Multiple sequence alignment - TraesCS5A01G491900
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
TraesCS5A01G491900
chr5A
100.000
2835
0
0
1
2835
660835432
660838266
0.000000e+00
5236.0
1
TraesCS5A01G491900
chr5A
93.214
280
19
0
1181
1460
502528695
502528416
2.030000e-111
412.0
2
TraesCS5A01G491900
chr4D
84.928
2070
115
73
1
1927
481885021
481883006
0.000000e+00
1912.0
3
TraesCS5A01G491900
chr4D
83.088
816
61
31
1945
2748
481883017
481882267
0.000000e+00
671.0
4
TraesCS5A01G491900
chr4D
93.286
283
19
0
1181
1463
211482126
211481844
4.370000e-113
418.0
5
TraesCS5A01G491900
chr4B
83.648
1957
121
82
587
2445
611321521
611319666
0.000000e+00
1657.0
6
TraesCS5A01G491900
chr4B
84.499
529
34
11
1
487
611401923
611401401
1.980000e-131
479.0
7
TraesCS5A01G491900
chr4B
85.373
335
27
9
2427
2751
611319645
611319323
7.570000e-86
327.0
8
TraesCS5A01G491900
chr4B
84.706
85
5
4
2606
2690
541243959
541243883
8.420000e-11
78.7
9
TraesCS5A01G491900
chr1B
91.011
356
29
1
1121
1473
665253068
665252713
7.110000e-131
477.0
10
TraesCS5A01G491900
chr5D
93.571
280
18
0
1181
1460
498728551
498728830
4.370000e-113
418.0
11
TraesCS5A01G491900
chr5D
85.366
82
4
4
2610
2690
495490159
495490085
8.420000e-11
78.7
12
TraesCS5A01G491900
chr7A
92.058
277
22
0
1187
1463
676070042
676069766
9.520000e-105
390.0
13
TraesCS5A01G491900
chr6B
88.489
278
20
5
1186
1463
716387819
716387554
2.720000e-85
326.0
14
TraesCS5A01G491900
chr2B
88.214
280
21
5
1181
1460
638526559
638526826
9.800000e-85
324.0
15
TraesCS5A01G491900
chr3D
84.706
85
5
2
2606
2690
447983660
447983584
8.420000e-11
78.7
16
TraesCS5A01G491900
chr3B
100.000
28
0
0
745
772
631611580
631611553
5.000000e-03
52.8
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
TraesCS5A01G491900
chr5A
660835432
660838266
2834
False
5236.0
5236
100.0000
1
2835
1
chr5A.!!$F1
2834
1
TraesCS5A01G491900
chr4D
481882267
481885021
2754
True
1291.5
1912
84.0080
1
2748
2
chr4D.!!$R2
2747
2
TraesCS5A01G491900
chr4B
611319323
611321521
2198
True
992.0
1657
84.5105
587
2751
2
chr4B.!!$R3
2164
3
TraesCS5A01G491900
chr4B
611401401
611401923
522
True
479.0
479
84.4990
1
487
1
chr4B.!!$R2
486
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
621
719
0.036732
TCTTGCACACCACCCTCATC
59.963
55.0
0.0
0.0
0.0
2.92
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2212
2413
0.169009
GTCCGCAAAATCTCCACTGC
59.831
55.0
0.0
0.0
0.0
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
39
40
2.586079
CGTGCTATCAGCCGGTGG
60.586
66.667
1.90
0.00
41.51
4.61
42
43
0.882042
GTGCTATCAGCCGGTGGATG
60.882
60.000
17.06
6.11
41.51
3.51
44
45
0.882042
GCTATCAGCCGGTGGATGTG
60.882
60.000
17.06
11.74
40.37
3.21
58
59
2.159184
TGGATGTGACGATCAGCTTCTC
60.159
50.000
0.00
0.00
0.00
2.87
72
73
2.452295
CTTCTCTGTGAAGCAGCTGA
57.548
50.000
20.43
0.00
44.62
4.26
99
104
4.451629
AAATTACTCCGCGAGAGAGAAA
57.548
40.909
25.01
17.13
46.50
2.52
137
152
1.936547
GAGATTTCAGACGGTGATGGC
59.063
52.381
0.00
0.00
34.17
4.40
209
254
1.966451
GCCTGAAACTGGACACCGG
60.966
63.158
0.00
0.00
35.68
5.28
228
273
0.185416
GTCGAGTCCCAGGGATAGGA
59.815
60.000
12.84
6.34
32.73
2.94
262
307
1.078426
AATCGTGGGAAAGGAGGCG
60.078
57.895
0.00
0.00
0.00
5.52
313
358
3.737172
CTTTTGGGACGGCGGCAG
61.737
66.667
17.61
0.00
0.00
4.85
437
482
2.136196
CTCGGCGGATAGGACAGAGC
62.136
65.000
7.21
0.00
0.00
4.09
438
483
2.737830
GGCGGATAGGACAGAGCC
59.262
66.667
0.00
0.00
37.61
4.70
459
506
0.171231
GCCAACTTTGATTCCGAGGC
59.829
55.000
0.00
0.00
0.00
4.70
460
507
0.447801
CCAACTTTGATTCCGAGGCG
59.552
55.000
0.00
0.00
0.00
5.52
461
508
1.438651
CAACTTTGATTCCGAGGCGA
58.561
50.000
0.00
0.00
0.00
5.54
462
509
1.128692
CAACTTTGATTCCGAGGCGAC
59.871
52.381
0.00
0.00
0.00
5.19
512
579
1.618861
GATCGCGATCGGGAATACTG
58.381
55.000
34.15
6.36
40.40
2.74
515
582
0.997226
CGCGATCGGGAATACTGACG
60.997
60.000
26.36
8.15
37.28
4.35
522
589
1.535437
CGGGAATACTGACGGTACTGC
60.535
57.143
0.23
0.00
32.72
4.40
542
609
1.792301
GGATGATGGATGCGATGCG
59.208
57.895
0.00
0.00
0.00
4.73
544
611
1.150827
GATGATGGATGCGATGCGAA
58.849
50.000
0.00
0.00
0.00
4.70
550
622
0.040958
GGATGCGATGCGAAATCCAC
60.041
55.000
13.60
0.00
39.63
4.02
600
685
2.571216
CCAGACACGGACGGACCTT
61.571
63.158
0.00
0.00
36.31
3.50
603
688
2.732658
ACACGGACGGACCTTGTC
59.267
61.111
2.98
0.00
46.04
3.18
604
689
1.831286
ACACGGACGGACCTTGTCT
60.831
57.895
2.98
0.00
46.04
3.41
617
714
0.466189
CTTGTCTTGCACACCACCCT
60.466
55.000
0.00
0.00
33.41
4.34
619
717
1.148273
GTCTTGCACACCACCCTCA
59.852
57.895
0.00
0.00
0.00
3.86
620
718
0.250901
GTCTTGCACACCACCCTCAT
60.251
55.000
0.00
0.00
0.00
2.90
621
719
0.036732
TCTTGCACACCACCCTCATC
59.963
55.000
0.00
0.00
0.00
2.92
622
720
0.250858
CTTGCACACCACCCTCATCA
60.251
55.000
0.00
0.00
0.00
3.07
623
721
0.405198
TTGCACACCACCCTCATCAT
59.595
50.000
0.00
0.00
0.00
2.45
624
722
0.322726
TGCACACCACCCTCATCATG
60.323
55.000
0.00
0.00
0.00
3.07
633
731
1.425066
ACCCTCATCATGGTGTTGTGT
59.575
47.619
5.73
0.00
32.36
3.72
933
1076
7.277981
ACGTGGAGAGCAGTAAATAAATACAAG
59.722
37.037
0.00
0.00
0.00
3.16
1085
1233
3.157949
CTCTCCTTCCTCCGCCCC
61.158
72.222
0.00
0.00
0.00
5.80
1126
1274
2.026945
GAGGAGCAGACCAGCTAGCC
62.027
65.000
12.13
0.00
46.75
3.93
1127
1275
2.105930
GAGCAGACCAGCTAGCCG
59.894
66.667
12.13
0.00
46.75
5.52
1128
1276
4.154347
AGCAGACCAGCTAGCCGC
62.154
66.667
12.13
4.96
44.50
6.53
1491
1663
4.637489
CCGGCCGAGCGATGAGAG
62.637
72.222
30.73
0.44
0.00
3.20
1492
1664
3.893763
CGGCCGAGCGATGAGAGT
61.894
66.667
24.07
0.00
0.00
3.24
1493
1665
2.279120
GGCCGAGCGATGAGAGTG
60.279
66.667
0.00
0.00
0.00
3.51
1494
1666
2.775856
GGCCGAGCGATGAGAGTGA
61.776
63.158
0.00
0.00
0.00
3.41
1495
1667
1.299014
GCCGAGCGATGAGAGTGAG
60.299
63.158
0.00
0.00
0.00
3.51
1498
1670
0.729690
CGAGCGATGAGAGTGAGACA
59.270
55.000
0.00
0.00
0.00
3.41
1576
1748
1.938577
CGATTCTTGATCCTGGCTGTG
59.061
52.381
0.00
0.00
0.00
3.66
1580
1752
3.726557
TCTTGATCCTGGCTGTGAATT
57.273
42.857
0.00
0.00
0.00
2.17
1584
1756
4.508551
TGATCCTGGCTGTGAATTACAT
57.491
40.909
0.00
0.00
38.92
2.29
1591
1763
5.416952
CCTGGCTGTGAATTACATCTTCTTT
59.583
40.000
0.00
0.00
38.92
2.52
1693
1873
7.348201
GTTTAAGATGATCGGAATGTAAGCAG
58.652
38.462
0.00
0.00
0.00
4.24
1719
1899
1.589993
CGCTACCTCAGTGCCGATG
60.590
63.158
0.00
0.00
0.00
3.84
1720
1900
1.816537
GCTACCTCAGTGCCGATGA
59.183
57.895
0.00
0.00
0.00
2.92
1721
1901
0.249238
GCTACCTCAGTGCCGATGAG
60.249
60.000
3.57
3.57
43.15
2.90
1723
1903
2.298610
CTACCTCAGTGCCGATGAGTA
58.701
52.381
8.55
2.55
42.18
2.59
1763
1955
5.794894
CCCGCAGATTAGTTGGATAAGTAT
58.205
41.667
0.00
0.00
0.00
2.12
1764
1956
5.869888
CCCGCAGATTAGTTGGATAAGTATC
59.130
44.000
0.00
0.00
0.00
2.24
1765
1957
5.573282
CCGCAGATTAGTTGGATAAGTATCG
59.427
44.000
0.00
0.00
33.52
2.92
1766
1958
6.150318
CGCAGATTAGTTGGATAAGTATCGT
58.850
40.000
0.00
0.00
33.52
3.73
1767
1959
7.303261
CGCAGATTAGTTGGATAAGTATCGTA
58.697
38.462
0.00
0.00
33.52
3.43
1768
1960
7.270793
CGCAGATTAGTTGGATAAGTATCGTAC
59.729
40.741
0.00
0.00
33.52
3.67
1769
1961
8.298140
GCAGATTAGTTGGATAAGTATCGTACT
58.702
37.037
0.00
8.25
41.73
2.73
1770
1962
9.828852
CAGATTAGTTGGATAAGTATCGTACTC
57.171
37.037
7.04
0.00
38.26
2.59
1771
1963
9.012161
AGATTAGTTGGATAAGTATCGTACTCC
57.988
37.037
7.04
0.00
38.26
3.85
1866
2064
4.566987
ACGTGGTAAATTCTCCTTCTCAC
58.433
43.478
0.00
0.00
0.00
3.51
1896
2094
0.969149
AGTGGCTGACAGTGATTCGA
59.031
50.000
3.99
0.00
0.00
3.71
1927
2125
0.178950
ACAGTCCACTCAGGCTCAGA
60.179
55.000
0.00
0.00
37.29
3.27
1928
2126
0.531657
CAGTCCACTCAGGCTCAGAG
59.468
60.000
0.00
0.00
39.04
3.35
1929
2127
0.614415
AGTCCACTCAGGCTCAGAGG
60.614
60.000
0.00
0.00
37.43
3.69
1930
2128
0.902516
GTCCACTCAGGCTCAGAGGT
60.903
60.000
1.29
0.00
37.43
3.85
1931
2129
0.178921
TCCACTCAGGCTCAGAGGTT
60.179
55.000
1.29
0.00
37.43
3.50
1932
2130
0.689623
CCACTCAGGCTCAGAGGTTT
59.310
55.000
0.00
0.00
37.43
3.27
1933
2131
1.072965
CCACTCAGGCTCAGAGGTTTT
59.927
52.381
0.00
0.00
37.43
2.43
1934
2132
2.487986
CCACTCAGGCTCAGAGGTTTTT
60.488
50.000
0.00
0.00
37.43
1.94
1955
2153
4.637483
TTTTTGAAACACTCAGGCTCAG
57.363
40.909
0.00
0.00
34.81
3.35
2032
2230
8.336080
CGATTCTGAAGTATTTTTAGGTTAGCC
58.664
37.037
0.00
0.00
0.00
3.93
2039
2237
7.334844
AGTATTTTTAGGTTAGCCTGCATTC
57.665
36.000
8.65
0.00
46.47
2.67
2040
2238
5.598416
ATTTTTAGGTTAGCCTGCATTCC
57.402
39.130
8.65
0.00
46.47
3.01
2041
2239
2.729028
TTAGGTTAGCCTGCATTCCC
57.271
50.000
8.65
0.00
46.47
3.97
2055
2253
1.208535
CATTCCCTAACCCGTGCTACA
59.791
52.381
0.00
0.00
0.00
2.74
2093
2291
1.298667
GCCGGGAAAGAAGCTGGTA
59.701
57.895
2.18
0.00
0.00
3.25
2094
2292
0.744771
GCCGGGAAAGAAGCTGGTAG
60.745
60.000
2.18
0.00
0.00
3.18
2095
2293
0.613777
CCGGGAAAGAAGCTGGTAGT
59.386
55.000
0.00
0.00
0.00
2.73
2096
2294
1.829222
CCGGGAAAGAAGCTGGTAGTA
59.171
52.381
0.00
0.00
0.00
1.82
2097
2295
2.434702
CCGGGAAAGAAGCTGGTAGTAT
59.565
50.000
0.00
0.00
0.00
2.12
2098
2296
3.118371
CCGGGAAAGAAGCTGGTAGTATT
60.118
47.826
0.00
0.00
0.00
1.89
2099
2297
4.100498
CCGGGAAAGAAGCTGGTAGTATTA
59.900
45.833
0.00
0.00
0.00
0.98
2146
2347
3.642705
TCATGGCTTAATGACGATCGAG
58.357
45.455
24.34
8.58
31.58
4.04
2171
2372
3.537471
CATGTACGCATGTGGCATG
57.463
52.632
22.46
22.46
45.48
4.06
2211
2412
1.999634
GCCTCCCCCATGTACTGCAT
62.000
60.000
0.00
0.00
38.60
3.96
2267
2468
1.562575
GGCAACTGTTGTACCGTCGG
61.563
60.000
20.57
10.48
0.00
4.79
2274
2475
0.509929
GTTGTACCGTCGGCTTCAAC
59.490
55.000
21.78
21.78
0.00
3.18
2310
2522
1.226802
CCGGCGTCAGTGAGAGATG
60.227
63.158
6.01
0.00
0.00
2.90
2311
2523
1.226802
CGGCGTCAGTGAGAGATGG
60.227
63.158
0.00
0.00
0.00
3.51
2322
2534
3.768757
AGTGAGAGATGGACTTGGAGAAG
59.231
47.826
0.00
0.00
35.07
2.85
2337
2549
1.738099
GAAGTCGTGCGTGGCTCAT
60.738
57.895
0.00
0.00
0.00
2.90
2342
2554
2.870372
GTGCGTGGCTCATTGTCC
59.130
61.111
0.00
0.00
0.00
4.02
2347
2559
1.374252
GTGGCTCATTGTCCGACGT
60.374
57.895
0.00
0.00
0.00
4.34
2433
2687
1.213013
CGGTCGTGGGAGAGAAGTG
59.787
63.158
0.00
0.00
0.00
3.16
2493
2747
0.316204
TGGTCGAAAACGAGAGGACC
59.684
55.000
1.68
1.68
45.75
4.46
2496
2750
0.890542
TCGAAAACGAGAGGACCGGA
60.891
55.000
9.46
0.00
0.00
5.14
2504
2758
1.604604
GAGAGGACCGGAGATGAGAG
58.395
60.000
9.46
0.00
0.00
3.20
2516
2782
3.490348
GAGATGAGAGGAGAAGAGGAGG
58.510
54.545
0.00
0.00
0.00
4.30
2526
2792
3.772572
GGAGAAGAGGAGGAGTAGCTTTT
59.227
47.826
0.00
0.00
0.00
2.27
2559
2825
0.745845
CCATGGGACGCTTCTCTTGG
60.746
60.000
10.17
10.17
40.30
3.61
2581
2847
0.594796
CTGCAAACGGACAAACCTGC
60.595
55.000
0.00
0.00
37.70
4.85
2640
2906
3.876198
CCGCGCCGCTGCTTTTAT
61.876
61.111
7.78
0.00
34.43
1.40
2641
2907
2.648724
CGCGCCGCTGCTTTTATG
60.649
61.111
7.78
0.00
34.43
1.90
2642
2908
2.485122
GCGCCGCTGCTTTTATGT
59.515
55.556
0.00
0.00
34.43
2.29
2643
2909
1.719117
GCGCCGCTGCTTTTATGTA
59.281
52.632
0.00
0.00
34.43
2.29
2644
2910
0.098025
GCGCCGCTGCTTTTATGTAA
59.902
50.000
0.00
0.00
34.43
2.41
2645
2911
1.856014
GCGCCGCTGCTTTTATGTAAG
60.856
52.381
0.00
0.00
34.43
2.34
2648
2914
3.543460
CGCCGCTGCTTTTATGTAAGTAC
60.543
47.826
0.00
0.00
34.43
2.73
2666
2932
1.558741
ACGTACGTGTTTTTCGAGCA
58.441
45.000
22.14
0.00
0.00
4.26
2685
2951
0.965439
AGATACGCTGCTGGATCCTC
59.035
55.000
14.23
5.46
0.00
3.71
2686
2952
0.387878
GATACGCTGCTGGATCCTCG
60.388
60.000
14.23
10.71
0.00
4.63
2687
2953
2.427540
ATACGCTGCTGGATCCTCGC
62.428
60.000
14.23
15.68
0.00
5.03
2748
3014
2.135933
GAGAGTTGTTTGACCGTCCAG
58.864
52.381
0.00
0.00
0.00
3.86
2761
3027
1.263217
CCGTCCAGGTTTCAGTTTTCG
59.737
52.381
0.00
0.00
34.51
3.46
2762
3028
1.333791
CGTCCAGGTTTCAGTTTTCGC
60.334
52.381
0.00
0.00
0.00
4.70
2763
3029
1.001706
GTCCAGGTTTCAGTTTTCGCC
60.002
52.381
0.00
0.00
0.00
5.54
2764
3030
1.133915
TCCAGGTTTCAGTTTTCGCCT
60.134
47.619
0.00
0.00
0.00
5.52
2765
3031
1.681264
CCAGGTTTCAGTTTTCGCCTT
59.319
47.619
0.00
0.00
0.00
4.35
2766
3032
2.287608
CCAGGTTTCAGTTTTCGCCTTC
60.288
50.000
0.00
0.00
0.00
3.46
2767
3033
1.954382
AGGTTTCAGTTTTCGCCTTCC
59.046
47.619
0.00
0.00
0.00
3.46
2768
3034
1.954382
GGTTTCAGTTTTCGCCTTCCT
59.046
47.619
0.00
0.00
0.00
3.36
2769
3035
2.361119
GGTTTCAGTTTTCGCCTTCCTT
59.639
45.455
0.00
0.00
0.00
3.36
2770
3036
3.566742
GGTTTCAGTTTTCGCCTTCCTTA
59.433
43.478
0.00
0.00
0.00
2.69
2771
3037
4.037089
GGTTTCAGTTTTCGCCTTCCTTAA
59.963
41.667
0.00
0.00
0.00
1.85
2772
3038
5.278808
GGTTTCAGTTTTCGCCTTCCTTAAT
60.279
40.000
0.00
0.00
0.00
1.40
2773
3039
6.213677
GTTTCAGTTTTCGCCTTCCTTAATT
58.786
36.000
0.00
0.00
0.00
1.40
2774
3040
6.399639
TTCAGTTTTCGCCTTCCTTAATTT
57.600
33.333
0.00
0.00
0.00
1.82
2775
3041
6.009115
TCAGTTTTCGCCTTCCTTAATTTC
57.991
37.500
0.00
0.00
0.00
2.17
2776
3042
5.768164
TCAGTTTTCGCCTTCCTTAATTTCT
59.232
36.000
0.00
0.00
0.00
2.52
2777
3043
6.264518
TCAGTTTTCGCCTTCCTTAATTTCTT
59.735
34.615
0.00
0.00
0.00
2.52
2778
3044
6.582672
CAGTTTTCGCCTTCCTTAATTTCTTC
59.417
38.462
0.00
0.00
0.00
2.87
2779
3045
6.490381
AGTTTTCGCCTTCCTTAATTTCTTCT
59.510
34.615
0.00
0.00
0.00
2.85
2780
3046
6.894339
TTTCGCCTTCCTTAATTTCTTCTT
57.106
33.333
0.00
0.00
0.00
2.52
2781
3047
6.894339
TTCGCCTTCCTTAATTTCTTCTTT
57.106
33.333
0.00
0.00
0.00
2.52
2782
3048
6.894339
TCGCCTTCCTTAATTTCTTCTTTT
57.106
33.333
0.00
0.00
0.00
2.27
2783
3049
7.284919
TCGCCTTCCTTAATTTCTTCTTTTT
57.715
32.000
0.00
0.00
0.00
1.94
2784
3050
8.398878
TCGCCTTCCTTAATTTCTTCTTTTTA
57.601
30.769
0.00
0.00
0.00
1.52
2785
3051
8.852135
TCGCCTTCCTTAATTTCTTCTTTTTAA
58.148
29.630
0.00
0.00
0.00
1.52
2786
3052
9.471084
CGCCTTCCTTAATTTCTTCTTTTTAAA
57.529
29.630
0.00
0.00
0.00
1.52
2791
3057
9.758651
TCCTTAATTTCTTCTTTTTAAAGTGGC
57.241
29.630
2.44
0.00
37.31
5.01
2792
3058
9.541143
CCTTAATTTCTTCTTTTTAAAGTGGCA
57.459
29.630
2.44
0.00
37.31
4.92
2794
3060
7.463469
AATTTCTTCTTTTTAAAGTGGCACG
57.537
32.000
12.71
0.00
37.31
5.34
2795
3061
4.561735
TCTTCTTTTTAAAGTGGCACGG
57.438
40.909
12.71
0.00
37.31
4.94
2796
3062
4.200874
TCTTCTTTTTAAAGTGGCACGGA
58.799
39.130
12.71
0.00
37.31
4.69
2797
3063
3.974871
TCTTTTTAAAGTGGCACGGAC
57.025
42.857
12.71
0.00
37.31
4.79
2798
3064
2.288458
TCTTTTTAAAGTGGCACGGACG
59.712
45.455
12.71
0.00
37.31
4.79
2799
3065
1.666054
TTTTAAAGTGGCACGGACGT
58.334
45.000
12.71
0.00
0.00
4.34
2800
3066
2.522836
TTTAAAGTGGCACGGACGTA
57.477
45.000
12.71
0.00
0.00
3.57
2801
3067
2.522836
TTAAAGTGGCACGGACGTAA
57.477
45.000
12.71
4.90
0.00
3.18
2802
3068
8.148962
TCTTTTTAAAGTGGCACGGACGTAAG
62.149
42.308
12.71
12.82
39.37
2.34
2830
3096
9.398170
ACGATTTTATGATGAAAACTTGACTTG
57.602
29.630
0.00
0.00
31.35
3.16
2831
3097
9.611284
CGATTTTATGATGAAAACTTGACTTGA
57.389
29.630
0.00
0.00
31.35
3.02
2834
3100
9.734620
TTTTATGATGAAAACTTGACTTGACAG
57.265
29.630
0.00
0.00
0.00
3.51
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
13
14
0.528466
CTGATAGCACGACCGCACAT
60.528
55.000
0.00
0.00
0.00
3.21
39
40
3.435105
AGAGAAGCTGATCGTCACATC
57.565
47.619
0.00
0.00
0.00
3.06
72
73
2.232941
TCTCGCGGAGTAATTTTGTCCT
59.767
45.455
6.13
0.00
0.00
3.85
137
152
0.099968
CAGCATCCGCACCTTGATTG
59.900
55.000
0.00
0.00
42.27
2.67
166
199
0.500178
CGATACTCGCACATGCTTCG
59.500
55.000
1.82
0.00
39.32
3.79
172
205
2.398498
GCAAGATCGATACTCGCACAT
58.602
47.619
0.00
0.00
40.21
3.21
191
224
1.966451
CCGGTGTCCAGTTTCAGGC
60.966
63.158
0.00
0.00
0.00
4.85
209
254
0.185416
TCCTATCCCTGGGACTCGAC
59.815
60.000
19.82
0.00
32.98
4.20
228
273
1.267806
CGATTCTGGCTGCAACAAACT
59.732
47.619
0.50
0.00
0.00
2.66
262
307
1.812922
CGCATGTGCTCCTCTCCAC
60.813
63.158
3.25
0.00
39.32
4.02
316
361
1.597742
ACATAAGTGGCGATCCATGC
58.402
50.000
0.00
0.00
45.62
4.06
317
362
3.002656
GTCAACATAAGTGGCGATCCATG
59.997
47.826
0.00
0.00
45.62
3.66
318
363
3.118261
AGTCAACATAAGTGGCGATCCAT
60.118
43.478
0.00
0.00
45.62
3.41
359
404
7.408756
TTGTCATGGGAATATTTTCTTCAGG
57.591
36.000
0.00
0.00
32.16
3.86
360
405
7.485913
CGTTTGTCATGGGAATATTTTCTTCAG
59.514
37.037
0.00
0.00
32.16
3.02
437
482
0.958382
TCGGAATCAAAGTTGGCCGG
60.958
55.000
15.62
0.00
37.89
6.13
438
483
0.447801
CTCGGAATCAAAGTTGGCCG
59.552
55.000
0.00
11.88
38.31
6.13
459
506
1.846541
AAACAAAAACCATGGCGTCG
58.153
45.000
13.04
0.00
0.00
5.12
460
507
2.933260
ACAAAACAAAAACCATGGCGTC
59.067
40.909
13.04
0.00
0.00
5.19
461
508
2.979240
ACAAAACAAAAACCATGGCGT
58.021
38.095
13.04
0.00
0.00
5.68
462
509
4.094212
CAAACAAAACAAAAACCATGGCG
58.906
39.130
13.04
0.00
0.00
5.69
467
515
7.065563
CCTCATCATCAAACAAAACAAAAACCA
59.934
33.333
0.00
0.00
0.00
3.67
515
582
0.687354
ATCCATCATCCGGCAGTACC
59.313
55.000
0.00
0.00
0.00
3.34
522
589
1.642037
GCATCGCATCCATCATCCGG
61.642
60.000
0.00
0.00
0.00
5.14
542
609
0.716108
CTCGTGCGTCTGTGGATTTC
59.284
55.000
0.00
0.00
0.00
2.17
544
611
1.738099
GCTCGTGCGTCTGTGGATT
60.738
57.895
0.00
0.00
0.00
3.01
550
622
3.756677
CGTGTGCTCGTGCGTCTG
61.757
66.667
4.84
0.00
43.34
3.51
579
664
1.526575
GGTCCGTCCGTGTCTGGTTA
61.527
60.000
0.00
0.00
0.00
2.85
600
685
1.148273
GAGGGTGGTGTGCAAGACA
59.852
57.895
0.00
0.00
0.00
3.41
602
687
0.036732
GATGAGGGTGGTGTGCAAGA
59.963
55.000
0.00
0.00
0.00
3.02
603
688
0.250858
TGATGAGGGTGGTGTGCAAG
60.251
55.000
0.00
0.00
0.00
4.01
604
689
0.405198
ATGATGAGGGTGGTGTGCAA
59.595
50.000
0.00
0.00
0.00
4.08
617
714
1.423161
TCCCACACAACACCATGATGA
59.577
47.619
0.00
0.00
0.00
2.92
619
717
1.881925
CGTCCCACACAACACCATGAT
60.882
52.381
0.00
0.00
0.00
2.45
620
718
0.533978
CGTCCCACACAACACCATGA
60.534
55.000
0.00
0.00
0.00
3.07
621
719
1.948508
CGTCCCACACAACACCATG
59.051
57.895
0.00
0.00
0.00
3.66
622
720
1.896660
GCGTCCCACACAACACCAT
60.897
57.895
0.00
0.00
0.00
3.55
623
721
2.515057
GCGTCCCACACAACACCA
60.515
61.111
0.00
0.00
0.00
4.17
624
722
1.852067
GATGCGTCCCACACAACACC
61.852
60.000
0.00
0.00
0.00
4.16
633
731
4.429212
CGTGTCGGATGCGTCCCA
62.429
66.667
19.51
9.54
41.83
4.37
761
863
3.905678
CTAGGACCAGAGGCGGCG
61.906
72.222
0.51
0.51
0.00
6.46
762
864
3.541713
CCTAGGACCAGAGGCGGC
61.542
72.222
1.05
0.00
0.00
6.53
763
865
0.976073
TTTCCTAGGACCAGAGGCGG
60.976
60.000
12.22
0.00
32.40
6.13
888
1026
4.136250
GGAATTAACCCGAGCCCG
57.864
61.111
0.00
0.00
0.00
6.13
933
1076
0.038526
TCCTTCTCTTTCACGACGCC
60.039
55.000
0.00
0.00
0.00
5.68
1099
1247
1.300542
GTCTGCTCCTCCTATGCGC
60.301
63.158
0.00
0.00
0.00
6.09
1128
1276
4.005472
GCCATTGCGATCGAGGCG
62.005
66.667
21.57
3.57
35.42
5.52
1491
1663
1.478510
AGATGGGATCGTGTGTCTCAC
59.521
52.381
0.00
0.00
43.03
3.51
1492
1664
1.751351
GAGATGGGATCGTGTGTCTCA
59.249
52.381
0.00
0.00
33.93
3.27
1493
1665
1.268794
CGAGATGGGATCGTGTGTCTC
60.269
57.143
0.00
0.00
35.48
3.36
1494
1666
0.741326
CGAGATGGGATCGTGTGTCT
59.259
55.000
0.00
0.00
35.48
3.41
1495
1667
0.249073
CCGAGATGGGATCGTGTGTC
60.249
60.000
0.00
0.00
38.50
3.67
1498
1670
2.021068
CTGCCGAGATGGGATCGTGT
62.021
60.000
0.00
0.00
37.50
4.49
1525
1697
0.390340
AACACTGATCGATGCGTGCT
60.390
50.000
18.53
8.17
0.00
4.40
1576
1748
8.105135
CGAGAGAAACGAAAGAAGATGTAATTC
58.895
37.037
0.00
0.00
0.00
2.17
1580
1752
5.048224
ACCGAGAGAAACGAAAGAAGATGTA
60.048
40.000
0.00
0.00
0.00
2.29
1584
1756
3.608707
CGACCGAGAGAAACGAAAGAAGA
60.609
47.826
0.00
0.00
0.00
2.87
1591
1763
1.081641
GTGCGACCGAGAGAAACGA
60.082
57.895
0.00
0.00
0.00
3.85
1693
1873
2.047274
TGAGGTAGCGGCAACTGC
60.047
61.111
1.45
0.00
41.14
4.40
1765
1957
2.900122
TTGCACGTACGTAGGAGTAC
57.100
50.000
22.34
5.40
42.48
2.73
1766
1958
4.439305
AAATTGCACGTACGTAGGAGTA
57.561
40.909
22.34
10.54
0.00
2.59
1767
1959
3.308438
AAATTGCACGTACGTAGGAGT
57.692
42.857
22.34
10.64
0.00
3.85
1768
1960
4.084223
ACAAAAATTGCACGTACGTAGGAG
60.084
41.667
22.34
14.50
0.00
3.69
1769
1961
3.808726
ACAAAAATTGCACGTACGTAGGA
59.191
39.130
22.34
13.76
0.00
2.94
1770
1962
3.903644
CACAAAAATTGCACGTACGTAGG
59.096
43.478
22.34
11.14
0.00
3.18
1771
1963
4.520078
ACACAAAAATTGCACGTACGTAG
58.480
39.130
22.34
16.04
0.00
3.51
1866
2064
0.964700
TCAGCCACTCACTCAGTCTG
59.035
55.000
0.00
0.00
30.26
3.51
1896
2094
0.900182
TGGACTGTCTGACTGCCGAT
60.900
55.000
13.73
0.00
0.00
4.18
1934
2132
4.016444
ACTGAGCCTGAGTGTTTCAAAAA
58.984
39.130
0.00
0.00
34.81
1.94
1935
2133
3.620488
ACTGAGCCTGAGTGTTTCAAAA
58.380
40.909
0.00
0.00
34.81
2.44
1936
2134
3.281727
ACTGAGCCTGAGTGTTTCAAA
57.718
42.857
0.00
0.00
34.81
2.69
1937
2135
3.281727
AACTGAGCCTGAGTGTTTCAA
57.718
42.857
0.00
0.00
34.81
2.69
1938
2136
4.040339
TCATAACTGAGCCTGAGTGTTTCA
59.960
41.667
0.00
0.00
0.00
2.69
1939
2137
4.390297
GTCATAACTGAGCCTGAGTGTTTC
59.610
45.833
0.00
0.00
30.18
2.78
1940
2138
4.040952
AGTCATAACTGAGCCTGAGTGTTT
59.959
41.667
0.00
0.00
33.32
2.83
1941
2139
3.580458
AGTCATAACTGAGCCTGAGTGTT
59.420
43.478
0.00
0.00
33.32
3.32
1942
2140
3.169099
AGTCATAACTGAGCCTGAGTGT
58.831
45.455
0.00
0.00
33.32
3.55
1943
2141
3.883830
AGTCATAACTGAGCCTGAGTG
57.116
47.619
0.00
0.00
33.32
3.51
1954
2152
1.618837
AGCACCGTGTCAGTCATAACT
59.381
47.619
0.00
0.00
35.60
2.24
1955
2153
2.080286
AGCACCGTGTCAGTCATAAC
57.920
50.000
0.00
0.00
0.00
1.89
2025
2223
2.298610
GTTAGGGAATGCAGGCTAACC
58.701
52.381
0.00
0.00
0.00
2.85
2026
2224
2.298610
GGTTAGGGAATGCAGGCTAAC
58.701
52.381
0.00
0.00
0.00
2.34
2032
2230
1.376609
GCACGGGTTAGGGAATGCAG
61.377
60.000
0.00
0.00
33.27
4.41
2039
2237
1.153429
GCTGTAGCACGGGTTAGGG
60.153
63.158
0.00
0.00
41.59
3.53
2040
2238
1.108776
TAGCTGTAGCACGGGTTAGG
58.891
55.000
6.65
0.00
45.16
2.69
2041
2239
1.202382
GGTAGCTGTAGCACGGGTTAG
60.202
57.143
6.65
0.00
45.16
2.34
2055
2253
2.606519
TGGCGTTCTGGGGTAGCT
60.607
61.111
0.00
0.00
0.00
3.32
2138
2339
2.123251
ATGGGGGAGCTCGATCGT
60.123
61.111
15.94
0.00
0.00
3.73
2146
2347
2.510906
ATGCGTACATGGGGGAGC
59.489
61.111
0.00
0.00
34.35
4.70
2165
2366
1.031571
GGAAGACGGATTGCATGCCA
61.032
55.000
16.68
4.04
0.00
4.92
2166
2367
1.031571
TGGAAGACGGATTGCATGCC
61.032
55.000
16.68
0.00
0.00
4.40
2167
2368
0.379669
CTGGAAGACGGATTGCATGC
59.620
55.000
11.82
11.82
34.07
4.06
2168
2369
2.028420
TCTGGAAGACGGATTGCATG
57.972
50.000
0.00
0.00
38.67
4.06
2211
2412
0.250684
TCCGCAAAATCTCCACTGCA
60.251
50.000
0.00
0.00
34.39
4.41
2212
2413
0.169009
GTCCGCAAAATCTCCACTGC
59.831
55.000
0.00
0.00
0.00
4.40
2213
2414
0.443869
CGTCCGCAAAATCTCCACTG
59.556
55.000
0.00
0.00
0.00
3.66
2214
2415
1.298859
GCGTCCGCAAAATCTCCACT
61.299
55.000
6.82
0.00
41.49
4.00
2215
2416
1.134694
GCGTCCGCAAAATCTCCAC
59.865
57.895
6.82
0.00
41.49
4.02
2260
2461
1.671054
CATGGTTGAAGCCGACGGT
60.671
57.895
16.73
0.00
0.00
4.83
2261
2462
3.039202
GCATGGTTGAAGCCGACGG
62.039
63.158
10.29
10.29
0.00
4.79
2267
2468
2.126346
GCCGTGCATGGTTGAAGC
60.126
61.111
25.67
6.82
0.00
3.86
2322
2534
2.227968
GACAATGAGCCACGCACGAC
62.228
60.000
0.00
0.00
0.00
4.34
2337
2549
1.067974
ACTGACATTGACGTCGGACAA
59.932
47.619
11.62
0.00
43.75
3.18
2342
2554
0.386858
ACCGACTGACATTGACGTCG
60.387
55.000
11.62
18.20
46.21
5.12
2347
2559
0.455464
CGCGTACCGACTGACATTGA
60.455
55.000
0.00
0.00
40.02
2.57
2493
2747
2.158682
TCCTCTTCTCCTCTCATCTCCG
60.159
54.545
0.00
0.00
0.00
4.63
2496
2750
3.130450
TCCTCCTCTTCTCCTCTCATCT
58.870
50.000
0.00
0.00
0.00
2.90
2504
2758
2.748209
AGCTACTCCTCCTCTTCTCC
57.252
55.000
0.00
0.00
0.00
3.71
2516
2782
1.003108
GAGCCTCGCAAAAGCTACTC
58.997
55.000
0.00
0.00
36.87
2.59
2526
2792
3.381983
ATGGACGTGAGCCTCGCA
61.382
61.111
6.04
0.00
0.00
5.10
2549
2815
0.670162
TTTGCAGCACCAAGAGAAGC
59.330
50.000
0.00
0.00
0.00
3.86
2559
2825
0.869880
GGTTTGTCCGTTTGCAGCAC
60.870
55.000
0.00
0.00
0.00
4.40
2581
2847
1.825285
CGATCGCGGCCAGATTCTTG
61.825
60.000
6.13
0.82
0.00
3.02
2638
2904
7.072647
TCGAAAAACACGTACGTACTTACATA
58.927
34.615
22.34
1.51
0.00
2.29
2639
2905
5.912396
TCGAAAAACACGTACGTACTTACAT
59.088
36.000
22.34
4.32
0.00
2.29
2640
2906
5.267009
TCGAAAAACACGTACGTACTTACA
58.733
37.500
22.34
0.00
0.00
2.41
2641
2907
5.660674
GCTCGAAAAACACGTACGTACTTAC
60.661
44.000
22.34
12.75
0.00
2.34
2642
2908
4.378616
GCTCGAAAAACACGTACGTACTTA
59.621
41.667
22.34
1.62
0.00
2.24
2643
2909
3.180387
GCTCGAAAAACACGTACGTACTT
59.820
43.478
22.34
14.05
0.00
2.24
2644
2910
2.721090
GCTCGAAAAACACGTACGTACT
59.279
45.455
22.34
8.16
0.00
2.73
2645
2911
2.467305
TGCTCGAAAAACACGTACGTAC
59.533
45.455
22.34
15.90
0.00
3.67
2648
2914
1.782569
TCTGCTCGAAAAACACGTACG
59.217
47.619
15.01
15.01
0.00
3.67
2666
2932
0.965439
GAGGATCCAGCAGCGTATCT
59.035
55.000
15.82
0.00
0.00
1.98
2724
2990
0.784778
CGGTCAAACAACTCTCTCGC
59.215
55.000
0.00
0.00
0.00
5.03
2727
2993
1.760613
TGGACGGTCAAACAACTCTCT
59.239
47.619
10.76
0.00
0.00
3.10
2730
2996
1.226746
CCTGGACGGTCAAACAACTC
58.773
55.000
10.76
0.00
0.00
3.01
2748
3014
1.954382
AGGAAGGCGAAAACTGAAACC
59.046
47.619
0.00
0.00
0.00
3.27
2751
3017
6.264518
AGAAATTAAGGAAGGCGAAAACTGAA
59.735
34.615
0.00
0.00
0.00
3.02
2752
3018
5.768164
AGAAATTAAGGAAGGCGAAAACTGA
59.232
36.000
0.00
0.00
0.00
3.41
2753
3019
6.013842
AGAAATTAAGGAAGGCGAAAACTG
57.986
37.500
0.00
0.00
0.00
3.16
2754
3020
6.490381
AGAAGAAATTAAGGAAGGCGAAAACT
59.510
34.615
0.00
0.00
0.00
2.66
2755
3021
6.678878
AGAAGAAATTAAGGAAGGCGAAAAC
58.321
36.000
0.00
0.00
0.00
2.43
2756
3022
6.894339
AGAAGAAATTAAGGAAGGCGAAAA
57.106
33.333
0.00
0.00
0.00
2.29
2757
3023
6.894339
AAGAAGAAATTAAGGAAGGCGAAA
57.106
33.333
0.00
0.00
0.00
3.46
2758
3024
6.894339
AAAGAAGAAATTAAGGAAGGCGAA
57.106
33.333
0.00
0.00
0.00
4.70
2759
3025
6.894339
AAAAGAAGAAATTAAGGAAGGCGA
57.106
33.333
0.00
0.00
0.00
5.54
2760
3026
9.471084
TTTAAAAAGAAGAAATTAAGGAAGGCG
57.529
29.630
0.00
0.00
0.00
5.52
2765
3031
9.758651
GCCACTTTAAAAAGAAGAAATTAAGGA
57.241
29.630
9.37
0.00
39.31
3.36
2766
3032
9.541143
TGCCACTTTAAAAAGAAGAAATTAAGG
57.459
29.630
9.37
0.00
39.31
2.69
2768
3034
9.026074
CGTGCCACTTTAAAAAGAAGAAATTAA
57.974
29.630
9.37
0.00
39.31
1.40
2769
3035
7.650104
CCGTGCCACTTTAAAAAGAAGAAATTA
59.350
33.333
9.37
0.00
39.31
1.40
2770
3036
6.478673
CCGTGCCACTTTAAAAAGAAGAAATT
59.521
34.615
9.37
0.00
39.31
1.82
2771
3037
5.983118
CCGTGCCACTTTAAAAAGAAGAAAT
59.017
36.000
9.37
0.00
39.31
2.17
2772
3038
5.125739
TCCGTGCCACTTTAAAAAGAAGAAA
59.874
36.000
9.37
0.00
39.31
2.52
2773
3039
4.641094
TCCGTGCCACTTTAAAAAGAAGAA
59.359
37.500
9.37
0.00
39.31
2.52
2774
3040
4.035909
GTCCGTGCCACTTTAAAAAGAAGA
59.964
41.667
9.37
0.00
39.31
2.87
2775
3041
4.287720
GTCCGTGCCACTTTAAAAAGAAG
58.712
43.478
9.37
1.66
39.31
2.85
2776
3042
3.242804
CGTCCGTGCCACTTTAAAAAGAA
60.243
43.478
9.37
0.00
39.31
2.52
2777
3043
2.288458
CGTCCGTGCCACTTTAAAAAGA
59.712
45.455
9.37
0.00
39.31
2.52
2778
3044
2.032426
ACGTCCGTGCCACTTTAAAAAG
59.968
45.455
0.90
0.90
41.73
2.27
2779
3045
2.015587
ACGTCCGTGCCACTTTAAAAA
58.984
42.857
0.00
0.00
0.00
1.94
2780
3046
1.666054
ACGTCCGTGCCACTTTAAAA
58.334
45.000
0.00
0.00
0.00
1.52
2781
3047
2.522836
TACGTCCGTGCCACTTTAAA
57.477
45.000
1.98
0.00
0.00
1.52
2782
3048
2.224018
ACTTACGTCCGTGCCACTTTAA
60.224
45.455
1.98
0.00
0.00
1.52
2783
3049
1.340889
ACTTACGTCCGTGCCACTTTA
59.659
47.619
1.98
0.00
0.00
1.85
2784
3050
0.105408
ACTTACGTCCGTGCCACTTT
59.895
50.000
1.98
0.00
0.00
2.66
2785
3051
0.961019
TACTTACGTCCGTGCCACTT
59.039
50.000
1.98
0.00
0.00
3.16
2786
3052
0.242017
GTACTTACGTCCGTGCCACT
59.758
55.000
1.98
0.00
0.00
4.00
2787
3053
1.067199
CGTACTTACGTCCGTGCCAC
61.067
60.000
1.98
0.00
44.13
5.01
2788
3054
1.209898
CGTACTTACGTCCGTGCCA
59.790
57.895
1.98
0.00
44.13
4.92
2789
3055
4.062183
CGTACTTACGTCCGTGCC
57.938
61.111
1.98
0.00
44.13
5.01
2804
3070
9.398170
CAAGTCAAGTTTTCATCATAAAATCGT
57.602
29.630
0.00
0.00
31.43
3.73
2805
3071
9.611284
TCAAGTCAAGTTTTCATCATAAAATCG
57.389
29.630
0.00
0.00
31.43
3.34
2808
3074
9.734620
CTGTCAAGTCAAGTTTTCATCATAAAA
57.265
29.630
0.00
0.00
0.00
1.52
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.