
1007
1.713647
TCCTCAGTCCTCACTCCTCTT
59.286
52.381
0.00
0.00
0.00
2.85
956
1008
2.099405
CCTCAGTCCTCACTCCTCTTC
58.901
57.143
0.00
0.00
0.00
2.87
957
1009
2.099405
CTCAGTCCTCACTCCTCTTCC
58.901
57.143
0.00
0.00
0.00
3.46
958
1010
1.429299
TCAGTCCTCACTCCTCTTCCA
59.571
52.381
0.00
0.00
0.00
3.53
959
1011
2.158310
TCAGTCCTCACTCCTCTTCCAA
60.158
50.000
0.00
0.00
0.00
3.53
960
1012
2.233431
CAGTCCTCACTCCTCTTCCAAG
59.767
54.545
0.00
0.00
0.00
3.61
961
1013
1.066502
GTCCTCACTCCTCTTCCAAGC
60.067
57.143
0.00
0.00
0.00
4.01
962
1014
0.108424
CCTCACTCCTCTTCCAAGCG
60.108
60.000
0.00
0.00
0.00
4.68
963
1015
0.605589
CTCACTCCTCTTCCAAGCGT
59.394
55.000
0.00
0.00
0.00
5.07
964
1016
0.318441
TCACTCCTCTTCCAAGCGTG
59.682
55.000
0.00
0.00
0.00
5.34
966
1018
1.743252
CTCCTCTTCCAAGCGTGGC
60.743
63.158
14.54
0.00
45.54
5.01
967
1019
2.747855
CCTCTTCCAAGCGTGGCC
60.748
66.667
14.54
0.00
45.54
5.36
968
1020
2.032528
CTCTTCCAAGCGTGGCCA
59.967
61.111
14.54
0.00
45.54
5.36
969
1021
2.032528
TCTTCCAAGCGTGGCCAG
59.967
61.111
14.54
12.04
45.54
4.85
970
1022
3.058160
CTTCCAAGCGTGGCCAGG
61.058
66.667
21.22
21.22
45.54
4.45
971
1023
3.850098
CTTCCAAGCGTGGCCAGGT
62.850
63.158
25.40
13.46
45.54
4.00
972
1024
3.842925
TTCCAAGCGTGGCCAGGTC
62.843
63.158
25.40
17.47
45.54
3.85
973
1025
4.335647
CCAAGCGTGGCCAGGTCT
62.336
66.667
25.40
19.28
38.35
3.85
974
1026
2.743928
CAAGCGTGGCCAGGTCTC
60.744
66.667
25.40
10.11
0.00
3.36
975
1027
2.925170
AAGCGTGGCCAGGTCTCT
60.925
61.111
25.40
12.24
0.00
3.10
1339
1454
2.425578
GGTCGATTTCTCCGATCCTC
57.574
55.000
0.00
0.00
38.38
3.71
1408
1535
1.079612
GGAGTTCGGTACAACCCCG
60.080
63.158
0.00
0.00
46.83
5.73
1670
1797
3.199071
ACCGTGCTGGATTGGTTTATCTA
59.801
43.478
2.38
0.00
42.00
1.98
1690
1817
1.523154
TTGGCAAACCGAGTCCATGC
61.523
55.000
0.00
0.00
39.70
4.06
1731
1858
4.855531
AGTACATTTTCGTGCTCAAAACC
58.144
39.130
0.00
0.00
0.00
3.27
1735
1862
3.701532
TTTTCGTGCTCAAAACCGATT
57.298
38.095
0.00
0.00
0.00
3.34
2007
3245
5.578005
TGACGGTTTTCAATGGTTTTGTA
57.422
34.783
0.00
0.00
0.00
2.41
2047
3312
5.125417
CCATGGAAAAATTACGTGGATCAGT
59.875
40.000
5.56
0.00
42.54
3.41
2048
3313
6.350110
CCATGGAAAAATTACGTGGATCAGTT
60.350
38.462
5.56
0.00
42.54
3.16
2049
3314
6.249035
TGGAAAAATTACGTGGATCAGTTC
57.751
37.500
0.00
0.00
0.00
3.01
2050
3315
5.765677
TGGAAAAATTACGTGGATCAGTTCA
59.234
36.000
0.00
0.00
0.00
3.18
2051
3316
6.263392
TGGAAAAATTACGTGGATCAGTTCAA
59.737
34.615
0.00
0.00
0.00
2.69
2052
3317
7.142680
GGAAAAATTACGTGGATCAGTTCAAA
58.857
34.615
0.00
0.00
0.00
2.69
2053
3318
7.650104
GGAAAAATTACGTGGATCAGTTCAAAA
59.350
33.333
0.00
0.00
0.00
2.44
2054
3319
7.924103
AAAATTACGTGGATCAGTTCAAAAC
57.076
32.000
0.00
0.00
0.00
2.43
2195
3460
7.176865
CCTTCTATGGAATACATCTCGGTAAGA
59.823
40.741
0.00
0.00
41.03
2.10
2445
3774
2.889678
GGGACCGAGGTTGTATAGTAGG
59.110
54.545
0.00
0.00
0.00
3.18
2570
3905
9.499479
AGATATAAAAGCTCCACATACAGAATG
57.501
33.333
0.00
0.00
46.00
2.67
2811
4478
7.293018
ACGTCGGTTTCAAATTTATGTCTTAC
58.707
34.615
0.00
0.00
0.00
2.34
3258
7204
9.047371
GTCTCCCTAAAAGCTAGATAAAATGAC
57.953
37.037
0.00
0.00
0.00
3.06
3361
7314
4.335416
TGTCACAGGAGGATTCAAAATCC
58.665
43.478
10.16
10.16
38.47
3.01
3386
7351
6.195600
AGGTTACTGGAAATGTTGGTCTTA
57.804
37.500
0.00
0.00
0.00
2.10
3400
7365
9.574516
AATGTTGGTCTTAAGAGTACAGAAAAT
57.425
29.630
5.12
0.00
0.00
1.82
3425
7390
8.213518
TGATTCATCAGTCCTTATAAAAGCAC
57.786
34.615
0.00
0.00
32.11
4.40
3511
7476
6.483307
CCTTCTCACTTTGTATTGACACTGAA
59.517
38.462
0.00
0.00
34.48
3.02
3791
7815
4.950434
TGTGTGATGATGTTATGTGCTG
57.050
40.909
0.00
0.00
0.00
4.41
3962
7995
7.359598
GCGAGCGAGTTTGAAGATCATATTAAT
60.360
37.037
0.00
0.00
0.00
1.40
3975
8008
7.224297
AGATCATATTAATTAAGGCGTGTGGT
58.776
34.615
3.94
0.00
0.00
4.16
3978
8011
6.824196
TCATATTAATTAAGGCGTGTGGTCAA
59.176
34.615
3.94
0.00
0.00
3.18
4046
8079
4.458989
TCCTTTCACCATGATGCTTGTAAC
59.541
41.667
0.00
0.00
0.00
2.50
4051
8084
3.374988
CACCATGATGCTTGTAACGTGAT
59.625
43.478
0.00
0.00
0.00
3.06
4053
8086
5.064579
CACCATGATGCTTGTAACGTGATAA
59.935
40.000
0.00
0.00
0.00
1.75
4055
8088
5.501715
CATGATGCTTGTAACGTGATAACC
58.498
41.667
0.00
0.00
0.00
2.85
4056
8089
3.615056
TGATGCTTGTAACGTGATAACCG
59.385
43.478
0.00
0.00
0.00
4.44
4057
8090
1.727880
TGCTTGTAACGTGATAACCGC
59.272
47.619
0.00
0.00
0.00
5.68
4058
8091
1.997606
GCTTGTAACGTGATAACCGCT
59.002
47.619
0.00
0.00
0.00
5.52
4063
8096
0.246635
AACGTGATAACCGCTCTGCT
59.753
50.000
0.00
0.00
0.00
4.24
4099
8135
3.534357
TGACCAAAAGATTAGGGCCAA
57.466
42.857
6.18
0.00
0.00
4.52
4135
8171
4.095483
GCCATCTGATCGTTGACAAAGATT
59.905
41.667
16.25
0.03
0.00
2.40
4141
8177
0.591170
CGTTGACAAAGATTGGCCGT
59.409
50.000
0.00
0.00
38.13
5.68
4158
8194
1.214062
GTGTCGAGAGCCACTGGAG
59.786
63.158
0.00
0.00
34.23
3.86
4174
8210
1.137614
GAGCAGTGTGATCGAGCGA
59.862
57.895
0.00
0.00
0.00
4.93
4180
8218
2.579787
GTGATCGAGCGACCACCG
60.580
66.667
6.10
0.00
32.63
4.94
4198
8236
1.651240
CGGCTAGCTGCTGCAACATT
61.651
55.000
18.42
0.00
41.61
2.71
4207
8245
0.385029
GCTGCAACATTGGTGACACA
59.615
50.000
5.72
0.00
42.67
3.72
4272
8311
0.037447
TCGGTCATGTTGCAATCCCA
59.963
50.000
0.59
0.00
0.00
4.37
4288
8345
3.121030
CAAGCCGAACGAGCAGGG
61.121
66.667
0.00
0.00
0.00
4.45
4289
8346
3.626924
AAGCCGAACGAGCAGGGT
61.627
61.111
0.00
0.00
37.35
4.34
4290
8347
3.883744
AAGCCGAACGAGCAGGGTG
62.884
63.158
0.00
0.00
35.74
4.61
4291
8348
4.681978
GCCGAACGAGCAGGGTGT
62.682
66.667
0.00
0.00
0.00
4.16
4292
8349
2.030562
CCGAACGAGCAGGGTGTT
59.969
61.111
0.00
0.00
0.00
3.32
4293
8350
1.290955
CCGAACGAGCAGGGTGTTA
59.709
57.895
0.00
0.00
0.00
2.41
4294
8351
0.736325
CCGAACGAGCAGGGTGTTAG
60.736
60.000
0.00
0.00
0.00
2.34
4295
8352
1.352156
CGAACGAGCAGGGTGTTAGC
61.352
60.000
0.00
0.00
0.00
3.09
4296
8353
1.003718
AACGAGCAGGGTGTTAGCC
60.004
57.895
0.00
0.00
35.59
3.93
4297
8354
2.509336
CGAGCAGGGTGTTAGCCG
60.509
66.667
0.00
0.00
41.56
5.52
4298
8355
2.820037
GAGCAGGGTGTTAGCCGC
60.820
66.667
0.00
0.00
41.56
6.53
4299
8356
4.760047
AGCAGGGTGTTAGCCGCG
62.760
66.667
0.00
0.00
41.56
6.46
4300
8357
4.752879
GCAGGGTGTTAGCCGCGA
62.753
66.667
8.23
0.00
41.56
5.87
4301
8358
2.509336
CAGGGTGTTAGCCGCGAG
60.509
66.667
8.23
0.00
41.56
5.03
4302
8359
4.452733
AGGGTGTTAGCCGCGAGC
62.453
66.667
8.23
9.98
41.56
5.03
4514
8580
4.319911
GCAACATTGAGTAGTTTGCGGTAA
60.320
41.667
0.00
0.00
0.00
2.85
4575
8641
1.069227
GCTGGGTGCTTTGTAGAAACG
60.069
52.381
0.00
0.00
38.95
3.60
4576
8642
0.948678
TGGGTGCTTTGTAGAAACGC
59.051
50.000
0.00
1.54
0.00
4.84
4582
8648
4.403453
GTGCTTTGTAGAAACGCAATAGG
58.597
43.478
9.79
0.00
31.42
2.57
4598
8667
3.611766
ATAGGCATACGATGTTAGGGC
57.388
47.619
0.00
0.00
0.00
5.19
4600
8669
1.699634
AGGCATACGATGTTAGGGCAT
59.300
47.619
0.00
0.00
0.00
4.40
4601
8670
2.076863
GGCATACGATGTTAGGGCATC
58.923
52.381
0.00
0.00
41.21
3.91
4605
8674
4.994852
GCATACGATGTTAGGGCATCTTTA
59.005
41.667
0.00
0.00
42.14
1.85
4606
8675
5.120830
GCATACGATGTTAGGGCATCTTTAG
59.879
44.000
0.00
0.00
42.14
1.85
4665
8744
9.468532
TGAGAGATATATTGAATCGAGTTGTTG
57.531
33.333
0.00
0.00
0.00
3.33
4666
8745
9.684448
GAGAGATATATTGAATCGAGTTGTTGA
57.316
33.333
0.00
0.00
0.00
3.18
4672
8751
6.668541
ATTGAATCGAGTTGTTGATAGGTG
57.331
37.500
0.00
0.00
0.00
4.00
4673
8752
4.503910
TGAATCGAGTTGTTGATAGGTGG
58.496
43.478
0.00
0.00
0.00
4.61
4674
8753
4.221924
TGAATCGAGTTGTTGATAGGTGGA
59.778
41.667
0.00
0.00
0.00
4.02
4675
8754
3.868757
TCGAGTTGTTGATAGGTGGAG
57.131
47.619
0.00
0.00
0.00
3.86
4676
8755
3.427573
TCGAGTTGTTGATAGGTGGAGA
58.572
45.455
0.00
0.00
0.00
3.71
4677
8756
3.192844
TCGAGTTGTTGATAGGTGGAGAC
59.807
47.826
0.00
0.00
0.00
3.36
4678
8757
3.676324
CGAGTTGTTGATAGGTGGAGACC
60.676
52.174
0.00
0.00
43.52
3.85
4679
8758
2.572104
AGTTGTTGATAGGTGGAGACCC
59.428
50.000
0.00
0.00
44.40
4.46
4680
8759
2.304761
GTTGTTGATAGGTGGAGACCCA
59.695
50.000
0.00
0.00
44.40
4.51
4681
8760
2.845659
TGTTGATAGGTGGAGACCCAT
58.154
47.619
0.00
0.00
45.68
4.00
4682
8761
4.002256
TGTTGATAGGTGGAGACCCATA
57.998
45.455
0.00
0.00
45.68
2.74
4683
8762
3.967326
TGTTGATAGGTGGAGACCCATAG
59.033
47.826
0.00
0.00
45.68
2.23
4684
8763
4.223953
GTTGATAGGTGGAGACCCATAGA
58.776
47.826
0.00
0.00
45.68
1.98
4685
8764
4.552883
TGATAGGTGGAGACCCATAGAA
57.447
45.455
0.00
0.00
45.68
2.10
4686
8765
4.223953
TGATAGGTGGAGACCCATAGAAC
58.776
47.826
0.00
0.00
45.68
3.01
4687
8766
1.486211
AGGTGGAGACCCATAGAACG
58.514
55.000
0.00
0.00
45.68
3.95
4688
8767
1.006758
AGGTGGAGACCCATAGAACGA
59.993
52.381
0.00
0.00
45.68
3.85
4689
8768
1.409427
GGTGGAGACCCATAGAACGAG
59.591
57.143
0.00
0.00
45.68
4.18
4690
8769
2.100989
GTGGAGACCCATAGAACGAGT
58.899
52.381
0.00
0.00
45.68
4.18
4691
8770
2.496470
GTGGAGACCCATAGAACGAGTT
59.504
50.000
0.00
0.00
45.68
3.01
4692
8771
2.758979
TGGAGACCCATAGAACGAGTTC
59.241
50.000
7.83
7.83
37.58
3.01
4693
8772
2.758979
GGAGACCCATAGAACGAGTTCA
59.241
50.000
17.00
5.00
41.84
3.18
4694
8773
3.429135
GGAGACCCATAGAACGAGTTCAC
60.429
52.174
17.00
0.00
41.84
3.18
4695
8774
2.163815
AGACCCATAGAACGAGTTCACG
59.836
50.000
17.00
5.74
41.84
4.35
4696
8775
1.278238
CCCATAGAACGAGTTCACGC
58.722
55.000
17.00
0.00
41.84
5.34
4697
8776
1.278238
CCATAGAACGAGTTCACGCC
58.722
55.000
17.00
0.00
41.84
5.68
4698
8777
1.135083
CCATAGAACGAGTTCACGCCT
60.135
52.381
17.00
0.16
41.84
5.52
4699
8778
1.920574
CATAGAACGAGTTCACGCCTG
59.079
52.381
17.00
4.46
41.84
4.85
4700
8779
1.241165
TAGAACGAGTTCACGCCTGA
58.759
50.000
17.00
0.00
41.84
3.86
4701
8780
0.039074
AGAACGAGTTCACGCCTGAG
60.039
55.000
17.00
0.00
41.84
3.35
4702
8781
1.006102
AACGAGTTCACGCCTGAGG
60.006
57.895
0.00
0.00
36.70
3.86
4703
8782
2.125912
CGAGTTCACGCCTGAGGG
60.126
66.667
0.00
0.00
0.00
4.30
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
10
11
3.866379
AATGCCGCTTCTGGGTGCA
62.866
57.895
0.00
0.00
37.00
4.57
30
31
0.179124
GCAGAAGCGATCGAGGAGTT
60.179
55.000
21.57
2.98
0.00
3.01
74
75
2.507471
TCAAATTTGGTGGCCCTTTGTT
59.493
40.909
17.90
0.00
0.00
2.83
92
93
2.477972
CGACAGCCTCGAGCACTCAA
62.478
60.000
6.99
0.00
46.14
3.02
128
129
2.224426
TGAGTATGTTGCAGGTTTCCGT
60.224
45.455
0.00
0.00
0.00
4.69
217
218
5.184864
GGACATCTTGATCTATCCAGTCGAT
59.815
44.000
0.00
0.00
34.73
3.59
246
247
3.781307
CGGAATGGAGGCCCGACA
61.781
66.667
0.00
0.00
45.58
4.35
248
249
3.467226
GACGGAATGGAGGCCCGA
61.467
66.667
0.00
0.00
45.58
5.14
251
252
2.514824
GCTGACGGAATGGAGGCC
60.515
66.667
0.00
0.00
0.00
5.19
256
257
1.503542
GCAACTGCTGACGGAATGG
59.496
57.895
0.00
0.00
38.21
3.16
277
278
0.099791
CGGCAACAGGTTTGTCGTTT
59.900
50.000
2.92
0.00
41.95
3.60
278
279
1.725066
CGGCAACAGGTTTGTCGTT
59.275
52.632
2.92
0.00
41.95
3.85
319
320
3.279875
GAATGGGGCGGCGATGAC
61.280
66.667
12.98
0.00
0.00
3.06
320
321
3.791586
TGAATGGGGCGGCGATGA
61.792
61.111
12.98
0.00
0.00
2.92
363
364
2.335011
CAGGACGTCTCGTGTGCA
59.665
61.111
16.46
0.00
41.37
4.57
388
389
0.174162
GCCGCAGCATTTTCCTGAAT
59.826
50.000
0.00
0.00
39.53
2.57
401
402
1.585521
CGTTAGTAGGTCGCCGCAG
60.586
63.158
0.00
0.00
0.00
5.18
406
407
0.585029
CGTCGTCGTTAGTAGGTCGC
60.585
60.000
0.00
0.00
0.00
5.19
477
481
3.895232
AAGAGAATACAGTGCGTCCAT
57.105
42.857
0.00
0.00
0.00
3.41
493
497
7.206687
AGCGAGAAGAATAAGGATACAAAGAG
58.793
38.462
0.00
0.00
41.41
2.85
497
501
7.174426
TCGATAGCGAGAAGAATAAGGATACAA
59.826
37.037
0.00
0.00
42.51
2.41
537
541
7.057264
GCTTTGGGATATTAGAAAAGAGGACT
58.943
38.462
0.00
0.00
31.01
3.85
538
542
6.828785
TGCTTTGGGATATTAGAAAAGAGGAC
59.171
38.462
0.00
0.00
31.01
3.85
539
543
6.969043
TGCTTTGGGATATTAGAAAAGAGGA
58.031
36.000
0.00
0.00
31.01
3.71
543
547
9.090692
CATTGTTGCTTTGGGATATTAGAAAAG
57.909
33.333
0.00
0.00
0.00
2.27
546
550
6.894654
TCCATTGTTGCTTTGGGATATTAGAA
59.105
34.615
0.00
0.00
0.00
2.10
547
551
6.430864
TCCATTGTTGCTTTGGGATATTAGA
58.569
36.000
0.00
0.00
0.00
2.10
548
552
6.713762
TCCATTGTTGCTTTGGGATATTAG
57.286
37.500
0.00
0.00
0.00
1.73
549
553
6.462768
GCATCCATTGTTGCTTTGGGATATTA
60.463
38.462
0.00
0.00
34.91
0.98
577
581
2.029020
TCTGATATGAGCCCGAAATCCG
60.029
50.000
0.00
0.00
38.18
4.18
631
635
2.358322
AAGGGCTTGAAGAACCGAAA
57.642
45.000
0.00
0.00
0.00
3.46
764
776
8.983724
GCAGTGCCAATTTTACATTTTTACTAA
58.016
29.630
2.85
0.00
0.00
2.24
827
844
4.141041
TCCTCCTCTTCTCTAGGGATGAAG
60.141
50.000
9.34
4.03
38.69
3.02
957
1009
2.743928
GAGACCTGGCCACGCTTG
60.744
66.667
0.00
0.00
0.00
4.01
958
1010
2.925170
AGAGACCTGGCCACGCTT
60.925
61.111
0.00
0.00
0.00
4.68
959
1011
3.699894
CAGAGACCTGGCCACGCT
61.700
66.667
0.00
0.00
36.77
5.07
960
1012
3.537206
AACAGAGACCTGGCCACGC
62.537
63.158
0.00
0.00
44.60
5.34
961
1013
0.535102
AAAACAGAGACCTGGCCACG
60.535
55.000
0.00
0.00
44.60
4.94
962
1014
1.239347
GAAAACAGAGACCTGGCCAC
58.761
55.000
0.00
0.00
44.60
5.01
963
1015
0.250295
CGAAAACAGAGACCTGGCCA
60.250
55.000
4.71
4.71
44.60
5.36
964
1016
1.578206
GCGAAAACAGAGACCTGGCC
61.578
60.000
0.00
0.00
44.60
5.36
965
1017
0.603975
AGCGAAAACAGAGACCTGGC
60.604
55.000
0.00
0.00
44.60
4.85
966
1018
1.532868
CAAGCGAAAACAGAGACCTGG
59.467
52.381
0.00
0.00
44.60
4.45
967
1019
2.478134
CTCAAGCGAAAACAGAGACCTG
59.522
50.000
0.00
0.00
45.76
4.00
968
1020
2.760374
CTCAAGCGAAAACAGAGACCT
58.240
47.619
0.00
0.00
0.00
3.85
969
1021
1.195674
GCTCAAGCGAAAACAGAGACC
59.804
52.381
0.00
0.00
0.00
3.85
970
1022
2.585888
GCTCAAGCGAAAACAGAGAC
57.414
50.000
0.00
0.00
0.00
3.36
1357
1481
1.218854
GGTGTTTGATGGCCATGGC
59.781
57.895
29.47
29.47
41.06
4.40
1408
1535
1.456165
GAGAAACAGAGCCGTCGTTTC
59.544
52.381
6.20
6.20
41.46
2.78
1670
1797
1.176527
CATGGACTCGGTTTGCCAAT
58.823
50.000
0.00
0.00
33.51
3.16
1690
1817
1.200252
CTCGCTGACATATACCCCGAG
59.800
57.143
0.00
0.00
35.46
4.63
1889
3127
2.786777
TGTGCAGCACAAATCTCTCAT
58.213
42.857
26.34
0.00
41.69
2.90
2047
3312
3.567397
TCCGGGGATTTGAAGTTTTGAA
58.433
40.909
0.00
0.00
0.00
2.69
2048
3313
3.153919
CTCCGGGGATTTGAAGTTTTGA
58.846
45.455
0.00
0.00
0.00
2.69
2049
3314
2.890945
ACTCCGGGGATTTGAAGTTTTG
59.109
45.455
9.33
0.00
0.00
2.44
2050
3315
2.890945
CACTCCGGGGATTTGAAGTTTT
59.109
45.455
9.33
0.00
0.00
2.43
2051
3316
2.514803
CACTCCGGGGATTTGAAGTTT
58.485
47.619
9.33
0.00
0.00
2.66
2052
3317
1.271926
CCACTCCGGGGATTTGAAGTT
60.272
52.381
9.33
0.00
0.00
2.66
2053
3318
0.328258
CCACTCCGGGGATTTGAAGT
59.672
55.000
9.33
0.00
0.00
3.01
2054
3319
0.328258
ACCACTCCGGGGATTTGAAG
59.672
55.000
9.33
0.00
40.22
3.02
2195
3460
3.091545
CCTTAGCACCATGGTCACATTT
58.908
45.455
16.53
0.00
34.35
2.32
2445
3774
2.863401
AAACGGAAAGTTGAGGTTGC
57.137
45.000
0.00
0.00
43.37
4.17
2923
4597
3.890756
GTGCCATTGGGATAATCATGTGA
59.109
43.478
4.53
0.00
35.59
3.58
3013
4693
5.065218
CGGACTTAATGGATGGCTAATATGC
59.935
44.000
0.00
0.00
0.00
3.14
3172
7077
8.381387
GCCTTCTAAAACGTTCTAAATCTACTG
58.619
37.037
0.00
0.00
0.00
2.74
3186
7132
2.218603
ACACCACTGCCTTCTAAAACG
58.781
47.619
0.00
0.00
0.00
3.60
3237
7183
8.964476
TCTGGTCATTTTATCTAGCTTTTAGG
57.036
34.615
0.00
0.00
0.00
2.69
3258
7204
6.234177
AGGGAATAGAATTTAGCGATTCTGG
58.766
40.000
17.65
0.00
44.05
3.86
3361
7314
3.408634
ACCAACATTTCCAGTAACCTCG
58.591
45.455
0.00
0.00
0.00
4.63
3386
7351
9.160496
GACTGATGAATCATTTTCTGTACTCTT
57.840
33.333
0.00
0.00
36.02
2.85
3400
7365
8.213518
GTGCTTTTATAAGGACTGATGAATCA
57.786
34.615
9.73
0.00
45.94
2.57
3791
7815
5.622233
GCCATCAGTGTTTATTCAGAAACCC
60.622
44.000
0.00
0.00
38.33
4.11
3901
7929
8.122330
GCACTTCTAAAACAAAAAGGGAAAATG
58.878
33.333
0.00
0.00
0.00
2.32
3962
7995
2.301870
AGAGATTGACCACACGCCTTAA
59.698
45.455
0.00
0.00
0.00
1.85
3975
8008
9.665719
TTACAGTTATTATGCAACAGAGATTGA
57.334
29.630
0.00
0.00
0.00
2.57
4046
8079
1.359848
AAAGCAGAGCGGTTATCACG
58.640
50.000
0.00
0.00
34.08
4.35
4099
8135
0.399454
AGATGGCCGAAGCATAGCAT
59.601
50.000
0.00
0.00
42.56
3.79
4141
8177
2.640302
GCTCCAGTGGCTCTCGACA
61.640
63.158
3.51
0.00
0.00
4.35
4158
8194
2.161486
GGTCGCTCGATCACACTGC
61.161
63.158
0.00
0.00
0.00
4.40
4198
8236
1.543208
GGTCAGATTGCTGTGTCACCA
60.543
52.381
0.00
0.00
42.84
4.17
4207
8245
1.089920
GATGTTGCGGTCAGATTGCT
58.910
50.000
0.00
0.00
0.00
3.91
4236
8274
1.227999
CGACATTGCGGCCGGATTAT
61.228
55.000
29.38
13.32
0.00
1.28
4272
8311
3.626924
ACCCTGCTCGTTCGGCTT
61.627
61.111
7.06
0.00
0.00
4.35
4288
8345
2.907897
ATCCTGCTCGCGGCTAACAC
62.908
60.000
18.14
0.00
42.39
3.32
4289
8346
2.721167
ATCCTGCTCGCGGCTAACA
61.721
57.895
18.14
4.58
42.39
2.41
4290
8347
2.107141
ATCCTGCTCGCGGCTAAC
59.893
61.111
18.14
0.25
42.39
2.34
4291
8348
2.106938
CATCCTGCTCGCGGCTAA
59.893
61.111
18.14
6.41
42.39
3.09
4292
8349
3.916544
CCATCCTGCTCGCGGCTA
61.917
66.667
18.14
6.69
42.39
3.93
4296
8353
3.869272
GTTGCCATCCTGCTCGCG
61.869
66.667
0.00
0.00
0.00
5.87
4297
8354
3.512516
GGTTGCCATCCTGCTCGC
61.513
66.667
0.00
0.00
0.00
5.03
4298
8355
3.197790
CGGTTGCCATCCTGCTCG
61.198
66.667
0.00
0.00
0.00
5.03
4299
8356
3.512516
GCGGTTGCCATCCTGCTC
61.513
66.667
2.68
0.00
33.98
4.26
4310
8367
2.025441
CAACACGGTTGGCGGTTG
59.975
61.111
8.40
0.00
35.25
3.77
4311
8368
3.894947
GCAACACGGTTGGCGGTT
61.895
61.111
15.52
0.00
0.00
4.44
4346
8403
1.003839
CAGAAGTACCGCCTTGCCA
60.004
57.895
0.00
0.00
0.00
4.92
4358
8415
3.884774
TGGCCCCGTTGCAGAAGT
61.885
61.111
0.00
0.00
0.00
3.01
4392
8449
2.239341
AATGCCATGTTGTCGTCGCG
62.239
55.000
0.00
0.00
0.00
5.87
4467
8532
1.007734
GACGCTCAAGGACGACACA
60.008
57.895
0.00
0.00
0.00
3.72
4494
8560
3.430895
CGTTACCGCAAACTACTCAATGT
59.569
43.478
0.00
0.00
0.00
2.71
4514
8580
4.656117
TGTCCACGATGCACGCGT
62.656
61.111
5.58
5.58
46.94
6.01
4519
8585
2.743538
GCTGCTGTCCACGATGCA
60.744
61.111
0.00
0.00
0.00
3.96
4575
8641
3.684788
CCCTAACATCGTATGCCTATTGC
59.315
47.826
0.00
0.00
41.77
3.56
4576
8642
3.684788
GCCCTAACATCGTATGCCTATTG
59.315
47.826
0.00
0.00
0.00
1.90
4598
8667
3.560636
AATCGTGTCCCCCTAAAGATG
57.439
47.619
0.00
0.00
0.00
2.90
4600
8669
3.307904
GGAAAATCGTGTCCCCCTAAAGA
60.308
47.826
0.00
0.00
0.00
2.52
4601
8670
3.014623
GGAAAATCGTGTCCCCCTAAAG
58.985
50.000
0.00
0.00
0.00
1.85
4605
8674
1.689412
GGGAAAATCGTGTCCCCCT
59.311
57.895
0.00
0.00
46.96
4.79
4606
8675
4.331622
GGGAAAATCGTGTCCCCC
57.668
61.111
0.00
0.00
46.96
5.40
4650
8729
4.935205
CCACCTATCAACAACTCGATTCAA
59.065
41.667
0.00
0.00
0.00
2.69
4656
8735
3.512680
GTCTCCACCTATCAACAACTCG
58.487
50.000
0.00
0.00
0.00
4.18
4669
8748
6.468115
GAACTCGTTCTATGGGTCTCCACC
62.468
54.167
2.66
0.00
40.01
4.61
4670
8749
3.429135
GAACTCGTTCTATGGGTCTCCAC
60.429
52.174
2.66
0.00
40.01
4.02
4671
8750
2.758979
GAACTCGTTCTATGGGTCTCCA
59.241
50.000
2.66
0.00
40.75
3.86
4672
8751
2.758979
TGAACTCGTTCTATGGGTCTCC
59.241
50.000
10.75
0.00
40.14
3.71
4673
8752
3.731264
CGTGAACTCGTTCTATGGGTCTC
60.731
52.174
10.75
0.00
40.14
3.36
4674
8753
2.163815
CGTGAACTCGTTCTATGGGTCT
59.836
50.000
10.75
0.00
40.14
3.85
4675
8754
2.527100
CGTGAACTCGTTCTATGGGTC
58.473
52.381
10.75
0.00
40.14
4.46
4676
8755
1.403780
GCGTGAACTCGTTCTATGGGT
60.404
52.381
10.75
0.00
40.14
4.51
4677
8756
1.278238
GCGTGAACTCGTTCTATGGG
58.722
55.000
10.75
0.00
40.14
4.00
4678
8757
1.135083
AGGCGTGAACTCGTTCTATGG
60.135
52.381
10.75
0.18
40.14
2.74
4679
8758
1.920574
CAGGCGTGAACTCGTTCTATG
59.079
52.381
0.00
4.80
40.14
2.23
4680
8759
1.816835
TCAGGCGTGAACTCGTTCTAT
59.183
47.619
6.64
0.00
40.14
1.98
4681
8760
1.199327
CTCAGGCGTGAACTCGTTCTA
59.801
52.381
10.76
0.00
40.14
2.10
4682
8761
0.039074
CTCAGGCGTGAACTCGTTCT
60.039
55.000
10.76
0.00
40.14
3.01
4683
8762
1.009389
CCTCAGGCGTGAACTCGTTC
61.009
60.000
10.76
2.92
39.91
3.95
4684
8763
1.006102
CCTCAGGCGTGAACTCGTT
60.006
57.895
10.76
0.00
30.14
3.85
4685
8764
2.651361
CCTCAGGCGTGAACTCGT
59.349
61.111
10.76
0.00
30.14
4.18
4686
8765
2.125912
CCCTCAGGCGTGAACTCG
60.126
66.667
10.76
0.00
30.14
4.18
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.