Multiple sequence alignment - TraesCS3B01G299000
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
TraesCS3B01G299000
chr3B
100.000
2516
0
0
1
2516
479888137
479885622
0.000000e+00
4647.0
1
TraesCS3B01G299000
chr3B
87.435
1743
202
11
1
1732
718831363
718829627
0.000000e+00
1989.0
2
TraesCS3B01G299000
chr3B
97.872
47
1
0
1996
2042
479886106
479886060
5.770000e-12
82.4
3
TraesCS3B01G299000
chr3B
97.872
47
1
0
2032
2078
479886142
479886096
5.770000e-12
82.4
4
TraesCS3B01G299000
chr3B
100.000
33
0
0
1605
1637
479886912
479886880
7.510000e-06
62.1
5
TraesCS3B01G299000
chr6B
85.507
2063
251
30
5
2023
567118189
567116131
0.000000e+00
2109.0
6
TraesCS3B01G299000
chr6B
85.621
1989
223
38
1
1942
446289943
446287971
0.000000e+00
2030.0
7
TraesCS3B01G299000
chr6B
87.493
1743
207
9
1
1732
147950693
147948951
0.000000e+00
2001.0
8
TraesCS3B01G299000
chr6B
100.000
33
0
0
1605
1637
147949462
147949430
7.510000e-06
62.1
9
TraesCS3B01G299000
chr6B
100.000
33
0
0
1605
1637
446288714
446288682
7.510000e-06
62.1
10
TraesCS3B01G299000
chr3D
85.778
2018
237
30
1
1972
558679297
558681310
0.000000e+00
2091.0
11
TraesCS3B01G299000
chr3D
100.000
33
0
0
1605
1637
558680528
558680560
7.510000e-06
62.1
12
TraesCS3B01G299000
chr4D
89.396
1622
160
9
1
1614
473971227
473969610
0.000000e+00
2032.0
13
TraesCS3B01G299000
chr4D
100.000
30
0
0
1608
1637
473969995
473969966
3.500000e-04
56.5
14
TraesCS3B01G299000
chr5B
87.730
1736
199
10
1
1726
659536134
659537865
0.000000e+00
2013.0
15
TraesCS3B01G299000
chr5B
89.006
1619
165
10
1
1611
649874488
649876101
0.000000e+00
1991.0
16
TraesCS3B01G299000
chr5B
100.000
33
0
0
1605
1637
659537365
659537397
7.510000e-06
62.1
17
TraesCS3B01G299000
chr7B
88.964
1622
166
9
1
1614
36428072
36426456
0.000000e+00
1991.0
18
TraesCS3B01G299000
chr7B
85.294
544
72
8
1522
2060
404760431
404759891
2.830000e-154
555.0
19
TraesCS3B01G299000
chr7B
82.736
307
27
10
2192
2492
404759831
404759545
1.490000e-62
250.0
20
TraesCS3B01G299000
chr7B
77.778
234
42
9
2033
2261
404759892
404760120
4.370000e-28
135.0
21
TraesCS3B01G299000
chr7B
100.000
33
0
0
1605
1637
36426844
36426812
7.510000e-06
62.1
22
TraesCS3B01G299000
chr2B
88.758
1610
171
8
1
1603
664330490
664328884
0.000000e+00
1962.0
23
TraesCS3B01G299000
chr7D
85.352
1420
171
28
514
1904
449978235
449976824
0.000000e+00
1435.0
24
TraesCS3B01G299000
chr6D
83.006
1324
182
18
720
2008
345634645
345635960
0.000000e+00
1158.0
25
TraesCS3B01G299000
chr5D
84.658
541
65
15
1509
2042
391235690
391236219
7.970000e-145
523.0
26
TraesCS3B01G299000
chr5D
88.095
252
28
2
2032
2281
391236173
391236424
5.260000e-77
298.0
27
TraesCS3B01G299000
chr5D
87.591
137
10
4
2381
2513
391236499
391236632
4.330000e-33
152.0
28
TraesCS3B01G299000
chr5D
96.970
33
1
0
1605
1637
387243004
387243036
3.500000e-04
56.5
29
TraesCS3B01G299000
chr5D
96.970
33
1
0
1605
1637
391235455
391235487
3.500000e-04
56.5
30
TraesCS3B01G299000
chr2D
100.000
33
0
0
1605
1637
12314846
12314814
7.510000e-06
62.1
31
TraesCS3B01G299000
chr1D
100.000
33
0
0
1605
1637
491070534
491070502
7.510000e-06
62.1
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
TraesCS3B01G299000
chr3B
479885622
479888137
2515
True
1218.475
4647
98.9360
1
2516
4
chr3B.!!$R2
2515
1
TraesCS3B01G299000
chr3B
718829627
718831363
1736
True
1989.000
1989
87.4350
1
1732
1
chr3B.!!$R1
1731
2
TraesCS3B01G299000
chr6B
567116131
567118189
2058
True
2109.000
2109
85.5070
5
2023
1
chr6B.!!$R1
2018
3
TraesCS3B01G299000
chr6B
446287971
446289943
1972
True
1046.050
2030
92.8105
1
1942
2
chr6B.!!$R3
1941
4
TraesCS3B01G299000
chr6B
147948951
147950693
1742
True
1031.550
2001
93.7465
1
1732
2
chr6B.!!$R2
1731
5
TraesCS3B01G299000
chr3D
558679297
558681310
2013
False
1076.550
2091
92.8890
1
1972
2
chr3D.!!$F1
1971
6
TraesCS3B01G299000
chr4D
473969610
473971227
1617
True
1044.250
2032
94.6980
1
1637
2
chr4D.!!$R1
1636
7
TraesCS3B01G299000
chr5B
649874488
649876101
1613
False
1991.000
1991
89.0060
1
1611
1
chr5B.!!$F1
1610
8
TraesCS3B01G299000
chr5B
659536134
659537865
1731
False
1037.550
2013
93.8650
1
1726
2
chr5B.!!$F2
1725
9
TraesCS3B01G299000
chr7B
36426456
36428072
1616
True
1026.550
1991
94.4820
1
1637
2
chr7B.!!$R1
1636
10
TraesCS3B01G299000
chr7B
404759545
404760431
886
True
402.500
555
84.0150
1522
2492
2
chr7B.!!$R2
970
11
TraesCS3B01G299000
chr2B
664328884
664330490
1606
True
1962.000
1962
88.7580
1
1603
1
chr2B.!!$R1
1602
12
TraesCS3B01G299000
chr7D
449976824
449978235
1411
True
1435.000
1435
85.3520
514
1904
1
chr7D.!!$R1
1390
13
TraesCS3B01G299000
chr6D
345634645
345635960
1315
False
1158.000
1158
83.0060
720
2008
1
chr6D.!!$F1
1288
14
TraesCS3B01G299000
chr5D
391235455
391236632
1177
False
257.375
523
89.3285
1509
2513
4
chr5D.!!$F2
1004
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
174
177
0.035056
GTGGACAAGCTAGGTGGCAT
60.035
55.0
0.0
0.0
34.17
4.4
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1528
1546
0.037882
TCTTCACGAGCAGCCTTCTG
60.038
55.0
0.0
0.0
43.16
3.02
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
57
58
5.163519
CGCCAAATGGATAGGTGAGAAAAAT
60.164
40.000
2.98
0.00
37.39
1.82
106
109
1.322442
GGTTTCAAGCAGGCAAGTCT
58.678
50.000
0.00
0.00
0.00
3.24
174
177
0.035056
GTGGACAAGCTAGGTGGCAT
60.035
55.000
0.00
0.00
34.17
4.40
184
187
2.418197
GCTAGGTGGCATAACACGAGAA
60.418
50.000
0.00
0.00
42.23
2.87
199
202
2.225963
ACGAGAAGGTGTGACTTACGAG
59.774
50.000
0.00
0.00
35.70
4.18
200
203
2.483106
CGAGAAGGTGTGACTTACGAGA
59.517
50.000
0.00
0.00
34.59
4.04
246
249
0.107214
AACCAGTGGTGTCAGTGTGG
60.107
55.000
17.56
0.00
41.52
4.17
247
250
0.980754
ACCAGTGGTGTCAGTGTGGA
60.981
55.000
15.86
0.00
41.52
4.02
262
265
4.040755
AGTGTGGAAGGCCTCATAAGTAT
58.959
43.478
5.23
0.00
39.63
2.12
283
286
3.386867
CTGGCCGTGCTCGCATTTC
62.387
63.158
1.89
0.00
35.54
2.17
312
315
0.884514
GCCAAGGAGAGAAACTTGCC
59.115
55.000
0.00
0.00
42.01
4.52
363
367
2.508526
GAGTTCACATTGGAAGCCACT
58.491
47.619
0.00
0.00
30.78
4.00
430
434
0.471617
GTGGCCTGAGTATGATGGCT
59.528
55.000
3.32
0.00
44.36
4.75
494
504
7.885922
GGGAAGAAGAAGAAAGAAGAGGTTTAT
59.114
37.037
0.00
0.00
0.00
1.40
547
557
5.304101
ACCAGAATGAAACAATTTGGTAGCA
59.696
36.000
0.78
0.00
39.69
3.49
553
563
5.771469
TGAAACAATTTGGTAGCAGTCATG
58.229
37.500
0.78
0.00
0.00
3.07
566
576
1.065636
CAGTCATGTCATGGAGCCACT
60.066
52.381
12.90
5.72
0.00
4.00
602
612
3.906660
GACAATGTGACGGTCCAGA
57.093
52.632
5.55
0.00
0.00
3.86
718
728
1.612442
GGAGGTAGGAGTGGTGGCA
60.612
63.158
0.00
0.00
0.00
4.92
728
738
2.447572
TGGTGGCAGTGGAGGACA
60.448
61.111
0.00
0.00
0.00
4.02
741
751
4.290196
AGTGGAGGACAGACTAGTCTTAGT
59.710
45.833
23.01
18.07
42.79
2.24
784
794
1.622607
TATTGGTGGGCGTGGAGGAG
61.623
60.000
0.00
0.00
0.00
3.69
795
805
0.610687
GTGGAGGAGGGACAAGTCTG
59.389
60.000
0.00
0.00
0.00
3.51
825
835
4.115199
GGGGGCGGTCATGCTTCT
62.115
66.667
0.00
0.00
34.52
2.85
827
837
2.268920
GGGCGGTCATGCTTCTGA
59.731
61.111
0.00
0.00
34.52
3.27
832
842
1.470098
GCGGTCATGCTTCTGATGTTT
59.530
47.619
0.00
0.00
0.00
2.83
845
855
3.769844
TCTGATGTTTCTAGGAGGTGGAC
59.230
47.826
0.00
0.00
0.00
4.02
883
894
7.462571
AGGCCTATTGACGTTTTTCTTAATT
57.537
32.000
1.29
0.00
0.00
1.40
886
897
7.238571
GCCTATTGACGTTTTTCTTAATTCGA
58.761
34.615
0.00
0.00
0.00
3.71
1011
1025
3.370840
TTTGTAGGCATGGCTTCATCT
57.629
42.857
28.30
4.19
0.00
2.90
1032
1046
4.804420
TCCATGAGGAGGCCGCCT
62.804
66.667
30.18
30.18
39.61
5.52
1048
1062
0.308993
GCCTTGTGCTGACTGTGAAC
59.691
55.000
0.00
0.00
36.87
3.18
1275
1289
5.671493
CCGGTATGGTCAAAGAGTAATCTT
58.329
41.667
0.00
0.00
0.00
2.40
1308
1325
7.965107
GGTTCAACTTCAAGTCATAATGCTAAG
59.035
37.037
0.00
0.00
0.00
2.18
1370
1388
4.769688
TGCAAGTACTTCACATGGATAGG
58.230
43.478
4.77
0.00
0.00
2.57
1381
1399
6.806668
TCACATGGATAGGTCAAGATGTTA
57.193
37.500
0.00
0.00
0.00
2.41
1410
1428
5.590259
AGATGTTCAAAAGGACCAATATCGG
59.410
40.000
0.00
0.00
0.00
4.18
1415
1433
5.515106
TCAAAAGGACCAATATCGGGATTT
58.485
37.500
0.00
0.00
0.00
2.17
1432
1450
2.943036
TTTTCTTAGGAGGCAACGGT
57.057
45.000
0.00
0.00
46.39
4.83
1459
1477
3.060003
CGAAGAAGCATATCAAAGAGCCG
60.060
47.826
0.00
0.00
0.00
5.52
1466
1484
2.533266
TATCAAAGAGCCGAGGATGC
57.467
50.000
0.00
0.00
0.00
3.91
1468
1486
0.324614
TCAAAGAGCCGAGGATGCAA
59.675
50.000
0.00
0.00
0.00
4.08
1479
1497
2.560861
GATGCAAAGCGCCGTCAA
59.439
55.556
2.29
0.00
41.33
3.18
1513
1531
2.622064
ACGAAAGAAGTGCAAGGAGT
57.378
45.000
0.00
0.00
0.00
3.85
1520
1538
2.180276
GAAGTGCAAGGAGTAGAGGGA
58.820
52.381
0.00
0.00
0.00
4.20
1528
1546
4.065789
CAAGGAGTAGAGGGAACACAAAC
58.934
47.826
0.00
0.00
0.00
2.93
1604
1622
0.179936
CAAGAGGAGGATGAGGCACC
59.820
60.000
0.00
0.00
0.00
5.01
1607
1625
0.467804
GAGGAGGATGAGGCACCTTC
59.532
60.000
0.00
0.00
36.57
3.46
1611
1629
0.329596
AGGATGAGGCACCTTCCAAC
59.670
55.000
9.57
0.00
34.01
3.77
1614
1632
2.238521
GATGAGGCACCTTCCAACAAA
58.761
47.619
0.00
0.00
0.00
2.83
1615
1633
1.398692
TGAGGCACCTTCCAACAAAC
58.601
50.000
0.00
0.00
0.00
2.93
1618
1636
1.299850
GCACCTTCCAACAAACGCC
60.300
57.895
0.00
0.00
0.00
5.68
1619
1637
1.734388
GCACCTTCCAACAAACGCCT
61.734
55.000
0.00
0.00
0.00
5.52
1621
1639
2.159382
CACCTTCCAACAAACGCCTAT
58.841
47.619
0.00
0.00
0.00
2.57
1623
1641
2.224670
ACCTTCCAACAAACGCCTATGA
60.225
45.455
0.00
0.00
0.00
2.15
1625
1643
1.434555
TCCAACAAACGCCTATGACG
58.565
50.000
0.00
0.00
0.00
4.35
1628
1646
2.093152
CCAACAAACGCCTATGACGTAC
59.907
50.000
0.00
0.00
44.30
3.67
1629
1647
2.000429
ACAAACGCCTATGACGTACC
58.000
50.000
0.00
0.00
44.30
3.34
1630
1648
1.273048
ACAAACGCCTATGACGTACCA
59.727
47.619
0.00
0.00
44.30
3.25
1631
1649
1.657094
CAAACGCCTATGACGTACCAC
59.343
52.381
0.00
0.00
44.30
4.16
1632
1650
0.174162
AACGCCTATGACGTACCACC
59.826
55.000
0.00
0.00
44.30
4.61
1633
1651
1.298863
CGCCTATGACGTACCACCG
60.299
63.158
0.00
0.00
0.00
4.94
1634
1652
1.066918
GCCTATGACGTACCACCGG
59.933
63.158
0.00
0.00
0.00
5.28
1636
1654
1.679139
CCTATGACGTACCACCGGTA
58.321
55.000
6.87
0.00
37.09
4.02
1668
1689
2.482485
GCGTTAGTGAAGTTGTACGC
57.518
50.000
0.00
0.00
45.73
4.42
1767
1846
9.783256
ACTTTAGTGTTAAAACAGACAAATGTC
57.217
29.630
5.40
5.40
45.08
3.06
1800
1879
7.848223
TGTGACTGAAATATTGTCAGGTATG
57.152
36.000
21.37
7.11
45.66
2.39
1965
2046
2.880879
CGCATCCGACCAGACACG
60.881
66.667
0.00
0.00
36.29
4.49
2006
2087
3.744003
TACCGAGCCCTACCGCCAT
62.744
63.158
0.00
0.00
0.00
4.40
2027
2108
4.221422
GAGCGGCGGTAGGATGCA
62.221
66.667
13.22
0.00
0.00
3.96
2028
2109
4.530857
AGCGGCGGTAGGATGCAC
62.531
66.667
11.06
0.00
0.00
4.57
2030
2111
4.155733
CGGCGGTAGGATGCACCA
62.156
66.667
0.00
0.00
42.04
4.17
2031
2112
2.513897
GGCGGTAGGATGCACCAC
60.514
66.667
7.86
4.50
42.04
4.16
2032
2113
2.513897
GCGGTAGGATGCACCACC
60.514
66.667
7.86
10.63
42.04
4.61
2033
2114
2.189521
CGGTAGGATGCACCACCC
59.810
66.667
7.86
5.90
42.04
4.61
2034
2115
2.367202
CGGTAGGATGCACCACCCT
61.367
63.158
7.86
6.15
42.04
4.34
2035
2116
1.046472
CGGTAGGATGCACCACCCTA
61.046
60.000
7.86
5.29
42.04
3.53
2037
2118
0.468648
GTAGGATGCACCACCCTACC
59.531
60.000
18.42
7.26
44.02
3.18
2038
2119
1.046472
TAGGATGCACCACCCTACCG
61.046
60.000
7.86
0.00
42.04
4.02
2039
2120
2.513897
GATGCACCACCCTACCGC
60.514
66.667
0.00
0.00
0.00
5.68
2040
2121
4.109675
ATGCACCACCCTACCGCC
62.110
66.667
0.00
0.00
0.00
6.13
2081
2162
3.319198
CCACCCTACCGCCACTGT
61.319
66.667
0.00
0.00
0.00
3.55
2121
2202
3.114616
ACTCGCACGCAGCATCAC
61.115
61.111
0.00
0.00
46.13
3.06
2128
2209
0.239082
CACGCAGCATCACACATGTT
59.761
50.000
0.00
0.00
0.00
2.71
2159
2240
0.824759
GCGTGAGAACCAGGGTCTAT
59.175
55.000
7.13
0.00
0.00
1.98
2160
2241
1.202428
GCGTGAGAACCAGGGTCTATC
60.202
57.143
7.13
2.54
0.00
2.08
2161
2242
1.065701
CGTGAGAACCAGGGTCTATCG
59.934
57.143
7.13
11.53
0.00
2.92
2162
2243
1.112113
TGAGAACCAGGGTCTATCGC
58.888
55.000
7.13
0.00
0.00
4.58
2163
2244
0.389757
GAGAACCAGGGTCTATCGCC
59.610
60.000
7.13
0.00
0.00
5.54
2164
2245
0.325296
AGAACCAGGGTCTATCGCCA
60.325
55.000
4.67
0.00
0.00
5.69
2165
2246
0.179081
GAACCAGGGTCTATCGCCAC
60.179
60.000
0.00
0.00
0.00
5.01
2166
2247
0.617820
AACCAGGGTCTATCGCCACT
60.618
55.000
0.00
0.00
0.00
4.00
2167
2248
1.330655
ACCAGGGTCTATCGCCACTG
61.331
60.000
0.00
0.00
0.00
3.66
2168
2249
1.330655
CCAGGGTCTATCGCCACTGT
61.331
60.000
0.00
0.00
0.00
3.55
2169
2250
0.103208
CAGGGTCTATCGCCACTGTC
59.897
60.000
0.00
0.00
0.00
3.51
2170
2251
0.033011
AGGGTCTATCGCCACTGTCT
60.033
55.000
0.00
0.00
0.00
3.41
2171
2252
0.386113
GGGTCTATCGCCACTGTCTC
59.614
60.000
0.00
0.00
0.00
3.36
2172
2253
0.386113
GGTCTATCGCCACTGTCTCC
59.614
60.000
0.00
0.00
0.00
3.71
2173
2254
0.029567
GTCTATCGCCACTGTCTCCG
59.970
60.000
0.00
0.00
0.00
4.63
2174
2255
1.101635
TCTATCGCCACTGTCTCCGG
61.102
60.000
0.00
0.00
0.00
5.14
2175
2256
2.685387
CTATCGCCACTGTCTCCGGC
62.685
65.000
0.00
0.00
42.64
6.13
2179
2260
3.066190
CCACTGTCTCCGGCGGTA
61.066
66.667
27.32
12.96
0.00
4.02
2180
2261
2.490217
CACTGTCTCCGGCGGTAG
59.510
66.667
27.32
20.80
0.00
3.18
2181
2262
3.450115
ACTGTCTCCGGCGGTAGC
61.450
66.667
27.32
16.58
44.18
3.58
2191
2272
2.357517
GCGGTAGCAGTGCACACT
60.358
61.111
21.04
17.92
44.35
3.55
2192
2273
2.383527
GCGGTAGCAGTGCACACTC
61.384
63.158
21.04
7.26
44.35
3.51
2193
2274
1.290324
CGGTAGCAGTGCACACTCT
59.710
57.895
21.04
14.40
40.20
3.24
2194
2275
0.526211
CGGTAGCAGTGCACACTCTA
59.474
55.000
21.04
13.39
40.20
2.43
2211
2328
0.898789
CTACCACCACAGACTCCGGT
60.899
60.000
0.00
0.00
0.00
5.28
2238
2355
2.301583
GGGCTAAATCCCTGCAAAACAA
59.698
45.455
0.00
0.00
43.13
2.83
2266
2383
4.666512
AGCAACATGTTAGACAGGGAAAT
58.333
39.130
11.53
0.00
33.62
2.17
2267
2384
4.460382
AGCAACATGTTAGACAGGGAAATG
59.540
41.667
11.53
0.00
33.62
2.32
2268
2385
4.458989
GCAACATGTTAGACAGGGAAATGA
59.541
41.667
11.53
0.00
33.62
2.57
2269
2386
5.048083
GCAACATGTTAGACAGGGAAATGAA
60.048
40.000
11.53
0.00
33.62
2.57
2270
2387
6.516527
GCAACATGTTAGACAGGGAAATGAAA
60.517
38.462
11.53
0.00
33.62
2.69
2271
2388
7.432869
CAACATGTTAGACAGGGAAATGAAAA
58.567
34.615
11.53
0.00
33.62
2.29
2272
2389
7.595819
ACATGTTAGACAGGGAAATGAAAAA
57.404
32.000
0.00
0.00
33.62
1.94
2273
2390
7.661040
ACATGTTAGACAGGGAAATGAAAAAG
58.339
34.615
0.00
0.00
33.62
2.27
2274
2391
7.505585
ACATGTTAGACAGGGAAATGAAAAAGA
59.494
33.333
0.00
0.00
33.62
2.52
2294
2411
9.665719
AAAAAGAATGTGTATCTTTTGGTTGTT
57.334
25.926
13.24
0.00
45.79
2.83
2309
2460
4.883083
TGGTTGTTAACTTTGTTGCACAA
58.117
34.783
7.22
0.00
36.11
3.33
2325
2476
7.824672
TGTTGCACAAGGAAAAATGAAAAATT
58.175
26.923
0.00
0.00
0.00
1.82
2369
2520
4.582240
TGGTAGTTCAAATGACATGCAACA
59.418
37.500
0.00
0.00
0.00
3.33
2370
2521
5.243507
TGGTAGTTCAAATGACATGCAACAT
59.756
36.000
0.00
0.00
0.00
2.71
2371
2522
5.801947
GGTAGTTCAAATGACATGCAACATC
59.198
40.000
0.00
0.00
0.00
3.06
2373
2524
3.490800
TCAAATGACATGCAACATCCG
57.509
42.857
0.00
0.00
0.00
4.18
2374
2525
3.080319
TCAAATGACATGCAACATCCGA
58.920
40.909
0.00
0.00
0.00
4.55
2376
2527
4.880696
TCAAATGACATGCAACATCCGATA
59.119
37.500
0.00
0.00
0.00
2.92
2377
2528
5.356470
TCAAATGACATGCAACATCCGATAA
59.644
36.000
0.00
0.00
0.00
1.75
2378
2529
6.039605
TCAAATGACATGCAACATCCGATAAT
59.960
34.615
0.00
0.00
0.00
1.28
2379
2530
7.228308
TCAAATGACATGCAACATCCGATAATA
59.772
33.333
0.00
0.00
0.00
0.98
2393
2544
9.173021
ACATCCGATAATAAGTTCAAATGACAA
57.827
29.630
0.00
0.00
0.00
3.18
2407
2558
6.148948
TCAAATGACAAAAATCATGTCCGAC
58.851
36.000
4.40
0.00
45.19
4.79
2422
2573
2.155155
GTCCGACAGCGTTAGTTCAAAG
59.845
50.000
0.00
0.00
35.23
2.77
2428
2579
2.096909
CAGCGTTAGTTCAAAGGACACG
60.097
50.000
0.00
0.00
0.00
4.49
2437
2588
2.503331
TCAAAGGACACGCATCATGTT
58.497
42.857
0.00
0.00
0.00
2.71
2491
2646
6.751888
GCCATTATAGTTCAAATGACCAACAC
59.248
38.462
0.00
0.00
35.53
3.32
2496
2651
3.059166
GTTCAAATGACCAACACCATGC
58.941
45.455
0.00
0.00
0.00
4.06
2498
2653
0.975887
AAATGACCAACACCATGCCC
59.024
50.000
0.00
0.00
0.00
5.36
2513
2668
0.756903
TGCCCGGTAGAATCCTAAGC
59.243
55.000
0.00
0.00
0.00
3.09
2514
2669
0.756903
GCCCGGTAGAATCCTAAGCA
59.243
55.000
0.00
0.00
0.00
3.91
2515
2670
1.348036
GCCCGGTAGAATCCTAAGCAT
59.652
52.381
0.00
0.00
0.00
3.79
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
57
58
6.961360
ATCATCAACCTTGTCGAGATACTA
57.039
37.500
0.00
0.00
0.00
1.82
64
66
3.417069
ACCAATCATCAACCTTGTCGA
57.583
42.857
0.00
0.00
0.00
4.20
106
109
7.760437
TGAATCTAATGATTTGTTGATGCGAA
58.240
30.769
0.00
0.00
42.43
4.70
174
177
4.555313
CGTAAGTCACACCTTCTCGTGTTA
60.555
45.833
0.00
0.00
44.57
2.41
184
187
2.584236
ACACTCTCGTAAGTCACACCT
58.416
47.619
0.00
0.00
39.48
4.00
246
249
4.636249
CCAGTGATACTTATGAGGCCTTC
58.364
47.826
6.77
0.10
0.00
3.46
247
250
3.181450
GCCAGTGATACTTATGAGGCCTT
60.181
47.826
6.77
0.00
34.94
4.35
283
286
4.776322
TCCTTGGCCGCCGTCATG
62.776
66.667
4.58
0.00
0.00
3.07
312
315
0.176680
CGGTCCTCCCATCAGAACAG
59.823
60.000
0.00
0.00
0.00
3.16
337
341
2.189594
TCCAATGTGAACTCCTGCAG
57.810
50.000
6.78
6.78
0.00
4.41
363
367
2.252072
GAGGCGCCCATGTCAACCTA
62.252
60.000
26.15
0.00
0.00
3.08
494
504
4.038883
CAGCTAGATCATCCATGTCACTCA
59.961
45.833
0.00
0.00
0.00
3.41
547
557
1.065636
CAGTGGCTCCATGACATGACT
60.066
52.381
17.24
8.77
35.31
3.41
553
563
0.674895
GTGTCCAGTGGCTCCATGAC
60.675
60.000
3.51
0.00
0.00
3.06
566
576
2.028130
GTCCACAATTGTTGGTGTCCA
58.972
47.619
8.77
0.00
33.19
4.02
602
612
3.758554
GGTGCATCTCCTAACATTGTGTT
59.241
43.478
0.00
0.67
43.88
3.32
698
708
0.910088
GCCACCACTCCTACCTCCTT
60.910
60.000
0.00
0.00
0.00
3.36
718
728
3.818295
AAGACTAGTCTGTCCTCCACT
57.182
47.619
25.83
4.12
40.36
4.00
728
738
4.701171
GTGCACTACCACTAAGACTAGTCT
59.299
45.833
20.00
20.00
36.14
3.24
741
751
3.056458
CCACCTCGTGCACTACCA
58.944
61.111
16.19
0.00
31.34
3.25
784
794
0.036858
GCACCTCTCAGACTTGTCCC
60.037
60.000
0.00
0.00
0.00
4.46
795
805
3.866582
CCCCCATCGGCACCTCTC
61.867
72.222
0.00
0.00
0.00
3.20
813
823
3.005554
AGAAACATCAGAAGCATGACCG
58.994
45.455
0.00
0.00
30.46
4.79
825
835
3.516586
TGTCCACCTCCTAGAAACATCA
58.483
45.455
0.00
0.00
0.00
3.07
827
837
5.014123
TCAATTGTCCACCTCCTAGAAACAT
59.986
40.000
5.13
0.00
0.00
2.71
832
842
5.777449
TCTATCAATTGTCCACCTCCTAGA
58.223
41.667
5.13
0.00
0.00
2.43
845
855
6.429385
GTCAATAGGCCTTCCTCTATCAATTG
59.571
42.308
12.58
10.95
43.06
2.32
958
972
9.912634
AGTGGTTGTTAGTGAAAAATATCAATG
57.087
29.630
0.00
0.00
0.00
2.82
1011
1025
2.669133
CGGCCTCCTCATGGAACCA
61.669
63.158
0.00
0.00
42.66
3.67
1032
1046
2.106477
TGTGTTCACAGTCAGCACAA
57.894
45.000
0.00
0.00
37.16
3.33
1042
1056
3.063316
CACTTGTTCGACATGTGTTCACA
59.937
43.478
1.15
8.09
44.42
3.58
1071
1085
4.834496
TCCTTCATCTTGTCAAATTTGGCT
59.166
37.500
22.47
0.29
33.01
4.75
1080
1094
9.519191
TTCATATCTTTTTCCTTCATCTTGTCA
57.481
29.630
0.00
0.00
0.00
3.58
1129
1143
3.561143
ACACCTTCACCTTGCAAACATA
58.439
40.909
0.00
0.00
0.00
2.29
1315
1333
5.401550
CGGTGACTGCATATGAAAAACATT
58.598
37.500
6.97
0.00
40.07
2.71
1316
1334
4.675146
GCGGTGACTGCATATGAAAAACAT
60.675
41.667
12.26
0.00
42.39
2.71
1370
1388
7.658179
TGAACATCTTCTGTAACATCTTGAC
57.342
36.000
0.00
0.00
36.98
3.18
1381
1399
4.792068
TGGTCCTTTTGAACATCTTCTGT
58.208
39.130
0.00
0.00
35.14
3.41
1410
1428
2.683362
CCGTTGCCTCCTAAGAAAATCC
59.317
50.000
0.00
0.00
0.00
3.01
1415
1433
1.418637
ACAACCGTTGCCTCCTAAGAA
59.581
47.619
11.29
0.00
0.00
2.52
1432
1450
6.402550
GCTCTTTGATATGCTTCTTCGAACAA
60.403
38.462
0.00
0.00
0.00
2.83
1466
1484
0.385974
CTCCTTTTGACGGCGCTTTG
60.386
55.000
6.90
0.00
0.00
2.77
1468
1486
0.534203
TTCTCCTTTTGACGGCGCTT
60.534
50.000
6.90
0.00
0.00
4.68
1479
1497
5.228945
TCTTTCGTTCCATCTTCTCCTTT
57.771
39.130
0.00
0.00
0.00
3.11
1513
1531
3.496160
GCCTTCTGTTTGTGTTCCCTCTA
60.496
47.826
0.00
0.00
0.00
2.43
1520
1538
1.678101
GAGCAGCCTTCTGTTTGTGTT
59.322
47.619
0.00
0.00
42.29
3.32
1528
1546
0.037882
TCTTCACGAGCAGCCTTCTG
60.038
55.000
0.00
0.00
43.16
3.02
1604
1622
2.159707
CGTCATAGGCGTTTGTTGGAAG
60.160
50.000
0.00
0.00
0.00
3.46
1607
1625
1.153353
ACGTCATAGGCGTTTGTTGG
58.847
50.000
0.00
0.00
39.79
3.77
1611
1629
1.657094
GTGGTACGTCATAGGCGTTTG
59.343
52.381
0.86
0.00
42.85
2.93
1614
1632
1.811860
GGTGGTACGTCATAGGCGT
59.188
57.895
1.34
1.34
45.11
5.68
1615
1633
1.298863
CGGTGGTACGTCATAGGCG
60.299
63.158
0.00
0.00
0.00
5.52
1626
1644
0.895100
ACAAGCTCGTACCGGTGGTA
60.895
55.000
19.93
0.22
37.09
3.25
1628
1646
1.736645
CACAAGCTCGTACCGGTGG
60.737
63.158
19.93
9.49
0.00
4.61
1629
1647
1.007336
GTCACAAGCTCGTACCGGTG
61.007
60.000
19.93
0.15
0.00
4.94
1630
1648
1.288127
GTCACAAGCTCGTACCGGT
59.712
57.895
13.98
13.98
0.00
5.28
1631
1649
1.800315
CGTCACAAGCTCGTACCGG
60.800
63.158
0.00
0.00
0.00
5.28
1632
1650
2.434134
GCGTCACAAGCTCGTACCG
61.434
63.158
0.00
0.00
0.00
4.02
1633
1651
2.434134
CGCGTCACAAGCTCGTACC
61.434
63.158
0.00
0.00
0.00
3.34
1634
1652
1.273455
AACGCGTCACAAGCTCGTAC
61.273
55.000
14.44
0.00
32.71
3.67
1636
1654
1.002250
CTAACGCGTCACAAGCTCGT
61.002
55.000
14.44
0.00
34.63
4.18
1637
1655
1.002250
ACTAACGCGTCACAAGCTCG
61.002
55.000
14.44
0.00
0.00
5.03
1640
1660
0.856641
TTCACTAACGCGTCACAAGC
59.143
50.000
14.44
0.00
0.00
4.01
1648
1668
1.201629
GCGTACAACTTCACTAACGCG
60.202
52.381
3.53
3.53
44.88
6.01
1668
1689
5.859114
CGAAATACCATCGAATAGTCTCAGG
59.141
44.000
0.00
0.00
42.76
3.86
1718
1754
8.340618
AGTTCAACATACATAGTTCAAGCATT
57.659
30.769
0.00
0.00
0.00
3.56
1767
1846
7.974675
ACAATATTTCAGTCACAAATAGGTCG
58.025
34.615
0.00
0.00
30.94
4.79
1800
1879
8.079809
ACATAACTAAACAAGCAACATTGGTAC
58.920
33.333
0.00
0.00
38.04
3.34
1866
1947
1.453762
CTCCGGCGGTAGGGTCTAAG
61.454
65.000
27.32
8.56
0.00
2.18
1965
2046
0.530744
TCCCGTGCAGTATCAGACAC
59.469
55.000
0.00
0.00
0.00
3.67
1982
2063
0.822944
GGTAGGGCTCGGTACTCTCC
60.823
65.000
0.00
0.00
0.00
3.71
2006
2087
4.862447
TCCTACCGCCGCTCGCTA
62.862
66.667
0.00
0.00
36.73
4.26
2010
2091
4.221422
TGCATCCTACCGCCGCTC
62.221
66.667
0.00
0.00
0.00
5.03
2011
2092
4.530857
GTGCATCCTACCGCCGCT
62.531
66.667
0.00
0.00
0.00
5.52
2013
2094
4.155733
TGGTGCATCCTACCGCCG
62.156
66.667
0.00
0.00
41.18
6.46
2023
2104
4.109675
GGCGGTAGGGTGGTGCAT
62.110
66.667
0.00
0.00
0.00
3.96
2025
2106
2.660258
CTATGGCGGTAGGGTGGTGC
62.660
65.000
0.00
0.00
0.00
5.01
2026
2107
1.445942
CTATGGCGGTAGGGTGGTG
59.554
63.158
0.00
0.00
0.00
4.17
2027
2108
2.440817
GCTATGGCGGTAGGGTGGT
61.441
63.158
0.00
0.00
0.00
4.16
2028
2109
2.426023
GCTATGGCGGTAGGGTGG
59.574
66.667
0.00
0.00
0.00
4.61
2081
2162
4.613143
GGGTCCTACCGCCATAGA
57.387
61.111
0.00
0.00
39.83
1.98
2104
2185
3.114616
GTGATGCTGCGTGCGAGT
61.115
61.111
0.00
0.00
46.63
4.18
2110
2191
0.953727
AAACATGTGTGATGCTGCGT
59.046
45.000
0.00
0.00
0.00
5.24
2121
2202
1.875963
GCCCGACCAGAAACATGTG
59.124
57.895
0.00
0.00
0.00
3.21
2162
2243
3.064987
CTACCGCCGGAGACAGTGG
62.065
68.421
11.71
0.00
39.63
4.00
2163
2244
2.490217
CTACCGCCGGAGACAGTG
59.510
66.667
11.71
0.00
0.00
3.66
2164
2245
3.450115
GCTACCGCCGGAGACAGT
61.450
66.667
11.71
0.00
0.00
3.55
2165
2246
3.417275
CTGCTACCGCCGGAGACAG
62.417
68.421
11.71
9.96
34.43
3.51
2166
2247
3.449227
CTGCTACCGCCGGAGACA
61.449
66.667
11.71
3.06
34.43
3.41
2167
2248
3.450115
ACTGCTACCGCCGGAGAC
61.450
66.667
11.71
0.00
34.43
3.36
2168
2249
3.449227
CACTGCTACCGCCGGAGA
61.449
66.667
11.71
0.00
34.43
3.71
2173
2254
3.423154
GTGTGCACTGCTACCGCC
61.423
66.667
19.41
0.00
34.43
6.13
2174
2255
2.357517
AGTGTGCACTGCTACCGC
60.358
61.111
19.41
0.00
40.75
5.68
2175
2256
0.526211
TAGAGTGTGCACTGCTACCG
59.474
55.000
19.41
0.00
42.66
4.02
2176
2257
1.404315
GGTAGAGTGTGCACTGCTACC
60.404
57.143
29.69
29.69
44.65
3.18
2177
2258
1.272490
TGGTAGAGTGTGCACTGCTAC
59.728
52.381
23.83
23.83
42.66
3.58
2178
2259
1.272490
GTGGTAGAGTGTGCACTGCTA
59.728
52.381
19.41
13.21
42.66
3.49
2179
2260
0.034059
GTGGTAGAGTGTGCACTGCT
59.966
55.000
19.41
15.77
42.66
4.24
2180
2261
0.951040
GGTGGTAGAGTGTGCACTGC
60.951
60.000
19.41
11.00
42.66
4.40
2181
2262
0.392706
TGGTGGTAGAGTGTGCACTG
59.607
55.000
19.41
0.00
42.66
3.66
2182
2263
0.393077
GTGGTGGTAGAGTGTGCACT
59.607
55.000
19.41
4.31
45.84
4.40
2183
2264
0.105964
TGTGGTGGTAGAGTGTGCAC
59.894
55.000
10.75
10.75
0.00
4.57
2184
2265
0.392706
CTGTGGTGGTAGAGTGTGCA
59.607
55.000
0.00
0.00
0.00
4.57
2185
2266
0.679505
TCTGTGGTGGTAGAGTGTGC
59.320
55.000
0.00
0.00
0.00
4.57
2186
2267
1.964223
AGTCTGTGGTGGTAGAGTGTG
59.036
52.381
0.00
0.00
0.00
3.82
2187
2268
2.240279
GAGTCTGTGGTGGTAGAGTGT
58.760
52.381
0.00
0.00
0.00
3.55
2188
2269
1.546476
GGAGTCTGTGGTGGTAGAGTG
59.454
57.143
0.00
0.00
0.00
3.51
2189
2270
1.887088
CGGAGTCTGTGGTGGTAGAGT
60.887
57.143
0.00
0.00
0.00
3.24
2190
2271
0.811915
CGGAGTCTGTGGTGGTAGAG
59.188
60.000
0.00
0.00
0.00
2.43
2191
2272
0.611062
CCGGAGTCTGTGGTGGTAGA
60.611
60.000
0.00
0.00
0.00
2.59
2192
2273
0.898789
ACCGGAGTCTGTGGTGGTAG
60.899
60.000
9.46
0.00
33.91
3.18
2193
2274
1.154454
ACCGGAGTCTGTGGTGGTA
59.846
57.895
9.46
0.00
33.91
3.25
2194
2275
2.122989
ACCGGAGTCTGTGGTGGT
60.123
61.111
9.46
0.00
33.91
4.16
2238
2355
5.010012
CCCTGTCTAACATGTTGCTTCTTTT
59.990
40.000
21.42
0.00
0.00
2.27
2266
2383
9.311916
CAACCAAAAGATACACATTCTTTTTCA
57.688
29.630
8.30
0.00
46.18
2.69
2267
2384
9.313118
ACAACCAAAAGATACACATTCTTTTTC
57.687
29.630
8.30
0.00
46.18
2.29
2268
2385
9.665719
AACAACCAAAAGATACACATTCTTTTT
57.334
25.926
8.30
0.00
46.18
1.94
2271
2388
9.744468
GTTAACAACCAAAAGATACACATTCTT
57.256
29.630
0.00
0.00
34.95
2.52
2272
2389
9.131791
AGTTAACAACCAAAAGATACACATTCT
57.868
29.630
8.61
0.00
0.00
2.40
2273
2390
9.744468
AAGTTAACAACCAAAAGATACACATTC
57.256
29.630
8.61
0.00
0.00
2.67
2325
2476
5.186409
ACCATTCGTTGCTAGTTCCTACTTA
59.814
40.000
0.00
0.00
35.78
2.24
2328
2479
3.858247
ACCATTCGTTGCTAGTTCCTAC
58.142
45.455
0.00
0.00
0.00
3.18
2332
2483
4.927425
TGAACTACCATTCGTTGCTAGTTC
59.073
41.667
18.81
18.81
45.59
3.01
2342
2493
5.030295
GCATGTCATTTGAACTACCATTCG
58.970
41.667
0.00
0.00
0.00
3.34
2378
2529
9.474920
GGACATGATTTTTGTCATTTGAACTTA
57.525
29.630
0.00
0.00
44.22
2.24
2379
2530
7.169645
CGGACATGATTTTTGTCATTTGAACTT
59.830
33.333
0.00
0.00
44.22
2.66
2393
2544
1.808411
ACGCTGTCGGACATGATTTT
58.192
45.000
11.86
0.00
40.69
1.82
2407
2558
2.096909
CGTGTCCTTTGAACTAACGCTG
60.097
50.000
0.00
0.00
0.00
5.18
2422
2573
1.290203
ATCGAACATGATGCGTGTCC
58.710
50.000
0.00
0.00
31.86
4.02
2428
2579
1.502231
ACCGCTATCGAACATGATGC
58.498
50.000
0.00
0.00
38.10
3.91
2437
2588
3.249320
GTGTGTCATACTACCGCTATCGA
59.751
47.826
0.00
0.00
38.10
3.59
2491
2646
1.348064
TAGGATTCTACCGGGCATGG
58.652
55.000
6.32
0.00
34.73
3.66
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.