Multiple sequence alignment - TraesCS3D01G068400
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
TraesCS3D01G068400
chr3D
100.000
4626
0
0
1
4626
30088938
30084313
0.000000e+00
8543.0
1
TraesCS3D01G068400
chr3D
82.920
363
50
9
2265
2618
608203284
608202925
2.690000e-82
316.0
2
TraesCS3D01G068400
chr3D
77.247
356
64
13
2292
2636
510649717
510649368
4.720000e-45
193.0
3
TraesCS3D01G068400
chr3D
79.439
214
41
3
2453
2664
95953356
95953144
1.040000e-31
148.0
4
TraesCS3D01G068400
chr3D
100.000
38
0
0
3348
3385
30085555
30085518
2.310000e-08
71.3
5
TraesCS3D01G068400
chr3D
100.000
38
0
0
3384
3421
30085591
30085554
2.310000e-08
71.3
6
TraesCS3D01G068400
chr3D
95.122
41
2
0
361
401
515957005
515957045
1.070000e-06
65.8
7
TraesCS3D01G068400
chr3A
96.953
3413
67
12
1
3385
41654176
41650773
0.000000e+00
5692.0
8
TraesCS3D01G068400
chr3A
97.549
612
14
1
3384
3995
41650810
41650200
0.000000e+00
1046.0
9
TraesCS3D01G068400
chr3A
96.822
409
9
1
3989
4397
41644948
41644544
0.000000e+00
680.0
10
TraesCS3D01G068400
chr3A
96.203
237
9
0
4390
4626
41643205
41642969
5.610000e-104
388.0
11
TraesCS3D01G068400
chr3A
78.149
389
60
18
2274
2650
42195566
42195941
1.670000e-54
224.0
12
TraesCS3D01G068400
chr7A
83.208
399
45
8
2281
2657
11356278
11355880
3.430000e-91
346.0
13
TraesCS3D01G068400
chr7A
75.873
315
62
11
2279
2587
216353704
216353398
1.040000e-31
148.0
14
TraesCS3D01G068400
chr5B
82.482
411
52
16
2265
2664
123767931
123767530
4.430000e-90
342.0
15
TraesCS3D01G068400
chr5B
95.238
42
2
0
364
405
540916202
540916243
2.990000e-07
67.6
16
TraesCS3D01G068400
chr4A
83.642
324
39
13
2347
2661
633052208
633052526
4.530000e-75
292.0
17
TraesCS3D01G068400
chr4A
94.545
55
2
1
1097
1150
734874293
734874239
2.970000e-12
84.2
18
TraesCS3D01G068400
chr4A
94.545
55
2
1
1097
1150
736112588
736112534
2.970000e-12
84.2
19
TraesCS3D01G068400
chr5A
80.914
372
56
10
2262
2626
555595516
555595153
3.520000e-71
279.0
20
TraesCS3D01G068400
chr5A
96.154
52
1
1
1099
1150
601437150
601437100
2.970000e-12
84.2
21
TraesCS3D01G068400
chr1A
79.562
411
65
14
2265
2660
98227461
98227055
4.560000e-70
276.0
22
TraesCS3D01G068400
chr5D
80.429
373
54
13
2262
2626
439979436
439979075
2.740000e-67
267.0
23
TraesCS3D01G068400
chr6A
79.656
349
50
13
2279
2618
403322970
403323306
1.000000e-56
231.0
24
TraesCS3D01G068400
chr6A
96.154
52
2
0
1099
1150
581742973
581742922
8.250000e-13
86.1
25
TraesCS3D01G068400
chr7D
76.368
402
63
14
2265
2661
51452263
51452637
2.200000e-43
187.0
26
TraesCS3D01G068400
chr7D
85.629
167
22
2
2266
2430
428025770
428025604
1.710000e-39
174.0
27
TraesCS3D01G068400
chr7D
78.205
234
33
8
2265
2491
476009948
476010170
2.900000e-27
134.0
28
TraesCS3D01G068400
chr7B
85.315
143
14
6
2291
2430
445664305
445664167
1.740000e-29
141.0
29
TraesCS3D01G068400
chr7B
92.857
56
2
2
1107
1162
165100268
165100215
3.840000e-11
80.5
30
TraesCS3D01G068400
chr4D
81.818
143
23
3
2290
2430
460302705
460302564
2.920000e-22
117.0
31
TraesCS3D01G068400
chr4D
92.857
56
3
1
1096
1150
447129610
447129555
3.840000e-11
80.5
32
TraesCS3D01G068400
chr6D
96.296
54
1
1
1098
1150
382611184
382611131
2.290000e-13
87.9
33
TraesCS3D01G068400
chr6D
88.060
67
5
3
1085
1148
30079493
30079427
4.960000e-10
76.8
34
TraesCS3D01G068400
chr3B
97.826
46
1
0
358
403
758520691
758520736
3.840000e-11
80.5
35
TraesCS3D01G068400
chr3B
97.826
46
1
0
358
403
758524736
758524781
3.840000e-11
80.5
36
TraesCS3D01G068400
chr3B
97.826
46
1
0
358
403
758528783
758528828
3.840000e-11
80.5
37
TraesCS3D01G068400
chr1D
91.228
57
4
1
350
405
387891091
387891035
4.960000e-10
76.8
38
TraesCS3D01G068400
chr6B
95.455
44
2
0
360
403
635069858
635069901
2.310000e-08
71.3
39
TraesCS3D01G068400
chr6B
93.182
44
2
1
364
407
707161243
707161201
3.860000e-06
63.9
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
TraesCS3D01G068400
chr3D
30084313
30088938
4625
True
2895.2
8543
100.0000
1
4626
3
chr3D.!!$R4
4625
1
TraesCS3D01G068400
chr3A
41650200
41654176
3976
True
3369.0
5692
97.2510
1
3995
2
chr3A.!!$R2
3994
2
TraesCS3D01G068400
chr3A
41642969
41644948
1979
True
534.0
680
96.5125
3989
4626
2
chr3A.!!$R1
637
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
573
592
0.039074
CCGATGCGAGTGGACTATCC
60.039
60.000
0.00
0.00
36.96
2.59
F
753
772
0.961019
CTTTGCCTAAAGGTGCAGCA
59.039
50.000
19.63
4.34
39.67
4.41
F
1436
1459
1.006102
CCCGAGCAGAGTTCGTGTT
60.006
57.895
2.82
0.00
36.37
3.32
F
3366
3394
0.035458
CCTTCTTCAGCGGAACAGGT
59.965
55.000
10.42
0.00
0.00
4.00
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2460
2483
0.179150
TTGTGTTCAAACAGCGCACC
60.179
50.000
11.47
0.0
40.05
5.01
R
2519
2542
2.996631
TGGTTGCAAAATTTGGTGCTT
58.003
38.095
14.29
0.0
41.48
3.91
R
3380
3408
0.034896
TGTTCCGCTGAAGAAGGACC
59.965
55.000
0.00
0.0
33.16
4.46
R
4197
4225
0.108041
AACCATTACCACGCCTACCG
60.108
55.000
0.00
0.0
44.21
4.02
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
198
200
3.428862
GCGAATTCCCAATAACAACAGGG
60.429
47.826
0.00
0.00
42.86
4.45
206
208
4.568804
CCCAATAACAACAGGGGTATCACA
60.569
45.833
0.00
0.00
37.66
3.58
238
240
2.277501
CTTGCGCTTGCGCCATAC
60.278
61.111
32.10
9.70
43.34
2.39
250
252
5.512753
TTGCGCCATACATAACAATCAAT
57.487
34.783
4.18
0.00
0.00
2.57
276
278
2.294979
GGACACCGGGTATGAAATTCC
58.705
52.381
6.32
0.00
32.19
3.01
300
302
3.049912
GTGTTTGCACGAATTTCTTCCC
58.950
45.455
0.00
0.00
35.75
3.97
305
307
3.153130
TGCACGAATTTCTTCCCATTGA
58.847
40.909
0.00
0.00
0.00
2.57
556
575
4.201679
TACGCATGGCCGTCTCCG
62.202
66.667
0.00
0.52
42.20
4.63
558
577
4.592192
CGCATGGCCGTCTCCGAT
62.592
66.667
0.00
0.00
35.63
4.18
559
578
2.969238
GCATGGCCGTCTCCGATG
60.969
66.667
0.00
0.00
35.63
3.84
560
579
2.969238
CATGGCCGTCTCCGATGC
60.969
66.667
0.00
0.00
35.63
3.91
561
580
4.592192
ATGGCCGTCTCCGATGCG
62.592
66.667
0.00
0.00
35.63
4.73
563
582
4.933064
GGCCGTCTCCGATGCGAG
62.933
72.222
0.00
0.00
35.63
5.03
573
592
0.039074
CCGATGCGAGTGGACTATCC
60.039
60.000
0.00
0.00
36.96
2.59
589
608
8.809468
TGGACTATCCAATACTACTAGCATAG
57.191
38.462
0.00
0.00
45.00
2.23
590
609
7.339721
TGGACTATCCAATACTACTAGCATAGC
59.660
40.741
0.00
0.00
45.00
2.97
753
772
0.961019
CTTTGCCTAAAGGTGCAGCA
59.039
50.000
19.63
4.34
39.67
4.41
858
877
7.896811
TCTAAGCATCATATAACCATCGTTCT
58.103
34.615
0.00
0.00
33.17
3.01
1063
1082
1.135972
CAAATCGAGCAACACGGGAAG
60.136
52.381
0.00
0.00
0.00
3.46
1117
1136
5.953571
AGGAAAATGTTTGTACTCCCTCTT
58.046
37.500
0.00
0.00
0.00
2.85
1237
1256
3.270877
AGTGTCTTGCTCAACTTTCGTT
58.729
40.909
0.00
0.00
0.00
3.85
1238
1257
4.439057
AGTGTCTTGCTCAACTTTCGTTA
58.561
39.130
0.00
0.00
0.00
3.18
1239
1258
4.270325
AGTGTCTTGCTCAACTTTCGTTAC
59.730
41.667
0.00
0.00
0.00
2.50
1240
1259
3.558418
TGTCTTGCTCAACTTTCGTTACC
59.442
43.478
0.00
0.00
0.00
2.85
1433
1456
2.344203
CCTCCCGAGCAGAGTTCGT
61.344
63.158
2.82
0.00
36.37
3.85
1436
1459
1.006102
CCCGAGCAGAGTTCGTGTT
60.006
57.895
2.82
0.00
36.37
3.32
1441
1464
2.059541
GAGCAGAGTTCGTGTTACACC
58.940
52.381
10.10
0.00
0.00
4.16
1442
1465
1.687123
AGCAGAGTTCGTGTTACACCT
59.313
47.619
10.10
1.06
0.00
4.00
1443
1466
2.102588
AGCAGAGTTCGTGTTACACCTT
59.897
45.455
10.10
0.00
0.00
3.50
1476
1499
7.777910
TCCTTCATTAATTACTGGGTATGGTTG
59.222
37.037
3.27
0.00
0.00
3.77
1511
1534
4.315803
CAACCTGATGAGTTTACTCCGTT
58.684
43.478
7.39
0.61
42.20
4.44
1531
1554
4.674362
CGTTGAATGACGAGGATGTGACTA
60.674
45.833
0.00
0.00
45.47
2.59
1538
1561
7.818997
ATGACGAGGATGTGACTAGTAATAA
57.181
36.000
0.00
0.00
0.00
1.40
1678
1701
6.949352
ATATAGTGAGCCATTCCACAAAAG
57.051
37.500
0.00
0.00
35.84
2.27
1814
1837
2.214376
TCGCTGTGAAATTGGGGATT
57.786
45.000
0.00
0.00
0.00
3.01
1858
1881
3.366374
GCGGAGAAAATCTGGAAAACTGG
60.366
47.826
0.00
0.00
34.56
4.00
1985
2008
6.591750
TGTAAACTTCTGTTGACCCAAAAA
57.408
33.333
0.00
0.00
36.85
1.94
2040
2063
3.756434
TCGCCCGAAAGATTCAGATTTTT
59.244
39.130
0.00
0.00
0.00
1.94
2113
2136
9.162764
TGGTTAAGAGAAATTTTCCTTCTATCG
57.837
33.333
12.97
0.00
33.24
2.92
2221
2244
3.821033
GTGGTCCATAGCTTTGTGACTTT
59.179
43.478
18.09
0.00
0.00
2.66
2329
2352
5.164002
CCCACGCAATAAAACATAGCAAAAC
60.164
40.000
0.00
0.00
0.00
2.43
2406
2429
4.582701
TGCAAAGTTAGGTGGTCAAATG
57.417
40.909
0.00
0.00
0.00
2.32
2429
2452
1.919240
TCCGAGGAGCTCTGTACAAA
58.081
50.000
14.64
0.00
0.00
2.83
2430
2453
2.457598
TCCGAGGAGCTCTGTACAAAT
58.542
47.619
14.64
0.00
0.00
2.32
2465
2488
4.712122
AATTACCCAAAATGTAGGTGCG
57.288
40.909
0.00
0.00
35.02
5.34
2519
2542
2.103094
CAGAGCTCCCGGATGTCATTTA
59.897
50.000
10.93
0.00
0.00
1.40
2646
2669
2.429930
CACCGAGCTGGGGTTCAA
59.570
61.111
19.90
0.00
44.64
2.69
2649
2672
2.429930
CGAGCTGGGGTTCAACCA
59.570
61.111
9.35
0.00
41.02
3.67
2704
2727
3.206150
TCTCCTGCAGAGTTTGTGTTTC
58.794
45.455
17.39
0.00
43.71
2.78
2837
2860
1.988293
TCGAAAATCCACCTTTGCCA
58.012
45.000
0.00
0.00
0.00
4.92
2875
2898
5.390387
AGTAAGCCATTCCACCAAAAGTAA
58.610
37.500
0.00
0.00
0.00
2.24
3077
3105
2.159787
GCAGATTATATCCAACTGCGCG
60.160
50.000
0.00
0.00
42.92
6.86
3098
3126
5.399301
CGCGAAAAATTCCATGGCTTAATAG
59.601
40.000
6.96
0.00
0.00
1.73
3099
3127
6.273071
GCGAAAAATTCCATGGCTTAATAGT
58.727
36.000
6.96
0.00
0.00
2.12
3131
3159
9.146586
TCCTAAAGGGGATTGATATTTTCATTG
57.853
33.333
0.00
0.00
32.77
2.82
3179
3207
0.037046
AGCATCTGTCATGTCGTGCA
60.037
50.000
13.79
0.00
35.17
4.57
3217
3245
0.609131
CGTTTGGGGATCTTGGCAGT
60.609
55.000
0.00
0.00
0.00
4.40
3264
3292
4.474226
ACTCACGACTCAAAATTGAAGC
57.526
40.909
0.00
0.00
36.64
3.86
3271
3299
6.678663
CACGACTCAAAATTGAAGCGTATTAG
59.321
38.462
17.04
6.78
41.71
1.73
3364
3392
0.321671
TCCCTTCTTCAGCGGAACAG
59.678
55.000
0.00
0.00
0.00
3.16
3365
3393
0.674895
CCCTTCTTCAGCGGAACAGG
60.675
60.000
11.28
11.28
31.86
4.00
3366
3394
0.035458
CCTTCTTCAGCGGAACAGGT
59.965
55.000
10.42
0.00
0.00
4.00
3367
3395
1.275291
CCTTCTTCAGCGGAACAGGTA
59.725
52.381
10.42
0.00
0.00
3.08
3368
3396
2.338500
CTTCTTCAGCGGAACAGGTAC
58.662
52.381
0.00
0.00
0.00
3.34
3369
3397
0.606604
TCTTCAGCGGAACAGGTACC
59.393
55.000
2.73
2.73
0.00
3.34
3370
3398
0.608640
CTTCAGCGGAACAGGTACCT
59.391
55.000
9.21
9.21
0.00
3.08
3371
3399
0.606604
TTCAGCGGAACAGGTACCTC
59.393
55.000
12.84
0.45
0.00
3.85
3372
3400
1.218316
CAGCGGAACAGGTACCTCC
59.782
63.158
12.84
10.17
0.00
4.30
3373
3401
1.988406
AGCGGAACAGGTACCTCCC
60.988
63.158
12.84
12.58
36.75
4.30
3374
3402
1.988406
GCGGAACAGGTACCTCCCT
60.988
63.158
12.84
0.00
36.75
4.20
3375
3403
1.957765
GCGGAACAGGTACCTCCCTC
61.958
65.000
12.84
8.60
36.75
4.30
3376
3404
1.328430
CGGAACAGGTACCTCCCTCC
61.328
65.000
12.84
16.27
36.75
4.30
3377
3405
0.981801
GGAACAGGTACCTCCCTCCC
60.982
65.000
12.84
5.55
36.75
4.30
3378
3406
0.252558
GAACAGGTACCTCCCTCCCA
60.253
60.000
12.84
0.00
36.75
4.37
3379
3407
0.546988
AACAGGTACCTCCCTCCCAC
60.547
60.000
12.84
0.00
36.75
4.61
3380
3408
2.058595
CAGGTACCTCCCTCCCACG
61.059
68.421
12.84
0.00
36.75
4.94
3381
3409
2.762875
GGTACCTCCCTCCCACGG
60.763
72.222
4.06
0.00
0.00
4.94
3382
3410
2.038490
GTACCTCCCTCCCACGGT
59.962
66.667
0.00
0.00
0.00
4.83
3383
3411
2.056815
GTACCTCCCTCCCACGGTC
61.057
68.421
0.00
0.00
0.00
4.79
3384
3412
3.307089
TACCTCCCTCCCACGGTCC
62.307
68.421
0.00
0.00
0.00
4.46
3385
3413
4.400251
CCTCCCTCCCACGGTCCT
62.400
72.222
0.00
0.00
0.00
3.85
3386
3414
2.284699
CTCCCTCCCACGGTCCTT
60.285
66.667
0.00
0.00
0.00
3.36
3387
3415
2.284405
TCCCTCCCACGGTCCTTC
60.284
66.667
0.00
0.00
0.00
3.46
3388
3416
2.284699
CCCTCCCACGGTCCTTCT
60.285
66.667
0.00
0.00
0.00
2.85
3389
3417
1.918800
CCCTCCCACGGTCCTTCTT
60.919
63.158
0.00
0.00
0.00
2.52
3390
3418
1.597461
CCTCCCACGGTCCTTCTTC
59.403
63.158
0.00
0.00
0.00
2.87
3391
3419
1.192146
CCTCCCACGGTCCTTCTTCA
61.192
60.000
0.00
0.00
0.00
3.02
3392
3420
0.247736
CTCCCACGGTCCTTCTTCAG
59.752
60.000
0.00
0.00
0.00
3.02
3393
3421
1.376037
CCCACGGTCCTTCTTCAGC
60.376
63.158
0.00
0.00
0.00
4.26
3394
3422
1.738099
CCACGGTCCTTCTTCAGCG
60.738
63.158
0.00
0.00
39.40
5.18
3395
3423
1.738099
CACGGTCCTTCTTCAGCGG
60.738
63.158
0.00
0.00
37.83
5.52
3396
3424
1.906824
ACGGTCCTTCTTCAGCGGA
60.907
57.895
0.00
0.00
37.83
5.54
3397
3425
1.292223
CGGTCCTTCTTCAGCGGAA
59.708
57.895
0.00
0.00
0.00
4.30
3398
3426
1.014564
CGGTCCTTCTTCAGCGGAAC
61.015
60.000
0.00
0.00
0.00
3.62
3399
3427
0.034896
GGTCCTTCTTCAGCGGAACA
59.965
55.000
0.00
0.00
34.64
3.18
3437
3465
0.471211
TCCCACGACCCAACTTCTCT
60.471
55.000
0.00
0.00
0.00
3.10
3441
3469
0.178929
ACGACCCAACTTCTCTCCCT
60.179
55.000
0.00
0.00
0.00
4.20
3478
3506
6.234920
CAAACATATATATGTCCCGACCCAA
58.765
40.000
25.01
0.00
45.55
4.12
3535
3563
1.525077
GAACGACTGTGGCACCCAA
60.525
57.895
16.26
0.00
34.18
4.12
3552
3580
5.507650
GCACCCAAAATTTCCACGTAAAGTA
60.508
40.000
0.00
0.00
0.00
2.24
3567
3595
4.214545
CGTAAAGTACTTGGGCAACATCAA
59.785
41.667
9.34
0.00
39.74
2.57
3620
3648
1.369091
CGAATCGCTGGACCCAAAGG
61.369
60.000
0.00
0.00
40.04
3.11
3768
3796
9.212641
CTTTATCATTCTATCGTGTGGATTCAT
57.787
33.333
0.00
0.00
36.55
2.57
3912
3940
6.868622
TGTTTTTACTAATGTGCTTTGTGGT
58.131
32.000
0.00
0.00
0.00
4.16
3925
3953
5.969435
GTGCTTTGTGGTTCTTACTAACAAC
59.031
40.000
0.00
0.00
34.42
3.32
3998
4026
1.202806
CCATCAACACCACACTCCACT
60.203
52.381
0.00
0.00
0.00
4.00
4001
4029
1.134521
TCAACACCACACTCCACTGTC
60.135
52.381
0.00
0.00
0.00
3.51
4011
4039
1.005450
ACTCCACTGTCTCCTCTCCTC
59.995
57.143
0.00
0.00
0.00
3.71
4028
4056
1.004560
TCGCTCTTGCCACTTCCTG
60.005
57.895
0.00
0.00
35.36
3.86
4126
4154
1.324736
CTTCGTTAATCAGGAGCACGC
59.675
52.381
0.00
0.00
0.00
5.34
4197
4225
0.819582
CAATGTCCATTGCCTCCCAC
59.180
55.000
7.05
0.00
41.27
4.61
4288
4316
1.035139
GGGAATCGCTCATGCCAATT
58.965
50.000
0.00
0.00
29.79
2.32
4371
4399
9.980780
CATTGTTGACGTATGTATTTATTGTGA
57.019
29.630
0.00
0.00
0.00
3.58
4427
5801
4.048504
GTTGACTATGCCAAAACCAACAC
58.951
43.478
0.00
0.00
34.35
3.32
4429
5803
1.611491
ACTATGCCAAAACCAACACCG
59.389
47.619
0.00
0.00
0.00
4.94
4430
5804
0.962489
TATGCCAAAACCAACACCGG
59.038
50.000
0.00
0.00
0.00
5.28
4440
5814
1.436195
CCAACACCGGCGATGTATGG
61.436
60.000
7.63
13.97
0.00
2.74
4548
5922
4.937620
TGTTTCTGTCAAGTGATGATAGCC
59.062
41.667
0.00
0.00
44.49
3.93
4584
5958
2.434336
TCACCTATAATGGCTCGTGCTT
59.566
45.455
9.61
0.00
39.59
3.91
4594
5968
0.654683
GCTCGTGCTTGATGACATCC
59.345
55.000
12.90
0.00
36.03
3.51
4616
5990
5.911178
TCCAAAGGGATATTCAGTCTATGGT
59.089
40.000
0.00
0.00
38.64
3.55
4619
5993
7.561356
CCAAAGGGATATTCAGTCTATGGTTTT
59.439
37.037
0.00
0.00
35.59
2.43
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
198
200
7.291411
AGTTCTGGTCTATATGTGTGATACC
57.709
40.000
0.00
0.00
0.00
2.73
206
208
3.133003
AGCGCAAGTTCTGGTCTATATGT
59.867
43.478
11.47
0.00
41.68
2.29
238
240
5.331902
GTGTCCCGTTGATTGATTGTTATG
58.668
41.667
0.00
0.00
0.00
1.90
266
268
3.057174
GTGCAAACACGGGGAATTTCATA
60.057
43.478
0.00
0.00
36.98
2.15
331
333
3.041940
CCGCCGTCCAACACTGTC
61.042
66.667
0.00
0.00
0.00
3.51
362
381
0.173255
CGCAAATTTCCTCCCGCATT
59.827
50.000
0.00
0.00
0.00
3.56
589
608
0.390340
TTCTCATCGTGAGCACTGGC
60.390
55.000
9.34
0.00
43.95
4.85
590
609
1.354040
GTTCTCATCGTGAGCACTGG
58.646
55.000
9.34
0.00
43.95
4.00
789
808
5.102313
GGATTCACCTTTAGCCAATTTTCG
58.898
41.667
0.00
0.00
35.41
3.46
1063
1082
6.072673
CCGGATATGAATTACTTACCTTTGGC
60.073
42.308
0.00
0.00
0.00
4.52
1237
1256
8.694540
CATGATTCATGAAATTTAACCCTGGTA
58.305
33.333
19.84
0.00
43.81
3.25
1238
1257
7.558604
CATGATTCATGAAATTTAACCCTGGT
58.441
34.615
19.84
0.00
43.81
4.00
1239
1258
6.480981
GCATGATTCATGAAATTTAACCCTGG
59.519
38.462
26.94
0.00
43.81
4.45
1240
1259
7.042950
TGCATGATTCATGAAATTTAACCCTG
58.957
34.615
26.94
0.84
43.81
4.45
1295
1318
2.736144
AGAGCGATGTACGTTTTCCA
57.264
45.000
0.00
0.00
44.60
3.53
1511
1534
4.017126
ACTAGTCACATCCTCGTCATTCA
58.983
43.478
0.00
0.00
0.00
2.57
1531
1554
7.172532
TGTTGTTGCTTCGTCTTCATTATTACT
59.827
33.333
0.00
0.00
0.00
2.24
1538
1561
3.466836
TCTGTTGTTGCTTCGTCTTCAT
58.533
40.909
0.00
0.00
0.00
2.57
1619
1642
5.613358
AGCTTTGCAACAGTACTATGTTC
57.387
39.130
0.00
0.00
41.41
3.18
1742
1765
4.005650
AGTGCAACATGAGACGATTTGAT
58.994
39.130
0.00
0.00
41.43
2.57
1814
1837
5.335583
CGCTCAACCACATCCAAAAATTAGA
60.336
40.000
0.00
0.00
0.00
2.10
2040
2063
9.877178
ACAACACTAACAATGGAAAAACAAATA
57.123
25.926
0.00
0.00
0.00
1.40
2113
2136
2.796593
GCAAAACAAGCAACATGGACTC
59.203
45.455
0.00
0.00
0.00
3.36
2221
2244
3.004171
CGACAATTTCGTATGACCCCAA
58.996
45.455
0.00
0.00
43.24
4.12
2255
2278
5.408604
GTGTAGAACAACCACTTCATCGAAT
59.591
40.000
0.00
0.00
0.00
3.34
2406
2429
1.335496
GTACAGAGCTCCTCGGATGTC
59.665
57.143
10.93
0.00
35.36
3.06
2460
2483
0.179150
TTGTGTTCAAACAGCGCACC
60.179
50.000
11.47
0.00
40.05
5.01
2465
2488
6.885735
AATTACAAGTTGTGTTCAAACAGC
57.114
33.333
18.90
0.00
41.98
4.40
2519
2542
2.996631
TGGTTGCAAAATTTGGTGCTT
58.003
38.095
14.29
0.00
41.48
3.91
2613
2636
4.697756
TGCAGCCACGCTACACCC
62.698
66.667
0.00
0.00
36.40
4.61
2646
2669
9.816787
TTAAATTCAAGTAGGGAAAGTAATGGT
57.183
29.630
0.00
0.00
0.00
3.55
2875
2898
5.404946
CCATGCGAATTTCAGAATGTTTCT
58.595
37.500
0.00
0.00
41.70
2.52
2925
2948
6.311815
AGCGATCTCTTCGATTGTCCAAAAA
61.312
40.000
0.00
0.00
45.90
1.94
3050
3078
7.439157
GCAGTTGGATATAATCTGCATGTTA
57.561
36.000
9.99
0.00
46.95
2.41
3059
3087
4.725556
TTTCGCGCAGTTGGATATAATC
57.274
40.909
8.75
0.00
0.00
1.75
3098
3126
9.588096
AATATCAATCCCCTTTAGGATGTTTAC
57.412
33.333
0.00
0.00
46.31
2.01
3364
3392
2.762875
CCGTGGGAGGGAGGTACC
60.763
72.222
2.73
2.73
38.08
3.34
3365
3393
2.038490
ACCGTGGGAGGGAGGTAC
59.962
66.667
0.00
0.00
34.83
3.34
3366
3394
2.361771
GACCGTGGGAGGGAGGTA
59.638
66.667
0.00
0.00
37.07
3.08
3367
3395
4.716977
GGACCGTGGGAGGGAGGT
62.717
72.222
0.00
0.00
40.11
3.85
3368
3396
3.925914
AAGGACCGTGGGAGGGAGG
62.926
68.421
0.00
0.00
35.02
4.30
3369
3397
2.284699
AAGGACCGTGGGAGGGAG
60.285
66.667
0.00
0.00
35.02
4.30
3370
3398
2.284405
GAAGGACCGTGGGAGGGA
60.284
66.667
0.00
0.00
35.02
4.20
3371
3399
1.900545
GAAGAAGGACCGTGGGAGGG
61.901
65.000
0.00
0.00
35.02
4.30
3372
3400
1.192146
TGAAGAAGGACCGTGGGAGG
61.192
60.000
0.00
0.00
37.30
4.30
3373
3401
0.247736
CTGAAGAAGGACCGTGGGAG
59.752
60.000
0.00
0.00
0.00
4.30
3374
3402
1.827399
GCTGAAGAAGGACCGTGGGA
61.827
60.000
0.00
0.00
0.00
4.37
3375
3403
1.376037
GCTGAAGAAGGACCGTGGG
60.376
63.158
0.00
0.00
0.00
4.61
3376
3404
1.738099
CGCTGAAGAAGGACCGTGG
60.738
63.158
0.00
0.00
0.00
4.94
3377
3405
1.738099
CCGCTGAAGAAGGACCGTG
60.738
63.158
0.00
0.00
0.00
4.94
3378
3406
1.469335
TTCCGCTGAAGAAGGACCGT
61.469
55.000
0.00
0.00
33.16
4.83
3379
3407
1.014564
GTTCCGCTGAAGAAGGACCG
61.015
60.000
0.00
0.00
33.16
4.79
3380
3408
0.034896
TGTTCCGCTGAAGAAGGACC
59.965
55.000
0.00
0.00
33.16
4.46
3381
3409
1.433534
CTGTTCCGCTGAAGAAGGAC
58.566
55.000
0.00
0.00
33.16
3.85
3382
3410
0.321671
CCTGTTCCGCTGAAGAAGGA
59.678
55.000
11.95
0.00
37.57
3.36
3383
3411
0.035458
ACCTGTTCCGCTGAAGAAGG
59.965
55.000
14.53
14.53
39.70
3.46
3384
3412
2.338500
GTACCTGTTCCGCTGAAGAAG
58.662
52.381
0.00
0.00
0.00
2.85
3385
3413
1.001633
GGTACCTGTTCCGCTGAAGAA
59.998
52.381
4.06
0.00
0.00
2.52
3386
3414
0.606604
GGTACCTGTTCCGCTGAAGA
59.393
55.000
4.06
0.00
0.00
2.87
3387
3415
0.608640
AGGTACCTGTTCCGCTGAAG
59.391
55.000
15.42
0.00
0.00
3.02
3388
3416
0.606604
GAGGTACCTGTTCCGCTGAA
59.393
55.000
22.10
0.00
0.00
3.02
3389
3417
1.255667
GGAGGTACCTGTTCCGCTGA
61.256
60.000
22.10
0.00
35.41
4.26
3390
3418
1.218316
GGAGGTACCTGTTCCGCTG
59.782
63.158
22.10
0.00
35.41
5.18
3391
3419
1.988406
GGGAGGTACCTGTTCCGCT
60.988
63.158
22.10
0.00
38.98
5.52
3392
3420
1.957765
GAGGGAGGTACCTGTTCCGC
61.958
65.000
22.10
15.41
42.10
5.54
3393
3421
1.328430
GGAGGGAGGTACCTGTTCCG
61.328
65.000
22.10
0.00
42.10
4.30
3394
3422
0.981801
GGGAGGGAGGTACCTGTTCC
60.982
65.000
22.10
21.02
42.10
3.62
3395
3423
0.252558
TGGGAGGGAGGTACCTGTTC
60.253
60.000
22.10
13.29
42.10
3.18
3396
3424
0.546988
GTGGGAGGGAGGTACCTGTT
60.547
60.000
22.10
3.87
42.10
3.16
3397
3425
1.080538
GTGGGAGGGAGGTACCTGT
59.919
63.158
22.10
2.98
42.10
4.00
3398
3426
2.058595
CGTGGGAGGGAGGTACCTG
61.059
68.421
22.10
0.00
42.10
4.00
3399
3427
2.363361
CGTGGGAGGGAGGTACCT
59.637
66.667
16.26
16.26
45.57
3.08
3424
3452
3.375699
TGATAGGGAGAGAAGTTGGGTC
58.624
50.000
0.00
0.00
0.00
4.46
3437
3465
5.601583
TGTTTGCTACGTAATGATAGGGA
57.398
39.130
0.00
0.00
0.00
4.20
3478
3506
4.478206
AGAAACGACATGTCAGGATCAT
57.522
40.909
24.93
4.06
0.00
2.45
3552
3580
0.179004
TCCGTTGATGTTGCCCAAGT
60.179
50.000
0.00
0.00
0.00
3.16
3620
3648
3.259902
ACTTCGGCGATTCCTTTTAGTC
58.740
45.455
11.76
0.00
0.00
2.59
3682
3710
4.540824
GAATGTGAACAGAGCAACCTTTC
58.459
43.478
0.00
0.00
0.00
2.62
3686
3714
1.873591
ACGAATGTGAACAGAGCAACC
59.126
47.619
0.00
0.00
0.00
3.77
3752
3780
5.582269
AGTCAAACATGAATCCACACGATAG
59.418
40.000
0.00
0.00
46.19
2.08
3880
3908
5.623673
GCACATTAGTAAAAACAGAACCACG
59.376
40.000
0.00
0.00
0.00
4.94
3912
3940
6.645790
AGGTCTTCTCGTTGTTAGTAAGAA
57.354
37.500
0.00
0.00
0.00
2.52
3925
3953
3.119316
AGTGCAGATTGTAGGTCTTCTCG
60.119
47.826
0.00
0.00
0.00
4.04
3998
4026
0.329931
AAGAGCGAGGAGAGGAGACA
59.670
55.000
0.00
0.00
0.00
3.41
4001
4029
1.437160
GCAAGAGCGAGGAGAGGAG
59.563
63.158
0.00
0.00
0.00
3.69
4011
4039
0.886490
AACAGGAAGTGGCAAGAGCG
60.886
55.000
0.00
0.00
43.41
5.03
4028
4056
3.338249
TCTCTAGAGCATTGCCACAAAC
58.662
45.455
15.35
0.00
0.00
2.93
4083
4111
2.636830
CAGTTCTTCCCATGTGCCTAG
58.363
52.381
0.00
0.00
0.00
3.02
4084
4112
1.340017
GCAGTTCTTCCCATGTGCCTA
60.340
52.381
0.00
0.00
0.00
3.93
4085
4113
0.610232
GCAGTTCTTCCCATGTGCCT
60.610
55.000
0.00
0.00
0.00
4.75
4086
4114
0.895100
TGCAGTTCTTCCCATGTGCC
60.895
55.000
0.00
0.00
0.00
5.01
4126
4154
1.475682
GATTCTTTCTTGCCCTGCTGG
59.524
52.381
1.89
1.89
37.09
4.85
4197
4225
0.108041
AACCATTACCACGCCTACCG
60.108
55.000
0.00
0.00
44.21
4.02
4288
4316
7.106439
TGCAAAACTTGAGACTTTTGGATAA
57.894
32.000
5.32
0.00
37.68
1.75
4343
4371
8.454894
ACAATAAATACATACGTCAACAATGCA
58.545
29.630
0.00
0.00
0.00
3.96
4371
4399
1.448985
GGACACGTGTGTTGCCATAT
58.551
50.000
28.82
0.00
45.05
1.78
4427
5801
2.327343
CCATGCCATACATCGCCGG
61.327
63.158
0.00
0.00
36.64
6.13
4429
5803
0.534877
TGTCCATGCCATACATCGCC
60.535
55.000
0.00
0.00
36.64
5.54
4430
5804
1.466167
GATGTCCATGCCATACATCGC
59.534
52.381
5.14
0.00
39.90
4.58
4440
5814
6.035843
ACAACAAATTTATCGATGTCCATGC
58.964
36.000
8.54
0.00
0.00
4.06
4548
5922
1.097547
GGTGATGCACAATCTCCCGG
61.098
60.000
0.00
0.00
41.33
5.73
4594
5968
8.408601
CAAAACCATAGACTGAATATCCCTTTG
58.591
37.037
0.00
0.00
0.00
2.77
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.