Multiple sequence alignment - TraesCS4B01G130500
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
TraesCS4B01G130500
chr4B
100.000
2408
0
0
1
2408
171120450
171122857
0.000000e+00
4447.0
1
TraesCS4B01G130500
chr4B
95.767
1441
60
1
1
1440
90758864
90760304
0.000000e+00
2322.0
2
TraesCS4B01G130500
chr4B
91.390
813
54
5
1602
2408
43809950
43809148
0.000000e+00
1099.0
3
TraesCS4B01G130500
chr4B
90.954
807
61
7
1603
2408
18434524
18433729
0.000000e+00
1075.0
4
TraesCS4B01G130500
chr4B
91.105
787
48
8
1601
2386
188180501
188181266
0.000000e+00
1046.0
5
TraesCS4B01G130500
chr4B
89.885
781
50
14
1629
2408
325999469
326000221
0.000000e+00
977.0
6
TraesCS4B01G130500
chr4B
90.909
121
11
0
1484
1604
171825861
171825741
1.920000e-36
163.0
7
TraesCS4B01G130500
chr1B
95.417
1440
62
4
4
1440
22438502
22437064
0.000000e+00
2290.0
8
TraesCS4B01G130500
chr1B
95.136
1439
67
3
4
1440
22565145
22563708
0.000000e+00
2266.0
9
TraesCS4B01G130500
chr1B
94.920
1437
70
3
4
1438
22498477
22497042
0.000000e+00
2246.0
10
TraesCS4B01G130500
chr1B
94.367
1438
80
1
4
1440
22378751
22377314
0.000000e+00
2206.0
11
TraesCS4B01G130500
chr1B
92.395
789
39
8
1602
2389
491366531
491365763
0.000000e+00
1105.0
12
TraesCS4B01G130500
chr1B
82.609
414
56
5
1015
1428
447244085
447243688
3.810000e-93
351.0
13
TraesCS4B01G130500
chr4A
95.076
1442
70
1
1
1441
674778437
674779878
0.000000e+00
2268.0
14
TraesCS4B01G130500
chr4A
95.043
807
37
2
1602
2408
651446744
651445941
0.000000e+00
1266.0
15
TraesCS4B01G130500
chr4A
93.277
119
8
0
1484
1602
466917027
466916909
2.460000e-40
176.0
16
TraesCS4B01G130500
chr7D
94.244
1442
80
3
1
1440
89059986
89061426
0.000000e+00
2200.0
17
TraesCS4B01G130500
chr7D
93.741
1438
72
10
4
1440
514921711
514920291
0.000000e+00
2141.0
18
TraesCS4B01G130500
chr4D
94.254
1427
81
1
1
1426
208377431
208378857
0.000000e+00
2180.0
19
TraesCS4B01G130500
chr4D
90.984
122
9
1
1484
1603
109919742
109919863
1.920000e-36
163.0
20
TraesCS4B01G130500
chr7B
92.278
790
40
6
1602
2389
468864770
468864000
0.000000e+00
1101.0
21
TraesCS4B01G130500
chr7B
92.381
735
50
5
1600
2331
733162065
733161334
0.000000e+00
1042.0
22
TraesCS4B01G130500
chr7B
89.550
823
65
10
1596
2408
546883520
546884331
0.000000e+00
1024.0
23
TraesCS4B01G130500
chr2B
90.965
808
62
6
1602
2408
76511628
76510831
0.000000e+00
1077.0
24
TraesCS4B01G130500
chr3B
90.864
810
46
14
1602
2408
678017296
678016512
0.000000e+00
1061.0
25
TraesCS4B01G130500
chr5B
90.959
365
24
4
1605
1969
379362110
379361755
1.290000e-132
483.0
26
TraesCS4B01G130500
chr3D
100.000
28
0
0
1441
1468
2766750
2766723
4.000000e-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
TraesCS4B01G130500
chr4B
171120450
171122857
2407
False
4447
4447
100.000
1
2408
1
chr4B.!!$F2
2407
1
TraesCS4B01G130500
chr4B
90758864
90760304
1440
False
2322
2322
95.767
1
1440
1
chr4B.!!$F1
1439
2
TraesCS4B01G130500
chr4B
43809148
43809950
802
True
1099
1099
91.390
1602
2408
1
chr4B.!!$R2
806
3
TraesCS4B01G130500
chr4B
18433729
18434524
795
True
1075
1075
90.954
1603
2408
1
chr4B.!!$R1
805
4
TraesCS4B01G130500
chr4B
188180501
188181266
765
False
1046
1046
91.105
1601
2386
1
chr4B.!!$F3
785
5
TraesCS4B01G130500
chr4B
325999469
326000221
752
False
977
977
89.885
1629
2408
1
chr4B.!!$F4
779
6
TraesCS4B01G130500
chr1B
22437064
22438502
1438
True
2290
2290
95.417
4
1440
1
chr1B.!!$R2
1436
7
TraesCS4B01G130500
chr1B
22563708
22565145
1437
True
2266
2266
95.136
4
1440
1
chr1B.!!$R4
1436
8
TraesCS4B01G130500
chr1B
22497042
22498477
1435
True
2246
2246
94.920
4
1438
1
chr1B.!!$R3
1434
9
TraesCS4B01G130500
chr1B
22377314
22378751
1437
True
2206
2206
94.367
4
1440
1
chr1B.!!$R1
1436
10
TraesCS4B01G130500
chr1B
491365763
491366531
768
True
1105
1105
92.395
1602
2389
1
chr1B.!!$R6
787
11
TraesCS4B01G130500
chr4A
674778437
674779878
1441
False
2268
2268
95.076
1
1441
1
chr4A.!!$F1
1440
12
TraesCS4B01G130500
chr4A
651445941
651446744
803
True
1266
1266
95.043
1602
2408
1
chr4A.!!$R2
806
13
TraesCS4B01G130500
chr7D
89059986
89061426
1440
False
2200
2200
94.244
1
1440
1
chr7D.!!$F1
1439
14
TraesCS4B01G130500
chr7D
514920291
514921711
1420
True
2141
2141
93.741
4
1440
1
chr7D.!!$R1
1436
15
TraesCS4B01G130500
chr4D
208377431
208378857
1426
False
2180
2180
94.254
1
1426
1
chr4D.!!$F2
1425
16
TraesCS4B01G130500
chr7B
468864000
468864770
770
True
1101
1101
92.278
1602
2389
1
chr7B.!!$R1
787
17
TraesCS4B01G130500
chr7B
733161334
733162065
731
True
1042
1042
92.381
1600
2331
1
chr7B.!!$R2
731
18
TraesCS4B01G130500
chr7B
546883520
546884331
811
False
1024
1024
89.550
1596
2408
1
chr7B.!!$F1
812
19
TraesCS4B01G130500
chr2B
76510831
76511628
797
True
1077
1077
90.965
1602
2408
1
chr2B.!!$R1
806
20
TraesCS4B01G130500
chr3B
678016512
678017296
784
True
1061
1061
90.864
1602
2408
1
chr3B.!!$R1
806
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
470
473
0.111253
AAGGCCCTTTGGTCAGTCAG
59.889
55.0
0.0
0.0
39.4
3.51
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1900
1905
0.178873
AGGGGAAGAACTGCCTGGTA
60.179
55.0
0.0
0.0
35.37
3.25
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
34
35
1.347707
TCATCTTCCTTCACTTGGCGT
59.652
47.619
0.00
0.00
0.00
5.68
177
179
1.002544
GATTCTCCCTATTCCGGCTGG
59.997
57.143
4.71
4.71
0.00
4.85
405
407
7.309770
ACTTCTTCTTCTCTACAAGTGGAAT
57.690
36.000
0.00
0.00
0.00
3.01
432
434
2.158755
AGGGTCTGGCTTCCAATATTCG
60.159
50.000
0.00
0.00
30.80
3.34
470
473
0.111253
AAGGCCCTTTGGTCAGTCAG
59.889
55.000
0.00
0.00
39.40
3.51
592
595
2.103432
TGTTTCTTCTGCAACCGGACTA
59.897
45.455
9.46
0.00
0.00
2.59
595
598
1.968493
TCTTCTGCAACCGGACTAAGT
59.032
47.619
9.46
0.00
0.00
2.24
622
625
1.350351
AGCATCTCTTCCTGCTGTGTT
59.650
47.619
0.00
0.00
46.55
3.32
628
631
1.768275
TCTTCCTGCTGTGTTCCTTCA
59.232
47.619
0.00
0.00
0.00
3.02
672
675
2.829741
AAGAGGAGTTCAGTGTCAGC
57.170
50.000
0.00
0.00
0.00
4.26
788
791
5.283763
TCTATGGCATATCTGGGAAGCTAT
58.716
41.667
7.81
0.00
0.00
2.97
904
907
1.632965
GCCTAAACCCGATCCCAGGT
61.633
60.000
0.00
0.00
38.27
4.00
915
918
1.208293
GATCCCAGGTGTGAGTCTTCC
59.792
57.143
0.00
0.00
0.00
3.46
928
931
5.119694
GTGAGTCTTCCTCTTCAACTGTTT
58.880
41.667
0.00
0.00
41.11
2.83
930
933
5.817816
TGAGTCTTCCTCTTCAACTGTTTTC
59.182
40.000
0.00
0.00
41.11
2.29
997
1000
2.803492
GCGCTGTTTCCTTCTATCCGAT
60.803
50.000
0.00
0.00
0.00
4.18
1082
1085
2.371510
AGCTTCAAGGCTTCTCTGAACT
59.628
45.455
0.00
0.00
39.86
3.01
1140
1143
2.632996
TGAGGTTTGTCGATCTGAAGGT
59.367
45.455
0.00
0.00
0.00
3.50
1154
1157
3.003275
TCTGAAGGTTGTTCGTCAATTGC
59.997
43.478
0.00
0.00
38.38
3.56
1177
1180
1.227205
GCATCTGACTGCCTCCTCG
60.227
63.158
2.04
0.00
36.10
4.63
1321
1324
2.242047
TGTAGCGGCACACAAACTAA
57.758
45.000
1.45
0.00
0.00
2.24
1325
1328
0.941542
GCGGCACACAAACTAACTCA
59.058
50.000
0.00
0.00
0.00
3.41
1343
1346
4.446994
CTCATAGTTGTGAGCACTCTGA
57.553
45.455
1.99
0.00
39.19
3.27
1395
1399
4.345859
TTGTATCAGGGACGAACTTTGT
57.654
40.909
0.00
0.00
0.00
2.83
1405
1409
4.439563
GGGACGAACTTTGTTGTGATGTTT
60.440
41.667
0.00
0.00
0.00
2.83
1458
1462
6.670695
AAAAAGTTCTCCCAATGTGCTTAT
57.329
33.333
0.00
0.00
0.00
1.73
1459
1463
6.670695
AAAAGTTCTCCCAATGTGCTTATT
57.329
33.333
0.00
0.00
0.00
1.40
1460
1464
6.670695
AAAGTTCTCCCAATGTGCTTATTT
57.329
33.333
0.00
0.00
0.00
1.40
1461
1465
5.904362
AGTTCTCCCAATGTGCTTATTTC
57.096
39.130
0.00
0.00
0.00
2.17
1462
1466
5.574188
AGTTCTCCCAATGTGCTTATTTCT
58.426
37.500
0.00
0.00
0.00
2.52
1463
1467
5.416952
AGTTCTCCCAATGTGCTTATTTCTG
59.583
40.000
0.00
0.00
0.00
3.02
1464
1468
4.272489
TCTCCCAATGTGCTTATTTCTGG
58.728
43.478
0.00
0.00
0.00
3.86
1465
1469
4.018506
TCTCCCAATGTGCTTATTTCTGGA
60.019
41.667
0.00
0.00
0.00
3.86
1466
1470
4.870636
TCCCAATGTGCTTATTTCTGGAT
58.129
39.130
0.00
0.00
0.00
3.41
1467
1471
6.012337
TCCCAATGTGCTTATTTCTGGATA
57.988
37.500
0.00
0.00
0.00
2.59
1468
1472
5.827797
TCCCAATGTGCTTATTTCTGGATAC
59.172
40.000
0.00
0.00
0.00
2.24
1469
1473
5.829924
CCCAATGTGCTTATTTCTGGATACT
59.170
40.000
0.00
0.00
37.61
2.12
1470
1474
6.322201
CCCAATGTGCTTATTTCTGGATACTT
59.678
38.462
0.00
0.00
37.61
2.24
1471
1475
7.198390
CCAATGTGCTTATTTCTGGATACTTG
58.802
38.462
0.00
0.00
37.61
3.16
1472
1476
5.818136
TGTGCTTATTTCTGGATACTTGC
57.182
39.130
0.00
0.00
37.61
4.01
1473
1477
4.332543
TGTGCTTATTTCTGGATACTTGCG
59.667
41.667
0.00
0.00
37.61
4.85
1474
1478
3.312421
TGCTTATTTCTGGATACTTGCGC
59.688
43.478
0.00
0.00
37.61
6.09
1475
1479
3.312421
GCTTATTTCTGGATACTTGCGCA
59.688
43.478
5.66
5.66
37.61
6.09
1476
1480
4.553547
GCTTATTTCTGGATACTTGCGCAG
60.554
45.833
11.31
7.81
37.61
5.18
1489
1493
4.767255
CGCAGCCCACTCCCACTC
62.767
72.222
0.00
0.00
0.00
3.51
1490
1494
3.325753
GCAGCCCACTCCCACTCT
61.326
66.667
0.00
0.00
0.00
3.24
1491
1495
1.990060
GCAGCCCACTCCCACTCTA
60.990
63.158
0.00
0.00
0.00
2.43
1492
1496
1.901085
CAGCCCACTCCCACTCTAC
59.099
63.158
0.00
0.00
0.00
2.59
1493
1497
0.904865
CAGCCCACTCCCACTCTACA
60.905
60.000
0.00
0.00
0.00
2.74
1494
1498
0.616111
AGCCCACTCCCACTCTACAG
60.616
60.000
0.00
0.00
0.00
2.74
1495
1499
1.617947
GCCCACTCCCACTCTACAGG
61.618
65.000
0.00
0.00
0.00
4.00
1496
1500
0.252284
CCCACTCCCACTCTACAGGT
60.252
60.000
0.00
0.00
0.00
4.00
1497
1501
1.645710
CCACTCCCACTCTACAGGTT
58.354
55.000
0.00
0.00
0.00
3.50
1498
1502
1.978580
CCACTCCCACTCTACAGGTTT
59.021
52.381
0.00
0.00
0.00
3.27
1499
1503
2.372172
CCACTCCCACTCTACAGGTTTT
59.628
50.000
0.00
0.00
0.00
2.43
1500
1504
3.403038
CACTCCCACTCTACAGGTTTTG
58.597
50.000
0.00
0.00
0.00
2.44
1501
1505
2.372172
ACTCCCACTCTACAGGTTTTGG
59.628
50.000
0.00
0.00
0.00
3.28
1502
1506
1.702957
TCCCACTCTACAGGTTTTGGG
59.297
52.381
0.00
0.00
44.51
4.12
1503
1507
1.702957
CCCACTCTACAGGTTTTGGGA
59.297
52.381
0.00
0.00
45.81
4.37
1504
1508
2.290323
CCCACTCTACAGGTTTTGGGAG
60.290
54.545
0.00
0.00
45.81
4.30
1505
1509
2.637872
CCACTCTACAGGTTTTGGGAGA
59.362
50.000
0.00
0.00
35.85
3.71
1506
1510
3.072476
CCACTCTACAGGTTTTGGGAGAA
59.928
47.826
0.00
0.00
35.85
2.87
1507
1511
4.319177
CACTCTACAGGTTTTGGGAGAAG
58.681
47.826
0.00
0.00
35.85
2.85
1508
1512
4.040461
CACTCTACAGGTTTTGGGAGAAGA
59.960
45.833
0.00
0.00
35.85
2.87
1509
1513
4.284746
ACTCTACAGGTTTTGGGAGAAGAG
59.715
45.833
0.00
0.00
35.85
2.85
1510
1514
4.489737
TCTACAGGTTTTGGGAGAAGAGA
58.510
43.478
0.00
0.00
0.00
3.10
1511
1515
3.778954
ACAGGTTTTGGGAGAAGAGAG
57.221
47.619
0.00
0.00
0.00
3.20
1512
1516
3.318313
ACAGGTTTTGGGAGAAGAGAGA
58.682
45.455
0.00
0.00
0.00
3.10
1513
1517
3.716872
ACAGGTTTTGGGAGAAGAGAGAA
59.283
43.478
0.00
0.00
0.00
2.87
1514
1518
4.166144
ACAGGTTTTGGGAGAAGAGAGAAA
59.834
41.667
0.00
0.00
0.00
2.52
1515
1519
4.759183
CAGGTTTTGGGAGAAGAGAGAAAG
59.241
45.833
0.00
0.00
0.00
2.62
1516
1520
4.660771
AGGTTTTGGGAGAAGAGAGAAAGA
59.339
41.667
0.00
0.00
0.00
2.52
1517
1521
5.132816
AGGTTTTGGGAGAAGAGAGAAAGAA
59.867
40.000
0.00
0.00
0.00
2.52
1518
1522
5.828328
GGTTTTGGGAGAAGAGAGAAAGAAA
59.172
40.000
0.00
0.00
0.00
2.52
1519
1523
6.321435
GGTTTTGGGAGAAGAGAGAAAGAAAA
59.679
38.462
0.00
0.00
0.00
2.29
1520
1524
7.014711
GGTTTTGGGAGAAGAGAGAAAGAAAAT
59.985
37.037
0.00
0.00
0.00
1.82
1521
1525
7.516198
TTTGGGAGAAGAGAGAAAGAAAATG
57.484
36.000
0.00
0.00
0.00
2.32
1522
1526
6.192970
TGGGAGAAGAGAGAAAGAAAATGT
57.807
37.500
0.00
0.00
0.00
2.71
1523
1527
6.234177
TGGGAGAAGAGAGAAAGAAAATGTC
58.766
40.000
0.00
0.00
0.00
3.06
1524
1528
5.350091
GGGAGAAGAGAGAAAGAAAATGTCG
59.650
44.000
0.00
0.00
0.00
4.35
1525
1529
6.159988
GGAGAAGAGAGAAAGAAAATGTCGA
58.840
40.000
0.00
0.00
0.00
4.20
1526
1530
6.816140
GGAGAAGAGAGAAAGAAAATGTCGAT
59.184
38.462
0.00
0.00
0.00
3.59
1527
1531
7.201513
GGAGAAGAGAGAAAGAAAATGTCGATG
60.202
40.741
0.00
0.00
0.00
3.84
1528
1532
6.593382
AGAAGAGAGAAAGAAAATGTCGATGG
59.407
38.462
0.00
0.00
0.00
3.51
1529
1533
4.633565
AGAGAGAAAGAAAATGTCGATGGC
59.366
41.667
0.00
0.00
0.00
4.40
1530
1534
4.583871
AGAGAAAGAAAATGTCGATGGCT
58.416
39.130
0.00
0.00
0.00
4.75
1531
1535
4.394300
AGAGAAAGAAAATGTCGATGGCTG
59.606
41.667
0.00
0.00
0.00
4.85
1532
1536
2.927553
AAGAAAATGTCGATGGCTGC
57.072
45.000
0.00
0.00
0.00
5.25
1533
1537
1.098050
AGAAAATGTCGATGGCTGCC
58.902
50.000
12.87
12.87
0.00
4.85
1534
1538
0.810648
GAAAATGTCGATGGCTGCCA
59.189
50.000
25.65
25.65
38.19
4.92
1535
1539
0.813184
AAAATGTCGATGGCTGCCAG
59.187
50.000
27.20
14.42
36.75
4.85
1536
1540
1.660560
AAATGTCGATGGCTGCCAGC
61.661
55.000
26.21
26.21
41.46
4.85
1541
1545
3.344215
GATGGCTGCCAGCGATCG
61.344
66.667
27.20
11.69
44.33
3.69
1542
1546
3.797225
GATGGCTGCCAGCGATCGA
62.797
63.158
27.20
0.00
44.33
3.59
1543
1547
3.804153
ATGGCTGCCAGCGATCGAG
62.804
63.158
27.20
10.27
43.62
4.04
1553
1557
4.899239
CGATCGAGGCAGGCCACC
62.899
72.222
10.26
6.01
38.92
4.61
1554
1558
3.785859
GATCGAGGCAGGCCACCA
61.786
66.667
16.52
0.00
38.92
4.17
1555
1559
3.092511
ATCGAGGCAGGCCACCAT
61.093
61.111
16.52
0.00
38.92
3.55
1556
1560
2.615227
GATCGAGGCAGGCCACCATT
62.615
60.000
16.52
0.00
38.92
3.16
1557
1561
2.898920
ATCGAGGCAGGCCACCATTG
62.899
60.000
16.52
0.85
38.92
2.82
1558
1562
2.356278
GAGGCAGGCCACCATTGA
59.644
61.111
16.52
0.00
38.92
2.57
1559
1563
1.076485
GAGGCAGGCCACCATTGAT
60.076
57.895
16.52
0.00
38.92
2.57
1560
1564
1.380785
AGGCAGGCCACCATTGATG
60.381
57.895
16.52
0.00
38.92
3.07
1572
1576
2.581216
CATTGATGGAGATGGGGGAG
57.419
55.000
0.00
0.00
0.00
4.30
1573
1577
2.060275
CATTGATGGAGATGGGGGAGA
58.940
52.381
0.00
0.00
0.00
3.71
1574
1578
2.285275
TTGATGGAGATGGGGGAGAA
57.715
50.000
0.00
0.00
0.00
2.87
1575
1579
1.811778
TGATGGAGATGGGGGAGAAG
58.188
55.000
0.00
0.00
0.00
2.85
1576
1580
1.063183
GATGGAGATGGGGGAGAAGG
58.937
60.000
0.00
0.00
0.00
3.46
1577
1581
0.348370
ATGGAGATGGGGGAGAAGGT
59.652
55.000
0.00
0.00
0.00
3.50
1578
1582
0.621571
TGGAGATGGGGGAGAAGGTG
60.622
60.000
0.00
0.00
0.00
4.00
1579
1583
1.348775
GGAGATGGGGGAGAAGGTGG
61.349
65.000
0.00
0.00
0.00
4.61
1580
1584
0.621862
GAGATGGGGGAGAAGGTGGT
60.622
60.000
0.00
0.00
0.00
4.16
1581
1585
0.916358
AGATGGGGGAGAAGGTGGTG
60.916
60.000
0.00
0.00
0.00
4.17
1582
1586
1.926426
GATGGGGGAGAAGGTGGTGG
61.926
65.000
0.00
0.00
0.00
4.61
1583
1587
3.339093
GGGGGAGAAGGTGGTGGG
61.339
72.222
0.00
0.00
0.00
4.61
1584
1588
4.048470
GGGGAGAAGGTGGTGGGC
62.048
72.222
0.00
0.00
0.00
5.36
1585
1589
4.410400
GGGAGAAGGTGGTGGGCG
62.410
72.222
0.00
0.00
0.00
6.13
1586
1590
3.637273
GGAGAAGGTGGTGGGCGT
61.637
66.667
0.00
0.00
0.00
5.68
1587
1591
2.358737
GAGAAGGTGGTGGGCGTG
60.359
66.667
0.00
0.00
0.00
5.34
1588
1592
4.643387
AGAAGGTGGTGGGCGTGC
62.643
66.667
0.00
0.00
0.00
5.34
1643
1647
3.441163
CTGATGCCCAAATCAAATCACG
58.559
45.455
0.00
0.00
36.16
4.35
1686
1690
4.640771
AATTCACTCTGCTGACCCTTTA
57.359
40.909
0.00
0.00
0.00
1.85
1835
1839
0.037697
CTAGGCGCCACACTGTAACA
60.038
55.000
31.54
0.00
0.00
2.41
1931
1937
0.183971
CTTCCCCTCTCCGCTCTCTA
59.816
60.000
0.00
0.00
0.00
2.43
1983
2009
4.169452
CCCCCACATCCCTCTCAA
57.831
61.111
0.00
0.00
0.00
3.02
2044
2070
3.950395
TCCTACTAGGTAAACTCTTCCGC
59.050
47.826
1.83
0.00
36.53
5.54
2069
2095
4.923281
CCCTTTCTTTTGCTCCGTAAATTG
59.077
41.667
0.00
0.00
0.00
2.32
2074
2100
4.339814
TCTTTTGCTCCGTAAATTGGTTGT
59.660
37.500
0.00
0.00
0.00
3.32
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
2
3
2.848694
AGGAAGATGATCTTGGCTTGGA
59.151
45.455
13.18
0.00
36.73
3.53
34
35
2.025155
TGACGCCCAAAAAGCAAACTA
58.975
42.857
0.00
0.00
0.00
2.24
390
392
2.265367
TGCCCATTCCACTTGTAGAGA
58.735
47.619
0.00
0.00
0.00
3.10
405
407
3.185203
AAGCCAGACCCTTGCCCA
61.185
61.111
0.00
0.00
0.00
5.36
470
473
7.538303
ACAATCTTCATTTTGTTTGGACAAC
57.462
32.000
0.00
0.00
45.01
3.32
592
595
2.289945
GGAAGAGATGCTCCACACACTT
60.290
50.000
0.00
0.00
0.00
3.16
595
598
1.277273
CAGGAAGAGATGCTCCACACA
59.723
52.381
0.00
0.00
0.00
3.72
650
653
4.241681
GCTGACACTGAACTCCTCTTTAG
58.758
47.826
0.00
0.00
0.00
1.85
672
675
7.362056
CCATTAACCATGTCTTTTCTACACAGG
60.362
40.741
0.00
0.00
33.68
4.00
749
752
4.443457
GCCATAGAGTGATAGCCAAGACAA
60.443
45.833
0.00
0.00
0.00
3.18
788
791
9.844790
CGGTATCATTATTACGTACCTCATTTA
57.155
33.333
0.00
0.00
34.12
1.40
915
918
4.513318
GGAGTCCAGAAAACAGTTGAAGAG
59.487
45.833
3.60
0.00
0.00
2.85
928
931
2.203788
AGGTGGCGGAGTCCAGAA
60.204
61.111
10.49
0.00
34.66
3.02
930
933
4.767255
GCAGGTGGCGGAGTCCAG
62.767
72.222
10.49
3.25
34.66
3.86
997
1000
1.686455
CAAAGCCCATGCCCATCCA
60.686
57.895
0.00
0.00
38.69
3.41
1082
1085
4.704833
GCGCCTCAGCCAACTCCA
62.705
66.667
0.00
0.00
34.57
3.86
1140
1143
2.468831
GCCAAAGCAATTGACGAACAA
58.531
42.857
10.34
0.00
41.85
2.83
1174
1177
4.273480
AGACTTGATTTTGTTCACCACGAG
59.727
41.667
0.00
0.00
0.00
4.18
1175
1178
4.196193
AGACTTGATTTTGTTCACCACGA
58.804
39.130
0.00
0.00
0.00
4.35
1177
1180
5.440685
CGTAGACTTGATTTTGTTCACCAC
58.559
41.667
0.00
0.00
0.00
4.16
1321
1324
3.829026
TCAGAGTGCTCACAACTATGAGT
59.171
43.478
2.63
0.00
46.65
3.41
1325
1328
7.358770
AGATTATCAGAGTGCTCACAACTAT
57.641
36.000
2.63
0.00
0.00
2.12
1356
1360
0.251165
AATCCGGAACCACACCAAGG
60.251
55.000
9.01
0.00
0.00
3.61
1441
1445
4.706476
CCAGAAATAAGCACATTGGGAGAA
59.294
41.667
0.00
0.00
0.00
2.87
1442
1446
4.018506
TCCAGAAATAAGCACATTGGGAGA
60.019
41.667
0.00
0.00
0.00
3.71
1443
1447
4.272489
TCCAGAAATAAGCACATTGGGAG
58.728
43.478
0.00
0.00
0.00
4.30
1444
1448
4.314522
TCCAGAAATAAGCACATTGGGA
57.685
40.909
0.00
0.00
0.00
4.37
1445
1449
5.829924
AGTATCCAGAAATAAGCACATTGGG
59.170
40.000
0.00
0.00
0.00
4.12
1446
1450
6.949352
AGTATCCAGAAATAAGCACATTGG
57.051
37.500
0.00
0.00
0.00
3.16
1447
1451
6.694411
GCAAGTATCCAGAAATAAGCACATTG
59.306
38.462
0.00
0.00
0.00
2.82
1448
1452
6.458751
CGCAAGTATCCAGAAATAAGCACATT
60.459
38.462
0.00
0.00
0.00
2.71
1449
1453
5.008019
CGCAAGTATCCAGAAATAAGCACAT
59.992
40.000
0.00
0.00
0.00
3.21
1450
1454
4.332543
CGCAAGTATCCAGAAATAAGCACA
59.667
41.667
0.00
0.00
0.00
4.57
1451
1455
4.786609
GCGCAAGTATCCAGAAATAAGCAC
60.787
45.833
0.30
0.00
41.68
4.40
1452
1456
3.312421
GCGCAAGTATCCAGAAATAAGCA
59.688
43.478
0.30
0.00
41.68
3.91
1453
1457
3.312421
TGCGCAAGTATCCAGAAATAAGC
59.688
43.478
8.16
0.00
41.68
3.09
1454
1458
4.553547
GCTGCGCAAGTATCCAGAAATAAG
60.554
45.833
13.05
0.00
41.68
1.73
1455
1459
3.312421
GCTGCGCAAGTATCCAGAAATAA
59.688
43.478
13.05
0.00
41.68
1.40
1456
1460
2.872245
GCTGCGCAAGTATCCAGAAATA
59.128
45.455
13.05
0.00
41.68
1.40
1457
1461
1.672881
GCTGCGCAAGTATCCAGAAAT
59.327
47.619
13.05
0.00
41.68
2.17
1458
1462
1.086696
GCTGCGCAAGTATCCAGAAA
58.913
50.000
13.05
0.00
41.68
2.52
1459
1463
0.744414
GGCTGCGCAAGTATCCAGAA
60.744
55.000
13.05
0.00
38.19
3.02
1460
1464
1.153369
GGCTGCGCAAGTATCCAGA
60.153
57.895
13.05
0.00
38.19
3.86
1461
1465
2.182842
GGGCTGCGCAAGTATCCAG
61.183
63.158
13.05
0.00
40.22
3.86
1462
1466
2.124736
GGGCTGCGCAAGTATCCA
60.125
61.111
13.05
0.00
40.22
3.41
1463
1467
2.124736
TGGGCTGCGCAAGTATCC
60.125
61.111
17.53
9.26
37.52
2.59
1464
1468
1.432270
GAGTGGGCTGCGCAAGTATC
61.432
60.000
21.38
12.67
41.68
2.24
1465
1469
1.450312
GAGTGGGCTGCGCAAGTAT
60.450
57.895
21.38
7.74
41.68
2.12
1466
1470
2.047274
GAGTGGGCTGCGCAAGTA
60.047
61.111
21.38
0.00
41.68
2.24
1472
1476
4.767255
GAGTGGGAGTGGGCTGCG
62.767
72.222
0.00
0.00
33.52
5.18
1473
1477
1.990060
TAGAGTGGGAGTGGGCTGC
60.990
63.158
0.00
0.00
0.00
5.25
1474
1478
0.904865
TGTAGAGTGGGAGTGGGCTG
60.905
60.000
0.00
0.00
0.00
4.85
1475
1479
0.616111
CTGTAGAGTGGGAGTGGGCT
60.616
60.000
0.00
0.00
0.00
5.19
1476
1480
1.617947
CCTGTAGAGTGGGAGTGGGC
61.618
65.000
0.00
0.00
0.00
5.36
1477
1481
0.252284
ACCTGTAGAGTGGGAGTGGG
60.252
60.000
0.00
0.00
0.00
4.61
1478
1482
1.645710
AACCTGTAGAGTGGGAGTGG
58.354
55.000
0.00
0.00
0.00
4.00
1479
1483
3.403038
CAAAACCTGTAGAGTGGGAGTG
58.597
50.000
0.00
0.00
0.00
3.51
1480
1484
2.372172
CCAAAACCTGTAGAGTGGGAGT
59.628
50.000
0.00
0.00
0.00
3.85
1481
1485
3.059352
CCAAAACCTGTAGAGTGGGAG
57.941
52.381
0.00
0.00
0.00
4.30
1483
1487
1.702957
TCCCAAAACCTGTAGAGTGGG
59.297
52.381
6.90
6.90
46.01
4.61
1484
1488
2.637872
TCTCCCAAAACCTGTAGAGTGG
59.362
50.000
0.00
0.00
0.00
4.00
1485
1489
4.040461
TCTTCTCCCAAAACCTGTAGAGTG
59.960
45.833
0.00
0.00
0.00
3.51
1486
1490
4.232091
TCTTCTCCCAAAACCTGTAGAGT
58.768
43.478
0.00
0.00
0.00
3.24
1487
1491
4.528596
TCTCTTCTCCCAAAACCTGTAGAG
59.471
45.833
0.00
0.00
0.00
2.43
1488
1492
4.489737
TCTCTTCTCCCAAAACCTGTAGA
58.510
43.478
0.00
0.00
0.00
2.59
1489
1493
4.528596
TCTCTCTTCTCCCAAAACCTGTAG
59.471
45.833
0.00
0.00
0.00
2.74
1490
1494
4.489737
TCTCTCTTCTCCCAAAACCTGTA
58.510
43.478
0.00
0.00
0.00
2.74
1491
1495
3.318313
TCTCTCTTCTCCCAAAACCTGT
58.682
45.455
0.00
0.00
0.00
4.00
1492
1496
4.357918
TTCTCTCTTCTCCCAAAACCTG
57.642
45.455
0.00
0.00
0.00
4.00
1493
1497
4.660771
TCTTTCTCTCTTCTCCCAAAACCT
59.339
41.667
0.00
0.00
0.00
3.50
1494
1498
4.974399
TCTTTCTCTCTTCTCCCAAAACC
58.026
43.478
0.00
0.00
0.00
3.27
1495
1499
6.944234
TTTCTTTCTCTCTTCTCCCAAAAC
57.056
37.500
0.00
0.00
0.00
2.43
1496
1500
7.561356
ACATTTTCTTTCTCTCTTCTCCCAAAA
59.439
33.333
0.00
0.00
0.00
2.44
1497
1501
7.062957
ACATTTTCTTTCTCTCTTCTCCCAAA
58.937
34.615
0.00
0.00
0.00
3.28
1498
1502
6.605119
ACATTTTCTTTCTCTCTTCTCCCAA
58.395
36.000
0.00
0.00
0.00
4.12
1499
1503
6.192970
ACATTTTCTTTCTCTCTTCTCCCA
57.807
37.500
0.00
0.00
0.00
4.37
1500
1504
5.350091
CGACATTTTCTTTCTCTCTTCTCCC
59.650
44.000
0.00
0.00
0.00
4.30
1501
1505
6.159988
TCGACATTTTCTTTCTCTCTTCTCC
58.840
40.000
0.00
0.00
0.00
3.71
1502
1506
7.201513
CCATCGACATTTTCTTTCTCTCTTCTC
60.202
40.741
0.00
0.00
0.00
2.87
1503
1507
6.593382
CCATCGACATTTTCTTTCTCTCTTCT
59.407
38.462
0.00
0.00
0.00
2.85
1504
1508
6.674278
GCCATCGACATTTTCTTTCTCTCTTC
60.674
42.308
0.00
0.00
0.00
2.87
1505
1509
5.123027
GCCATCGACATTTTCTTTCTCTCTT
59.877
40.000
0.00
0.00
0.00
2.85
1506
1510
4.633565
GCCATCGACATTTTCTTTCTCTCT
59.366
41.667
0.00
0.00
0.00
3.10
1507
1511
4.633565
AGCCATCGACATTTTCTTTCTCTC
59.366
41.667
0.00
0.00
0.00
3.20
1508
1512
4.394300
CAGCCATCGACATTTTCTTTCTCT
59.606
41.667
0.00
0.00
0.00
3.10
1509
1513
4.656041
CAGCCATCGACATTTTCTTTCTC
58.344
43.478
0.00
0.00
0.00
2.87
1510
1514
3.119708
GCAGCCATCGACATTTTCTTTCT
60.120
43.478
0.00
0.00
0.00
2.52
1511
1515
3.174375
GCAGCCATCGACATTTTCTTTC
58.826
45.455
0.00
0.00
0.00
2.62
1512
1516
2.094545
GGCAGCCATCGACATTTTCTTT
60.095
45.455
6.55
0.00
0.00
2.52
1513
1517
1.474077
GGCAGCCATCGACATTTTCTT
59.526
47.619
6.55
0.00
0.00
2.52
1514
1518
1.098050
GGCAGCCATCGACATTTTCT
58.902
50.000
6.55
0.00
0.00
2.52
1515
1519
0.810648
TGGCAGCCATCGACATTTTC
59.189
50.000
11.22
0.00
0.00
2.29
1516
1520
0.813184
CTGGCAGCCATCGACATTTT
59.187
50.000
16.64
0.00
30.82
1.82
1517
1521
1.660560
GCTGGCAGCCATCGACATTT
61.661
55.000
28.87
0.00
34.48
2.32
1518
1522
2.117156
GCTGGCAGCCATCGACATT
61.117
57.895
28.87
0.00
34.48
2.71
1519
1523
2.515523
GCTGGCAGCCATCGACAT
60.516
61.111
28.87
0.00
34.48
3.06
1521
1525
4.819761
TCGCTGGCAGCCATCGAC
62.820
66.667
31.66
13.83
45.23
4.20
1523
1527
3.344215
GATCGCTGGCAGCCATCG
61.344
66.667
32.08
28.28
43.38
3.84
1524
1528
3.344215
CGATCGCTGGCAGCCATC
61.344
66.667
29.85
29.85
38.18
3.51
1525
1529
3.804153
CTCGATCGCTGGCAGCCAT
62.804
63.158
32.08
26.20
38.18
4.40
1526
1530
4.519437
CTCGATCGCTGGCAGCCA
62.519
66.667
32.08
22.26
38.18
4.75
1536
1540
4.899239
GGTGGCCTGCCTCGATCG
62.899
72.222
9.36
9.36
36.94
3.69
1537
1541
2.615227
AATGGTGGCCTGCCTCGATC
62.615
60.000
16.05
0.00
36.94
3.69
1538
1542
2.683465
AATGGTGGCCTGCCTCGAT
61.683
57.895
16.05
5.84
36.94
3.59
1539
1543
3.329889
AATGGTGGCCTGCCTCGA
61.330
61.111
16.05
3.46
36.94
4.04
1540
1544
2.898920
ATCAATGGTGGCCTGCCTCG
62.899
60.000
16.05
6.51
36.94
4.63
1541
1545
1.076485
ATCAATGGTGGCCTGCCTC
60.076
57.895
16.05
5.67
36.94
4.70
1542
1546
1.380785
CATCAATGGTGGCCTGCCT
60.381
57.895
16.05
1.95
36.94
4.75
1543
1547
2.428925
CCATCAATGGTGGCCTGCC
61.429
63.158
3.32
7.19
43.05
4.85
1544
1548
3.213264
CCATCAATGGTGGCCTGC
58.787
61.111
3.32
0.00
43.05
4.85
1553
1557
2.060275
TCTCCCCCATCTCCATCAATG
58.940
52.381
0.00
0.00
0.00
2.82
1554
1558
2.520188
TCTCCCCCATCTCCATCAAT
57.480
50.000
0.00
0.00
0.00
2.57
1555
1559
2.130193
CTTCTCCCCCATCTCCATCAA
58.870
52.381
0.00
0.00
0.00
2.57
1556
1560
1.696965
CCTTCTCCCCCATCTCCATCA
60.697
57.143
0.00
0.00
0.00
3.07
1557
1561
1.063183
CCTTCTCCCCCATCTCCATC
58.937
60.000
0.00
0.00
0.00
3.51
1558
1562
0.348370
ACCTTCTCCCCCATCTCCAT
59.652
55.000
0.00
0.00
0.00
3.41
1559
1563
0.621571
CACCTTCTCCCCCATCTCCA
60.622
60.000
0.00
0.00
0.00
3.86
1560
1564
1.348775
CCACCTTCTCCCCCATCTCC
61.349
65.000
0.00
0.00
0.00
3.71
1561
1565
0.621862
ACCACCTTCTCCCCCATCTC
60.622
60.000
0.00
0.00
0.00
2.75
1562
1566
0.916358
CACCACCTTCTCCCCCATCT
60.916
60.000
0.00
0.00
0.00
2.90
1563
1567
1.609783
CACCACCTTCTCCCCCATC
59.390
63.158
0.00
0.00
0.00
3.51
1564
1568
1.930656
CCACCACCTTCTCCCCCAT
60.931
63.158
0.00
0.00
0.00
4.00
1565
1569
2.531685
CCACCACCTTCTCCCCCA
60.532
66.667
0.00
0.00
0.00
4.96
1566
1570
3.339093
CCCACCACCTTCTCCCCC
61.339
72.222
0.00
0.00
0.00
5.40
1567
1571
4.048470
GCCCACCACCTTCTCCCC
62.048
72.222
0.00
0.00
0.00
4.81
1568
1572
4.410400
CGCCCACCACCTTCTCCC
62.410
72.222
0.00
0.00
0.00
4.30
1569
1573
3.637273
ACGCCCACCACCTTCTCC
61.637
66.667
0.00
0.00
0.00
3.71
1570
1574
2.358737
CACGCCCACCACCTTCTC
60.359
66.667
0.00
0.00
0.00
2.87
1571
1575
4.643387
GCACGCCCACCACCTTCT
62.643
66.667
0.00
0.00
0.00
2.85
1584
1588
3.792047
CTCATGCCACACCGCACG
61.792
66.667
0.00
0.00
42.70
5.34
1585
1589
3.434319
CCTCATGCCACACCGCAC
61.434
66.667
0.00
0.00
42.70
5.34
1588
1592
3.129502
CTGCCTCATGCCACACCG
61.130
66.667
0.00
0.00
40.16
4.94
1589
1593
0.895100
TTTCTGCCTCATGCCACACC
60.895
55.000
0.00
0.00
40.16
4.16
1590
1594
1.133790
GATTTCTGCCTCATGCCACAC
59.866
52.381
0.00
0.00
40.16
3.82
1591
1595
1.005097
AGATTTCTGCCTCATGCCACA
59.995
47.619
0.00
0.00
40.16
4.17
1592
1596
1.674962
GAGATTTCTGCCTCATGCCAC
59.325
52.381
0.00
0.00
40.16
5.01
1593
1597
1.282738
TGAGATTTCTGCCTCATGCCA
59.717
47.619
0.00
0.00
40.16
4.92
1594
1598
2.048444
TGAGATTTCTGCCTCATGCC
57.952
50.000
0.00
0.00
40.16
4.40
1611
1615
3.949586
TGGGCATCAGGTCAAATATGA
57.050
42.857
0.00
0.00
0.00
2.15
1643
1647
3.963383
TTTTCGAAAGCAGGTCAGTTC
57.037
42.857
10.98
0.00
0.00
3.01
1798
1802
2.032528
AGCTTAGGCGCTGCACAA
59.967
55.556
7.64
0.00
44.37
3.33
1835
1839
0.471617
CTAAGGGCTAGGCACTGCAT
59.528
55.000
19.14
0.00
43.87
3.96
1900
1905
0.178873
AGGGGAAGAACTGCCTGGTA
60.179
55.000
0.00
0.00
35.37
3.25
1931
1937
4.127040
CGCCGCTGCTCTCTGTCT
62.127
66.667
0.00
0.00
34.43
3.41
1983
2009
7.040617
CGAATCCATGGATCAAATCTTCAGATT
60.041
37.037
27.45
7.43
38.92
2.40
2044
2070
1.897560
ACGGAGCAAAAGAAAGGGAG
58.102
50.000
0.00
0.00
0.00
4.30
2069
2095
7.214467
TGGACAAATCTCTAAAATGACAACC
57.786
36.000
0.00
0.00
0.00
3.77
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.