Multiple sequence alignment - TraesCS1B01G336200
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
TraesCS1B01G336200
chr1B
100.000
3115
0
0
1
3115
563024033
563027147
0.000000e+00
5753.0
1
TraesCS1B01G336200
chr1B
76.699
103
20
4
468
568
591956075
591955975
2.000000e-03
54.7
2
TraesCS1B01G336200
chr1D
86.339
2562
170
61
638
3115
416468448
416470913
0.000000e+00
2627.0
3
TraesCS1B01G336200
chr1A
91.793
987
55
11
638
1603
513732541
513733522
0.000000e+00
1351.0
4
TraesCS1B01G336200
chr1A
83.827
878
79
33
1662
2514
513733548
513734387
0.000000e+00
776.0
5
TraesCS1B01G336200
chr1A
80.203
394
18
15
2737
3115
513734558
513734906
1.120000e-59
241.0
6
TraesCS1B01G336200
chr4B
89.043
575
47
8
1
566
75542990
75543557
0.000000e+00
699.0
7
TraesCS1B01G336200
chr2B
87.895
570
57
8
1
567
588160463
588161023
0.000000e+00
660.0
8
TraesCS1B01G336200
chr2B
84.348
575
71
7
1
566
572708550
572707986
2.110000e-151
545.0
9
TraesCS1B01G336200
chr5B
85.962
577
56
11
2
569
255338688
255338128
7.440000e-166
593.0
10
TraesCS1B01G336200
chr4D
88.446
502
36
10
1
487
12306386
12305892
1.240000e-163
586.0
11
TraesCS1B01G336200
chr7D
86.774
499
48
8
1
487
501797239
501796747
9.830000e-150
540.0
12
TraesCS1B01G336200
chr7D
86.869
396
38
7
4
393
626621554
626621167
6.170000e-117
431.0
13
TraesCS1B01G336200
chr7D
88.281
128
15
0
442
569
28219133
28219006
1.500000e-33
154.0
14
TraesCS1B01G336200
chr5D
87.387
444
40
7
1
435
494290474
494290910
2.160000e-136
496.0
15
TraesCS1B01G336200
chr3A
86.216
399
40
8
1
393
688022319
688022708
4.800000e-113
418.0
16
TraesCS1B01G336200
chr3A
93.750
48
3
0
1082
1129
558515671
558515718
4.310000e-09
73.1
17
TraesCS1B01G336200
chr2A
86.375
389
36
10
1
382
712182322
712182700
2.890000e-110
409.0
18
TraesCS1B01G336200
chr7B
85.122
410
38
11
1
394
543847473
543847071
6.260000e-107
398.0
19
TraesCS1B01G336200
chr2D
86.719
128
15
2
442
568
476805904
476806030
1.160000e-29
141.0
20
TraesCS1B01G336200
chr3D
94.231
52
3
0
1081
1132
427631935
427631884
2.580000e-11
80.5
21
TraesCS1B01G336200
chr3B
83.721
86
12
2
1081
1165
559109913
559109829
2.580000e-11
80.5
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
TraesCS1B01G336200
chr1B
563024033
563027147
3114
False
5753.000000
5753
100.000000
1
3115
1
chr1B.!!$F1
3114
1
TraesCS1B01G336200
chr1D
416468448
416470913
2465
False
2627.000000
2627
86.339000
638
3115
1
chr1D.!!$F1
2477
2
TraesCS1B01G336200
chr1A
513732541
513734906
2365
False
789.333333
1351
85.274333
638
3115
3
chr1A.!!$F1
2477
3
TraesCS1B01G336200
chr4B
75542990
75543557
567
False
699.000000
699
89.043000
1
566
1
chr4B.!!$F1
565
4
TraesCS1B01G336200
chr2B
588160463
588161023
560
False
660.000000
660
87.895000
1
567
1
chr2B.!!$F1
566
5
TraesCS1B01G336200
chr2B
572707986
572708550
564
True
545.000000
545
84.348000
1
566
1
chr2B.!!$R1
565
6
TraesCS1B01G336200
chr5B
255338128
255338688
560
True
593.000000
593
85.962000
2
569
1
chr5B.!!$R1
567
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
628
648
0.031994
GCACGACCAAGTTTTGCCAT
59.968
50.000
0.0
0.0
0.0
4.40
F
630
650
1.066908
CACGACCAAGTTTTGCCATGT
59.933
47.619
0.0
0.0
0.0
3.21
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1856
1915
0.170561
CTTACTGACGGACTCACGGG
59.829
60.0
0.00
0.0
38.39
5.28
R
2382
2485
0.179094
GATCGGCCCGTTGACATACA
60.179
55.0
1.63
0.0
0.00
2.29
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
22
23
0.260816
AAGCTCACCATGGCATCCAT
59.739
50.000
13.04
0.00
46.37
3.41
63
64
2.741092
GGTTCTGACGGCTCCACA
59.259
61.111
0.00
0.00
0.00
4.17
178
179
0.386113
GATTCGTCCCCTCTCCTTCG
59.614
60.000
0.00
0.00
0.00
3.79
180
181
2.044252
CGTCCCCTCTCCTTCGGA
60.044
66.667
0.00
0.00
0.00
4.55
196
199
2.507324
GAGGTCGACGGAAGCTGC
60.507
66.667
9.92
0.00
0.00
5.25
238
242
1.671054
ACGACATTGCCTTGGACGG
60.671
57.895
0.00
0.00
0.00
4.79
291
301
4.489771
CCGGCCCGCTCAGGAATT
62.490
66.667
0.00
0.00
45.00
2.17
299
309
2.476320
GCTCAGGAATTGCCTCCGC
61.476
63.158
0.00
0.00
46.97
5.54
300
310
1.821332
CTCAGGAATTGCCTCCGCC
60.821
63.158
0.00
0.00
46.97
6.13
301
311
2.262774
CTCAGGAATTGCCTCCGCCT
62.263
60.000
0.00
0.00
46.97
5.52
302
312
1.821332
CAGGAATTGCCTCCGCCTC
60.821
63.158
0.00
0.00
46.97
4.70
303
313
2.517166
GGAATTGCCTCCGCCTCC
60.517
66.667
0.00
0.00
0.00
4.30
304
314
2.897350
GAATTGCCTCCGCCTCCG
60.897
66.667
0.00
0.00
0.00
4.63
346
356
0.857681
TCCCCCAAATCCCCAATCCA
60.858
55.000
0.00
0.00
0.00
3.41
426
446
1.092921
GTTGACACTGGCCACGTCAA
61.093
55.000
29.61
29.61
44.95
3.18
468
488
3.572255
GCACTAAGGTTTGATTTGGACCA
59.428
43.478
0.00
0.00
35.89
4.02
485
505
6.884472
TGGACCAGGATTCATTAGTTTAGA
57.116
37.500
0.00
0.00
0.00
2.10
494
514
8.816894
AGGATTCATTAGTTTAGAGTGAGAACA
58.183
33.333
0.00
0.00
0.00
3.18
506
526
4.103153
AGAGTGAGAACAACAGGGATTTCA
59.897
41.667
0.00
0.00
0.00
2.69
511
531
5.656416
TGAGAACAACAGGGATTTCAACTTT
59.344
36.000
0.00
0.00
0.00
2.66
523
543
7.292356
AGGGATTTCAACTTTAGGGTTTGATTT
59.708
33.333
0.00
0.00
0.00
2.17
536
556
3.004944
GGTTTGATTTGCCGAACACCTAA
59.995
43.478
0.00
0.00
33.20
2.69
569
589
7.959175
AGGTTTAAAATGGACTTTTTCCCTAC
58.041
34.615
0.00
0.00
45.17
3.18
570
590
7.565768
AGGTTTAAAATGGACTTTTTCCCTACA
59.434
33.333
0.00
0.00
45.17
2.74
571
591
7.870954
GGTTTAAAATGGACTTTTTCCCTACAG
59.129
37.037
0.00
0.00
45.17
2.74
572
592
8.635328
GTTTAAAATGGACTTTTTCCCTACAGA
58.365
33.333
0.00
0.00
45.17
3.41
573
593
6.650427
AAAATGGACTTTTTCCCTACAGAC
57.350
37.500
0.00
0.00
45.17
3.51
574
594
4.993705
ATGGACTTTTTCCCTACAGACA
57.006
40.909
0.00
0.00
45.17
3.41
575
595
4.993705
TGGACTTTTTCCCTACAGACAT
57.006
40.909
0.00
0.00
45.17
3.06
576
596
6.636454
ATGGACTTTTTCCCTACAGACATA
57.364
37.500
0.00
0.00
45.17
2.29
577
597
6.049955
TGGACTTTTTCCCTACAGACATAG
57.950
41.667
0.00
0.00
45.17
2.23
578
598
4.876679
GGACTTTTTCCCTACAGACATAGC
59.123
45.833
0.00
0.00
38.70
2.97
579
599
4.844884
ACTTTTTCCCTACAGACATAGCC
58.155
43.478
0.00
0.00
0.00
3.93
580
600
4.288626
ACTTTTTCCCTACAGACATAGCCA
59.711
41.667
0.00
0.00
0.00
4.75
581
601
5.044846
ACTTTTTCCCTACAGACATAGCCAT
60.045
40.000
0.00
0.00
0.00
4.40
582
602
4.422073
TTTCCCTACAGACATAGCCATG
57.578
45.455
0.00
0.00
38.21
3.66
584
604
3.384168
TCCCTACAGACATAGCCATGTT
58.616
45.455
0.00
0.00
45.58
2.71
585
605
4.552674
TCCCTACAGACATAGCCATGTTA
58.447
43.478
0.00
0.00
45.58
2.41
586
606
4.344102
TCCCTACAGACATAGCCATGTTAC
59.656
45.833
0.00
0.00
45.58
2.50
587
607
4.100963
CCCTACAGACATAGCCATGTTACA
59.899
45.833
0.00
0.00
45.58
2.41
588
608
5.396324
CCCTACAGACATAGCCATGTTACAA
60.396
44.000
0.00
0.00
45.58
2.41
589
609
6.291377
CCTACAGACATAGCCATGTTACAAT
58.709
40.000
0.00
0.00
45.58
2.71
590
610
6.203530
CCTACAGACATAGCCATGTTACAATG
59.796
42.308
0.00
0.00
45.58
2.82
591
611
5.500234
ACAGACATAGCCATGTTACAATGT
58.500
37.500
0.00
0.00
45.58
2.71
592
612
5.355071
ACAGACATAGCCATGTTACAATGTG
59.645
40.000
0.00
0.00
45.58
3.21
593
613
4.336433
AGACATAGCCATGTTACAATGTGC
59.664
41.667
0.00
0.00
45.58
4.57
594
614
4.272489
ACATAGCCATGTTACAATGTGCT
58.728
39.130
0.00
0.00
42.98
4.40
595
615
4.096833
ACATAGCCATGTTACAATGTGCTG
59.903
41.667
0.00
0.00
42.98
4.41
596
616
2.517959
AGCCATGTTACAATGTGCTGT
58.482
42.857
0.00
0.00
34.69
4.40
597
617
2.489329
AGCCATGTTACAATGTGCTGTC
59.511
45.455
0.00
0.00
34.69
3.51
598
618
2.415893
GCCATGTTACAATGTGCTGTCC
60.416
50.000
0.00
0.00
0.00
4.02
599
619
3.084039
CCATGTTACAATGTGCTGTCCT
58.916
45.455
0.00
0.00
0.00
3.85
600
620
3.507233
CCATGTTACAATGTGCTGTCCTT
59.493
43.478
0.00
0.00
0.00
3.36
601
621
4.379813
CCATGTTACAATGTGCTGTCCTTC
60.380
45.833
0.00
0.00
0.00
3.46
602
622
4.085357
TGTTACAATGTGCTGTCCTTCT
57.915
40.909
0.00
0.00
0.00
2.85
603
623
4.460263
TGTTACAATGTGCTGTCCTTCTT
58.540
39.130
0.00
0.00
0.00
2.52
604
624
4.887071
TGTTACAATGTGCTGTCCTTCTTT
59.113
37.500
0.00
0.00
0.00
2.52
605
625
5.008613
TGTTACAATGTGCTGTCCTTCTTTC
59.991
40.000
0.00
0.00
0.00
2.62
606
626
3.825328
ACAATGTGCTGTCCTTCTTTCT
58.175
40.909
0.00
0.00
0.00
2.52
607
627
3.567164
ACAATGTGCTGTCCTTCTTTCTG
59.433
43.478
0.00
0.00
0.00
3.02
608
628
3.498774
ATGTGCTGTCCTTCTTTCTGT
57.501
42.857
0.00
0.00
0.00
3.41
609
629
2.564771
TGTGCTGTCCTTCTTTCTGTG
58.435
47.619
0.00
0.00
0.00
3.66
610
630
1.265365
GTGCTGTCCTTCTTTCTGTGC
59.735
52.381
0.00
0.00
0.00
4.57
611
631
1.134128
TGCTGTCCTTCTTTCTGTGCA
60.134
47.619
0.00
0.00
0.00
4.57
612
632
1.265365
GCTGTCCTTCTTTCTGTGCAC
59.735
52.381
10.75
10.75
0.00
4.57
613
633
1.528586
CTGTCCTTCTTTCTGTGCACG
59.471
52.381
13.13
7.36
0.00
5.34
614
634
1.138069
TGTCCTTCTTTCTGTGCACGA
59.862
47.619
13.13
9.76
0.00
4.35
615
635
1.527311
GTCCTTCTTTCTGTGCACGAC
59.473
52.381
13.13
6.18
0.00
4.34
616
636
0.868406
CCTTCTTTCTGTGCACGACC
59.132
55.000
13.13
0.00
0.00
4.79
617
637
1.581934
CTTCTTTCTGTGCACGACCA
58.418
50.000
13.13
0.00
0.00
4.02
618
638
1.939934
CTTCTTTCTGTGCACGACCAA
59.060
47.619
13.13
4.35
0.00
3.67
619
639
1.581934
TCTTTCTGTGCACGACCAAG
58.418
50.000
13.13
12.89
0.00
3.61
620
640
1.134521
TCTTTCTGTGCACGACCAAGT
60.135
47.619
13.13
0.00
0.00
3.16
621
641
1.670811
CTTTCTGTGCACGACCAAGTT
59.329
47.619
13.13
0.00
0.00
2.66
622
642
1.745232
TTCTGTGCACGACCAAGTTT
58.255
45.000
13.13
0.00
0.00
2.66
623
643
1.745232
TCTGTGCACGACCAAGTTTT
58.255
45.000
13.13
0.00
0.00
2.43
624
644
1.400142
TCTGTGCACGACCAAGTTTTG
59.600
47.619
13.13
0.00
0.00
2.44
625
645
0.179150
TGTGCACGACCAAGTTTTGC
60.179
50.000
13.13
0.00
0.00
3.68
626
646
0.869880
GTGCACGACCAAGTTTTGCC
60.870
55.000
0.00
0.00
31.94
4.52
627
647
1.315981
TGCACGACCAAGTTTTGCCA
61.316
50.000
0.00
0.00
31.94
4.92
628
648
0.031994
GCACGACCAAGTTTTGCCAT
59.968
50.000
0.00
0.00
0.00
4.40
629
649
1.769733
CACGACCAAGTTTTGCCATG
58.230
50.000
0.00
0.00
0.00
3.66
630
650
1.066908
CACGACCAAGTTTTGCCATGT
59.933
47.619
0.00
0.00
0.00
3.21
631
651
1.754226
ACGACCAAGTTTTGCCATGTT
59.246
42.857
0.00
0.00
0.00
2.71
632
652
2.952978
ACGACCAAGTTTTGCCATGTTA
59.047
40.909
0.00
0.00
0.00
2.41
633
653
3.243267
ACGACCAAGTTTTGCCATGTTAC
60.243
43.478
0.00
0.00
0.00
2.50
634
654
3.243234
CGACCAAGTTTTGCCATGTTACA
60.243
43.478
0.00
0.00
0.00
2.41
635
655
4.298332
GACCAAGTTTTGCCATGTTACAG
58.702
43.478
0.00
0.00
0.00
2.74
636
656
3.704061
ACCAAGTTTTGCCATGTTACAGT
59.296
39.130
0.00
0.00
0.00
3.55
670
690
3.000727
GGTCGTGAATACCACTTTCCAG
58.999
50.000
0.00
0.00
43.53
3.86
701
721
5.905331
AGAACATGACCCCTGATCAGTATTA
59.095
40.000
21.11
3.78
0.00
0.98
713
733
7.816995
CCCTGATCAGTATTATAAGCTCAACTC
59.183
40.741
21.11
0.00
0.00
3.01
724
746
8.858003
TTATAAGCTCAACTCTCAGATAAACG
57.142
34.615
0.00
0.00
0.00
3.60
787
809
3.625897
TCTCCCACCACACTGCCG
61.626
66.667
0.00
0.00
0.00
5.69
830
862
2.223782
GGCTCACACAAATCAAAGCACA
60.224
45.455
0.00
0.00
0.00
4.57
901
935
2.689034
CCCCTGTCTGTCCCTCCC
60.689
72.222
0.00
0.00
0.00
4.30
902
936
2.452114
CCCTGTCTGTCCCTCCCT
59.548
66.667
0.00
0.00
0.00
4.20
903
937
1.687493
CCCTGTCTGTCCCTCCCTC
60.687
68.421
0.00
0.00
0.00
4.30
904
938
1.687493
CCTGTCTGTCCCTCCCTCC
60.687
68.421
0.00
0.00
0.00
4.30
905
939
1.687493
CTGTCTGTCCCTCCCTCCC
60.687
68.421
0.00
0.00
0.00
4.30
908
942
2.041405
CTGTCCCTCCCTCCCTCC
60.041
72.222
0.00
0.00
0.00
4.30
983
1021
1.067821
CTAGAAGCCTGGTAGAAGCGG
59.932
57.143
0.00
0.00
0.00
5.52
1695
1748
2.181021
CACGGTCCTCCTACGCAC
59.819
66.667
0.00
0.00
0.00
5.34
1701
1754
1.906333
TCCTCCTACGCACTGTGCA
60.906
57.895
29.86
12.63
45.36
4.57
1812
1871
2.359967
GGAGTCCCTGGAGAACCCG
61.360
68.421
0.00
0.00
37.93
5.28
1848
1907
5.591877
GGAATGCTTCATCTTCCTGTAACAT
59.408
40.000
0.00
0.00
36.36
2.71
1850
1909
6.690194
ATGCTTCATCTTCCTGTAACATTC
57.310
37.500
0.00
0.00
0.00
2.67
1851
1910
5.559770
TGCTTCATCTTCCTGTAACATTCA
58.440
37.500
0.00
0.00
0.00
2.57
1852
1911
6.182627
TGCTTCATCTTCCTGTAACATTCAT
58.817
36.000
0.00
0.00
0.00
2.57
1856
1915
6.586344
TCATCTTCCTGTAACATTCATCCTC
58.414
40.000
0.00
0.00
0.00
3.71
1857
1916
5.359194
TCTTCCTGTAACATTCATCCTCC
57.641
43.478
0.00
0.00
0.00
4.30
1858
1917
4.164221
TCTTCCTGTAACATTCATCCTCCC
59.836
45.833
0.00
0.00
0.00
4.30
1859
1918
2.434336
TCCTGTAACATTCATCCTCCCG
59.566
50.000
0.00
0.00
0.00
5.14
1860
1919
2.170607
CCTGTAACATTCATCCTCCCGT
59.829
50.000
0.00
0.00
0.00
5.28
1861
1920
3.198068
CTGTAACATTCATCCTCCCGTG
58.802
50.000
0.00
0.00
0.00
4.94
1864
1923
1.573108
ACATTCATCCTCCCGTGAGT
58.427
50.000
0.00
0.00
36.86
3.41
1867
1926
1.320344
TTCATCCTCCCGTGAGTCCG
61.320
60.000
0.00
0.00
36.86
4.79
1969
2039
1.301677
CTGGCAACTTCTTCTCGGGC
61.302
60.000
0.00
0.00
37.61
6.13
1994
2064
3.577805
ATTTTGTATCCCGGGGAAGAG
57.422
47.619
23.50
0.00
34.34
2.85
2021
2091
1.586541
CAGCTCTCTGGTGTACGCA
59.413
57.895
8.97
0.00
39.17
5.24
2022
2092
0.174389
CAGCTCTCTGGTGTACGCAT
59.826
55.000
8.97
0.00
39.17
4.73
2023
2093
0.457851
AGCTCTCTGGTGTACGCATC
59.542
55.000
8.97
0.00
0.00
3.91
2024
2094
0.457851
GCTCTCTGGTGTACGCATCT
59.542
55.000
8.97
0.00
0.00
2.90
2025
2095
1.800655
GCTCTCTGGTGTACGCATCTG
60.801
57.143
8.97
0.00
0.00
2.90
2026
2096
1.474478
CTCTCTGGTGTACGCATCTGT
59.526
52.381
8.97
0.00
0.00
3.41
2049
2119
3.947626
CAACTAGTTTGTTTGGTGTCCG
58.052
45.455
5.07
0.00
0.00
4.79
2050
2120
2.567985
ACTAGTTTGTTTGGTGTCCGG
58.432
47.619
0.00
0.00
0.00
5.14
2122
2205
6.017605
GGGTATCTCTGTAATGAACTGCATTG
60.018
42.308
0.00
0.00
46.38
2.82
2132
2215
5.831702
ATGAACTGCATTGATTCCTCTTC
57.168
39.130
0.00
0.00
31.73
2.87
2140
2235
4.141390
GCATTGATTCCTCTTCCCTTCCTA
60.141
45.833
0.00
0.00
0.00
2.94
2141
2236
5.372373
CATTGATTCCTCTTCCCTTCCTAC
58.628
45.833
0.00
0.00
0.00
3.18
2142
2237
4.354208
TGATTCCTCTTCCCTTCCTACT
57.646
45.455
0.00
0.00
0.00
2.57
2143
2238
4.699994
TGATTCCTCTTCCCTTCCTACTT
58.300
43.478
0.00
0.00
0.00
2.24
2144
2239
4.717280
TGATTCCTCTTCCCTTCCTACTTC
59.283
45.833
0.00
0.00
0.00
3.01
2145
2240
3.117552
TCCTCTTCCCTTCCTACTTCC
57.882
52.381
0.00
0.00
0.00
3.46
2146
2241
2.660556
TCCTCTTCCCTTCCTACTTCCT
59.339
50.000
0.00
0.00
0.00
3.36
2155
2250
7.229951
TCCCTTCCTACTTCCTAGTACATTA
57.770
40.000
0.00
0.00
35.78
1.90
2185
2280
2.589014
CGATCTTTCTTGTGCAAAGCC
58.411
47.619
0.00
0.00
31.85
4.35
2205
2300
1.468520
CGGAGTTGCCACTTATGTTGG
59.531
52.381
0.00
0.00
35.94
3.77
2206
2301
1.818674
GGAGTTGCCACTTATGTTGGG
59.181
52.381
0.00
0.00
36.34
4.12
2207
2302
1.818674
GAGTTGCCACTTATGTTGGGG
59.181
52.381
0.00
0.00
31.22
4.96
2208
2303
0.894835
GTTGCCACTTATGTTGGGGG
59.105
55.000
0.00
0.00
0.00
5.40
2230
2325
5.523438
GATCCGATCCAATCCTATCCTAC
57.477
47.826
0.00
0.00
0.00
3.18
2318
2421
2.601905
GCATTCAATGGCCCCTTATCT
58.398
47.619
0.00
0.00
0.00
1.98
2324
2427
2.701951
CAATGGCCCCTTATCTGCATTT
59.298
45.455
0.00
0.00
0.00
2.32
2426
2536
1.439353
CTGCGTATTCAATGCCCGCT
61.439
55.000
10.85
0.00
44.32
5.52
2468
2578
1.569493
CGGGCGTTATGCTATGCAC
59.431
57.895
0.00
0.00
43.04
4.57
2469
2579
1.157257
CGGGCGTTATGCTATGCACA
61.157
55.000
0.00
0.00
43.04
4.57
2470
2580
0.588252
GGGCGTTATGCTATGCACAG
59.412
55.000
0.00
0.00
43.04
3.66
2471
2581
0.588252
GGCGTTATGCTATGCACAGG
59.412
55.000
0.00
0.00
43.04
4.00
2506
2620
1.019278
AGTCGAACAAATGCGCCGAT
61.019
50.000
4.18
0.00
0.00
4.18
2534
2657
0.957395
AGAACATGTGCTTGCTCCGG
60.957
55.000
0.00
0.00
0.00
5.14
2535
2658
1.228245
AACATGTGCTTGCTCCGGT
60.228
52.632
0.00
0.00
0.00
5.28
2538
2661
1.228245
ATGTGCTTGCTCCGGTGTT
60.228
52.632
0.00
0.00
0.00
3.32
2540
2663
1.282875
GTGCTTGCTCCGGTGTTTC
59.717
57.895
0.00
0.00
0.00
2.78
2547
2670
1.071542
TGCTCCGGTGTTTCAGATTCA
59.928
47.619
0.00
0.00
0.00
2.57
2549
2672
3.055458
TGCTCCGGTGTTTCAGATTCATA
60.055
43.478
0.00
0.00
0.00
2.15
2820
2984
0.601576
TTTTAGCAGAGCACGGCGAA
60.602
50.000
16.62
0.00
41.73
4.70
2883
3047
2.098233
CCACGGTGCGATGGTGTAC
61.098
63.158
1.68
0.00
0.00
2.90
2884
3048
2.098233
CACGGTGCGATGGTGTACC
61.098
63.158
0.00
0.00
40.78
3.34
2886
3050
2.510691
GGTGCGATGGTGTACCGG
60.511
66.667
0.00
0.00
39.43
5.28
2897
3061
2.280552
TGTACCGGACTGGAGCACC
61.281
63.158
9.46
0.00
42.00
5.01
2907
3071
1.893801
ACTGGAGCACCTGTACTGTAC
59.106
52.381
10.93
10.98
44.49
2.90
2908
3072
2.171840
CTGGAGCACCTGTACTGTACT
58.828
52.381
17.98
0.00
37.04
2.73
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
22
23
3.612251
GGAGGTACTACGCCTGCA
58.388
61.111
0.00
0.00
41.55
4.41
63
64
1.690219
AAGGCGCCGAGATGGATCTT
61.690
55.000
23.20
2.00
42.00
2.40
178
179
2.182030
CAGCTTCCGTCGACCTCC
59.818
66.667
10.58
0.00
0.00
4.30
180
181
4.421479
CGCAGCTTCCGTCGACCT
62.421
66.667
10.58
0.00
0.00
3.85
182
185
3.173240
GTCGCAGCTTCCGTCGAC
61.173
66.667
5.18
5.18
43.23
4.20
196
199
1.859427
TTCGGGTCGTTCTCAGGTCG
61.859
60.000
0.00
0.00
0.00
4.79
315
325
2.045242
GGGGGAAGAAACGAGGGC
60.045
66.667
0.00
0.00
0.00
5.19
320
330
1.182667
GGGATTTGGGGGAAGAAACG
58.817
55.000
0.00
0.00
0.00
3.60
346
356
1.579429
GCGAGGGCGAACAACAAAT
59.421
52.632
0.00
0.00
40.82
2.32
372
382
1.676248
TGGTGGGCCAGGTTATAACT
58.324
50.000
6.40
0.00
40.46
2.24
439
459
3.701532
TCAAACCTTAGTGCCGTTTTG
57.298
42.857
0.00
0.00
0.00
2.44
468
488
8.816894
TGTTCTCACTCTAAACTAATGAATCCT
58.183
33.333
0.00
0.00
0.00
3.24
485
505
4.437682
TGAAATCCCTGTTGTTCTCACT
57.562
40.909
0.00
0.00
0.00
3.41
494
514
5.074746
ACCCTAAAGTTGAAATCCCTGTT
57.925
39.130
0.00
0.00
0.00
3.16
506
526
3.892588
TCGGCAAATCAAACCCTAAAGTT
59.107
39.130
0.00
0.00
0.00
2.66
511
531
2.554893
GTGTTCGGCAAATCAAACCCTA
59.445
45.455
0.00
0.00
0.00
3.53
540
560
8.902540
GGAAAAAGTCCATTTTAAACCTTGAT
57.097
30.769
0.00
0.00
46.97
2.57
569
589
5.731406
GCACATTGTAACATGGCTATGTCTG
60.731
44.000
16.73
11.03
46.54
3.51
570
590
4.336433
GCACATTGTAACATGGCTATGTCT
59.664
41.667
16.73
9.24
46.54
3.41
571
591
4.336433
AGCACATTGTAACATGGCTATGTC
59.664
41.667
16.73
5.57
46.54
3.06
573
593
4.096833
ACAGCACATTGTAACATGGCTATG
59.903
41.667
8.74
8.74
40.24
2.23
574
594
4.272489
ACAGCACATTGTAACATGGCTAT
58.728
39.130
0.00
0.00
0.00
2.97
575
595
3.684908
ACAGCACATTGTAACATGGCTA
58.315
40.909
0.00
0.00
0.00
3.93
576
596
2.489329
GACAGCACATTGTAACATGGCT
59.511
45.455
0.00
0.00
0.00
4.75
577
597
2.415893
GGACAGCACATTGTAACATGGC
60.416
50.000
0.00
0.00
0.00
4.40
578
598
3.084039
AGGACAGCACATTGTAACATGG
58.916
45.455
0.00
0.00
0.00
3.66
579
599
4.456911
AGAAGGACAGCACATTGTAACATG
59.543
41.667
0.00
0.00
0.00
3.21
580
600
4.655963
AGAAGGACAGCACATTGTAACAT
58.344
39.130
0.00
0.00
0.00
2.71
581
601
4.085357
AGAAGGACAGCACATTGTAACA
57.915
40.909
0.00
0.00
0.00
2.41
582
602
5.239525
AGAAAGAAGGACAGCACATTGTAAC
59.760
40.000
0.00
0.00
0.00
2.50
583
603
5.239306
CAGAAAGAAGGACAGCACATTGTAA
59.761
40.000
0.00
0.00
0.00
2.41
584
604
4.756642
CAGAAAGAAGGACAGCACATTGTA
59.243
41.667
0.00
0.00
0.00
2.41
585
605
3.567164
CAGAAAGAAGGACAGCACATTGT
59.433
43.478
0.00
0.00
0.00
2.71
586
606
3.567164
ACAGAAAGAAGGACAGCACATTG
59.433
43.478
0.00
0.00
0.00
2.82
587
607
3.567164
CACAGAAAGAAGGACAGCACATT
59.433
43.478
0.00
0.00
0.00
2.71
588
608
3.144506
CACAGAAAGAAGGACAGCACAT
58.855
45.455
0.00
0.00
0.00
3.21
589
609
2.564771
CACAGAAAGAAGGACAGCACA
58.435
47.619
0.00
0.00
0.00
4.57
590
610
1.265365
GCACAGAAAGAAGGACAGCAC
59.735
52.381
0.00
0.00
0.00
4.40
591
611
1.134128
TGCACAGAAAGAAGGACAGCA
60.134
47.619
0.00
0.00
0.00
4.41
592
612
1.265365
GTGCACAGAAAGAAGGACAGC
59.735
52.381
13.17
0.00
0.00
4.40
593
613
1.528586
CGTGCACAGAAAGAAGGACAG
59.471
52.381
18.64
0.00
0.00
3.51
594
614
1.138069
TCGTGCACAGAAAGAAGGACA
59.862
47.619
18.64
0.00
0.00
4.02
595
615
1.527311
GTCGTGCACAGAAAGAAGGAC
59.473
52.381
18.64
8.71
0.00
3.85
596
616
1.540363
GGTCGTGCACAGAAAGAAGGA
60.540
52.381
18.64
0.00
0.00
3.36
597
617
0.868406
GGTCGTGCACAGAAAGAAGG
59.132
55.000
18.64
0.00
0.00
3.46
598
618
1.581934
TGGTCGTGCACAGAAAGAAG
58.418
50.000
18.64
0.00
0.00
2.85
599
619
1.939934
CTTGGTCGTGCACAGAAAGAA
59.060
47.619
18.64
7.60
0.00
2.52
600
620
1.134521
ACTTGGTCGTGCACAGAAAGA
60.135
47.619
18.64
2.07
0.00
2.52
601
621
1.299541
ACTTGGTCGTGCACAGAAAG
58.700
50.000
18.64
15.71
0.00
2.62
602
622
1.745232
AACTTGGTCGTGCACAGAAA
58.255
45.000
18.64
4.45
0.00
2.52
603
623
1.745232
AAACTTGGTCGTGCACAGAA
58.255
45.000
18.64
2.27
0.00
3.02
604
624
1.400142
CAAAACTTGGTCGTGCACAGA
59.600
47.619
18.64
12.26
0.00
3.41
605
625
1.826327
CAAAACTTGGTCGTGCACAG
58.174
50.000
18.64
8.66
0.00
3.66
606
626
0.179150
GCAAAACTTGGTCGTGCACA
60.179
50.000
18.64
0.81
35.28
4.57
607
627
0.869880
GGCAAAACTTGGTCGTGCAC
60.870
55.000
6.82
6.82
36.93
4.57
608
628
1.315981
TGGCAAAACTTGGTCGTGCA
61.316
50.000
0.00
0.00
36.93
4.57
609
629
0.031994
ATGGCAAAACTTGGTCGTGC
59.968
50.000
0.00
0.00
34.42
5.34
610
630
1.066908
ACATGGCAAAACTTGGTCGTG
59.933
47.619
0.00
0.00
0.00
4.35
611
631
1.398692
ACATGGCAAAACTTGGTCGT
58.601
45.000
0.00
0.00
0.00
4.34
612
632
2.507339
AACATGGCAAAACTTGGTCG
57.493
45.000
0.00
0.00
0.00
4.79
613
633
4.202111
ACTGTAACATGGCAAAACTTGGTC
60.202
41.667
0.00
0.00
0.00
4.02
614
634
3.704061
ACTGTAACATGGCAAAACTTGGT
59.296
39.130
0.00
0.00
0.00
3.67
615
635
4.050553
CACTGTAACATGGCAAAACTTGG
58.949
43.478
0.00
0.00
0.00
3.61
616
636
4.930963
TCACTGTAACATGGCAAAACTTG
58.069
39.130
0.00
0.00
0.00
3.16
617
637
5.590530
TTCACTGTAACATGGCAAAACTT
57.409
34.783
0.00
0.00
0.00
2.66
618
638
5.590530
TTTCACTGTAACATGGCAAAACT
57.409
34.783
0.00
0.00
0.00
2.66
619
639
6.654793
TTTTTCACTGTAACATGGCAAAAC
57.345
33.333
0.00
0.00
0.00
2.43
658
678
2.703536
TCTTGCTCACTGGAAAGTGGTA
59.296
45.455
6.06
0.00
40.03
3.25
670
690
1.168714
GGGGTCATGTTCTTGCTCAC
58.831
55.000
0.00
0.00
0.00
3.51
701
721
5.751028
GCGTTTATCTGAGAGTTGAGCTTAT
59.249
40.000
0.00
0.00
0.00
1.73
713
733
7.568497
GCTCTAATTAAGCTGCGTTTATCTGAG
60.568
40.741
10.54
0.00
36.80
3.35
743
765
2.027653
AGTCAAAAGGGCTCAGCTACTC
60.028
50.000
0.00
0.00
0.00
2.59
814
846
2.425312
TCCGTTGTGCTTTGATTTGTGT
59.575
40.909
0.00
0.00
0.00
3.72
830
862
0.826256
GCTTTGGGTTTCCCTCCGTT
60.826
55.000
6.38
0.00
45.70
4.44
901
935
2.664081
GGTGGTGAGCAGGAGGGAG
61.664
68.421
0.00
0.00
0.00
4.30
902
936
2.607750
GGTGGTGAGCAGGAGGGA
60.608
66.667
0.00
0.00
0.00
4.20
903
937
2.262774
GATGGTGGTGAGCAGGAGGG
62.263
65.000
0.00
0.00
31.77
4.30
904
938
1.222936
GATGGTGGTGAGCAGGAGG
59.777
63.158
0.00
0.00
31.77
4.30
905
939
0.107800
CTGATGGTGGTGAGCAGGAG
60.108
60.000
0.00
0.00
31.77
3.69
908
942
0.392193
GGTCTGATGGTGGTGAGCAG
60.392
60.000
0.00
0.00
31.77
4.24
972
1006
1.601419
CGTCCTTCCCGCTTCTACCA
61.601
60.000
0.00
0.00
0.00
3.25
1626
1667
4.065281
GGCGCCTCCTGTGTACGT
62.065
66.667
22.15
0.00
0.00
3.57
1779
1838
1.990060
CTCCTTCCCCTCGCCTTCA
60.990
63.158
0.00
0.00
0.00
3.02
1782
1841
2.364448
GACTCCTTCCCCTCGCCT
60.364
66.667
0.00
0.00
0.00
5.52
1812
1871
0.682209
AGCATTCCATGGACACCAGC
60.682
55.000
15.91
13.80
36.75
4.85
1848
1907
1.320344
CGGACTCACGGGAGGATGAA
61.320
60.000
20.91
0.00
45.81
2.57
1850
1909
2.005960
GACGGACTCACGGGAGGATG
62.006
65.000
20.91
10.15
45.81
3.51
1851
1910
1.753463
GACGGACTCACGGGAGGAT
60.753
63.158
20.91
0.00
45.81
3.24
1852
1911
2.360852
GACGGACTCACGGGAGGA
60.361
66.667
20.91
0.00
45.81
3.71
1856
1915
0.170561
CTTACTGACGGACTCACGGG
59.829
60.000
0.00
0.00
38.39
5.28
1857
1916
0.879765
ACTTACTGACGGACTCACGG
59.120
55.000
0.00
0.00
38.39
4.94
1858
1917
3.818961
TTACTTACTGACGGACTCACG
57.181
47.619
0.00
0.00
40.31
4.35
1859
1918
5.106237
ACTGATTACTTACTGACGGACTCAC
60.106
44.000
0.00
0.00
0.00
3.51
1860
1919
5.008331
ACTGATTACTTACTGACGGACTCA
58.992
41.667
0.00
0.00
0.00
3.41
1861
1920
5.333513
CACTGATTACTTACTGACGGACTC
58.666
45.833
0.00
0.00
0.00
3.36
1864
1923
3.762288
AGCACTGATTACTTACTGACGGA
59.238
43.478
0.00
0.00
0.00
4.69
1867
1926
5.073311
TGGAGCACTGATTACTTACTGAC
57.927
43.478
0.00
0.00
0.00
3.51
1969
2039
2.092103
TCCCCGGGATACAAAATTCCAG
60.092
50.000
26.32
0.00
39.74
3.86
2010
2080
2.647529
TGTACAGATGCGTACACCAG
57.352
50.000
0.00
0.00
45.18
4.00
2029
2099
2.946990
CCGGACACCAAACAAACTAGTT
59.053
45.455
1.12
1.12
0.00
2.24
2034
2104
0.812549
ACACCGGACACCAAACAAAC
59.187
50.000
9.46
0.00
0.00
2.93
2049
2119
4.463186
ACAGTCTACAGGACAGATTACACC
59.537
45.833
0.00
0.00
46.72
4.16
2050
2120
5.646577
ACAGTCTACAGGACAGATTACAC
57.353
43.478
0.00
0.00
46.72
2.90
2122
2205
4.101898
GGAAGTAGGAAGGGAAGAGGAATC
59.898
50.000
0.00
0.00
0.00
2.52
2132
2215
7.564292
AGTTAATGTACTAGGAAGTAGGAAGGG
59.436
40.741
0.00
0.00
38.89
3.95
2140
2235
4.159879
AGCGCAGTTAATGTACTAGGAAGT
59.840
41.667
11.47
0.00
39.91
3.01
2141
2236
4.683832
AGCGCAGTTAATGTACTAGGAAG
58.316
43.478
11.47
0.00
0.00
3.46
2142
2237
4.441079
GGAGCGCAGTTAATGTACTAGGAA
60.441
45.833
11.47
0.00
0.00
3.36
2143
2238
3.067742
GGAGCGCAGTTAATGTACTAGGA
59.932
47.826
11.47
0.00
0.00
2.94
2144
2239
3.381949
GGAGCGCAGTTAATGTACTAGG
58.618
50.000
11.47
0.00
0.00
3.02
2145
2240
3.043586
CGGAGCGCAGTTAATGTACTAG
58.956
50.000
11.47
0.00
0.00
2.57
2146
2241
2.684374
TCGGAGCGCAGTTAATGTACTA
59.316
45.455
11.47
0.00
0.00
1.82
2155
2250
0.247736
AGAAAGATCGGAGCGCAGTT
59.752
50.000
11.47
0.00
0.00
3.16
2185
2280
1.468520
CCAACATAAGTGGCAACTCCG
59.531
52.381
0.00
0.00
34.77
4.63
2208
2303
4.342665
GGTAGGATAGGATTGGATCGGATC
59.657
50.000
9.54
9.54
0.00
3.36
2218
2313
4.114597
CCATCCATGGGTAGGATAGGATT
58.885
47.826
13.02
0.00
43.90
3.01
2310
2413
1.684983
CTGGGCAAATGCAGATAAGGG
59.315
52.381
7.80
0.00
44.36
3.95
2314
2417
3.084536
TGAACTGGGCAAATGCAGATA
57.915
42.857
7.80
0.00
44.36
1.98
2318
2421
3.577848
AGTTATTGAACTGGGCAAATGCA
59.422
39.130
7.80
0.00
44.50
3.96
2382
2485
0.179094
GATCGGCCCGTTGACATACA
60.179
55.000
1.63
0.00
0.00
2.29
2386
2489
4.444838
CGGATCGGCCCGTTGACA
62.445
66.667
1.63
0.00
44.23
3.58
2447
2557
1.566018
GCATAGCATAACGCCCGGTC
61.566
60.000
0.00
0.00
44.04
4.79
2453
2563
1.261619
GTCCTGTGCATAGCATAACGC
59.738
52.381
4.68
0.00
41.91
4.84
2454
2564
2.285220
GTGTCCTGTGCATAGCATAACG
59.715
50.000
4.68
0.00
41.91
3.18
2456
2566
2.167487
TCGTGTCCTGTGCATAGCATAA
59.833
45.455
4.68
0.00
41.91
1.90
2488
2602
0.586502
GATCGGCGCATTTGTTCGAC
60.587
55.000
10.83
0.00
32.60
4.20
2517
2631
1.228245
ACCGGAGCAAGCACATGTT
60.228
52.632
9.46
0.00
0.00
2.71
2518
2632
1.968017
CACCGGAGCAAGCACATGT
60.968
57.895
9.46
0.00
0.00
3.21
2519
2633
1.518056
AACACCGGAGCAAGCACATG
61.518
55.000
9.46
0.00
0.00
3.21
2520
2634
0.823356
AAACACCGGAGCAAGCACAT
60.823
50.000
9.46
0.00
0.00
3.21
2521
2635
1.444119
GAAACACCGGAGCAAGCACA
61.444
55.000
9.46
0.00
0.00
4.57
2522
2636
1.282875
GAAACACCGGAGCAAGCAC
59.717
57.895
9.46
0.00
0.00
4.40
2534
2657
5.119694
GTCCCTCCTATGAATCTGAAACAC
58.880
45.833
0.00
0.00
0.00
3.32
2535
2658
4.782691
TGTCCCTCCTATGAATCTGAAACA
59.217
41.667
0.00
0.00
0.00
2.83
2538
2661
3.389329
GCTGTCCCTCCTATGAATCTGAA
59.611
47.826
0.00
0.00
0.00
3.02
2540
2663
2.288702
CGCTGTCCCTCCTATGAATCTG
60.289
54.545
0.00
0.00
0.00
2.90
2547
2670
3.227276
CGCCGCTGTCCCTCCTAT
61.227
66.667
0.00
0.00
0.00
2.57
2883
3047
1.982395
TACAGGTGCTCCAGTCCGG
60.982
63.158
6.09
0.00
35.16
5.14
2884
3048
1.215647
GTACAGGTGCTCCAGTCCG
59.784
63.158
6.09
0.00
35.16
4.79
2885
3049
0.247736
CAGTACAGGTGCTCCAGTCC
59.752
60.000
6.09
0.00
35.16
3.85
2886
3050
0.969894
ACAGTACAGGTGCTCCAGTC
59.030
55.000
6.09
0.00
35.16
3.51
2907
3071
8.102047
AGGCAGTACAGTAGTATACCAGTATAG
58.898
40.741
0.00
0.00
44.47
1.31
2908
3072
7.881751
CAGGCAGTACAGTAGTATACCAGTATA
59.118
40.741
0.00
0.00
44.47
1.47
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.