Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014358.1 Kokia drynarioides strain JFW-HI SEQ_129395, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 74361
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:3688 original size:86 final size:85
Alignment explanation
Indices: 3532--3693 Score: 202
Period size: 86 Copynumber: 1.9 Consensus size: 85
3522 TCGAGGGCAA
* *
3532 AAAAAAGTAATTTCTAGAAGCTTGGGGGTAAAATGGTAATTTTCAAAAATTTAGGGGTAAAATGG
1 AAAAAAGTAATTTCTAGAAGCTTGGGGGTAAAATGGAAATTTTCAAAAAGTTAGGGGTAAAATGG
3597 TAATTTTTGGAAGTTAAAGT
66 TAATTTTTGGAAGTTAAAGT
* * *** * *
3617 AAAAAAGTAAATTTTTAGAAG-TTAGGGGGTAAAATTGAAATTTTTGGAAAGTTCGAGGTTAAAA
1 AAAAAAGT-AATTTCTAGAAGCTT-GGGGGTAAAATGGAAATTTTCAAAAAGTTAG-GGGTAAAA
3681 TGG-AATTTTTGGA
63 TGGTAATTTTTGGA
3694 CATTCGAGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
85 10 0.15
86 45 0.69
87 10 0.15
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (85 bp):
AAAAAAGTAATTTCTAGAAGCTTGGGGGTAAAATGGAAATTTTCAAAAAGTTAGGGGTAAAATGG
TAATTTTTGGAAGTTAAAGT
Found at i:3717 original size:58 final size:59
Alignment explanation
Indices: 3655--3783 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
3645 GTAAAATTGA
* * * * *
3655 AATTTTTGGAAAGTTCGAGGT-TAAAATGGAATTTTTGGACATTCGAGGGAAAAAAGGT
1 AATTTTTGGAAAGTTCGAGGTCAAAAATAGAATTTTTGCAAATTCAAGGGAAAAAAGGT
* * *
3713 AATTTTTGGAAAGTTCGAGGTCAAAAATAGATTTTTTGCAAATTCAAGGGTAAAATGGT
1 AATTTTTGGAAAGTTCGAGGTCAAAAATAGAATTTTTGCAAATTCAAGGGAAAAAAGGT
3772 AATTTTTGGAAA
1 AATTTTTGGAAA
3784 TTTGGGAGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
58 21 0.34
59 41 0.66
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.33
Consensus pattern (59 bp):
AATTTTTGGAAAGTTCGAGGTCAAAAATAGAATTTTTGCAAATTCAAGGGAAAAAAGGT
Found at i:3863 original size:28 final size:28
Alignment explanation
Indices: 3586--3985 Score: 248
Period size: 29 Copynumber: 13.9 Consensus size: 28
3576 AAAAATTTAG
3586 GGGTAAAATGGTAATTTTTGGAAGTT--A
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGA
** * * * *
3613 AAGTAAAAAAGTAAATTTTTAGAAGTTAGG
1 GGGT-AAAATGT-AATTTTTGGAAGTTCGA
*
3643 GGGTAAAATTGAAATTTTTGGAAAGTTCGA
1 GGGTAAAA-TGTAATTTTTGG-AAGTTCGA
* *
3673 GGTTAAAATGGAATTTTTGGACA-TTCGA
1 GGGTAAAATGTAATTTTTGGA-AGTTCGA
* *
3701 GGGAAAAAAGGTAATTTTTGGAAAGTTCGA
1 GGG-TAAAATGTAATTTTTGG-AAGTTCGA
* * * *
3731 -GGTCAAAAATAG-ATTTTTTGCAAATTCAA
1 GGGT--AAAAT-GTAATTTTTGGAAGTTCGA
* *
3760 GGGTAAAATGGTAATTTTTGGAAATTTG-
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGA
* *
3788 GGAGCAAAATGGTAATTTTTGAAAAGTTCG-
1 GG-GTAAAAT-GTAATTTTTG-GAAGTTCGA
3818 GGGTTAAGAATG--ATATTTTGGAAGTTCGA
1 GGG-TAA-AATGTAAT-TTTTGGAAGTTCGA
* * *
3847 GGGTAAAATCGTAA--TTTAGAAGTTTGG
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGA
* *
3874 GGGCAAAATGTGATTTTTGGAAGTTCGA
1 GGGTAAAATGTAATTTTTGGAAGTTCGA
* *
3902 GGGTAAAATGCAATTTTTTGAAGTTC-A
1 GGGTAAAATGTAATTTTTGGAAGTTCGA
* *
3929 GGGGCAAAAATATAATTTTTGTGAAGTTCGA
1 -GGG-TAAAATGTAATTTTTG-GAAGTTCGA
*
3960 GGGAAAAATGTAATTTTTGTGAAGTT
1 GGGTAAAATGTAATTTTTG-GAAGTT
3986 AAGGGTTAAA
Statistics
Matches: 291, Mismatches: 52, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
26 3 0.01
27 26 0.09
28 81 0.28
29 119 0.41
30 57 0.20
31 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTCGA
Found at i:3898 original size:55 final size:55
Alignment explanation
Indices: 3827--3975 Score: 183
Period size: 55 Copynumber: 2.6 Consensus size: 55
3817 GGGGTTAAGA
**
3827 ATGATATTTTGGAAGTTCGAGGGTAAAATCGTAATTTAGAAGTTTGGGGGC-AAAAT
1 ATGAT-TTTTGGAAGTTCGAGGGTAAAAT-GTAATTTAGAAGTTCAGGGGCAAAAAT
* * *
3883 GTGATTTTTGGAAGTTCGAGGGTAAAATGCAATTTTTTGAAGTTCAGGGGCAAAAAT
1 ATGATTTTTGGAAGTTCGAGGGTAAAATGTAA--TTTAGAAGTTCAGGGGCAAAAAT
* *
3940 ATAATTTTTGTGAAGTTCGAGGGAAAAATGTAATTT
1 ATGATTTTTG-GAAGTTCGAGGGTAAAATGTAATTT
3976 TTGTGAAGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
54 3 0.04
55 23 0.29
56 21 0.26
57 13 0.16
58 20 0.25
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (55 bp):
ATGATTTTTGGAAGTTCGAGGGTAAAATGTAATTTAGAAGTTCAGGGGCAAAAAT
Found at i:4004 original size:29 final size:29
Alignment explanation
Indices: 3886--4005 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
3876 GCAAAATGTG
* * **
3886 ATTTTTG-GAAGTTCGAGGGTAAAATGCA
1 ATTTTTGTGAAGTTCAAGGGAAAAATATA
*
3914 ATTTTT-TGAAGTTCAGGGGCAAAAATATA
1 ATTTTTGTGAAGTTCAAGGG-AAAAATATA
* *
3943 ATTTTTGTGAAGTTCGAGGGAAAAATGTA
1 ATTTTTGTGAAGTTCAAGGGAAAAATATA
* *
3972 ATTTTTGTGAAGTT-AAGGGTTAAAATATT
1 ATTTTTGTGAAGTTCAAGGG-AAAAATATA
4001 ATTTT
1 ATTTT
4006 AGAAAAGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
28 20 0.26
29 45 0.59
30 11 0.14
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
ATTTTTGTGAAGTTCAAGGGAAAAATATA
Found at i:4014 original size:58 final size:58
Alignment explanation
Indices: 3894--4014 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 58
3884 TGATTTTTGG
* * * **
3894 AAGTTCGAGGGTAAAATGCAATTTTTTGAAGTTCAGGGGCAAAAATATAATTTTTGTG
1 AAGTTCGAGGGAAAAATGCAATTTTTTGAAGTTCAAGGGCAAAAATATAATTTTAGAA
* ** *
3952 AAGTTCGAGGGAAAAATGTAATTTTTGTGAAGTT-AAGGGTTAAAATATTATTTTAGAA
1 AAGTTCGAGGGAAAAATGCAATTTTT-TGAAGTTCAAGGGCAAAAATATAATTTTAGAA
4010 AAGTT
1 AAGTT
4015 TGGGTATCAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 46 0.87
59 7 0.13
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (58 bp):
AAGTTCGAGGGAAAAATGCAATTTTTTGAAGTTCAAGGGCAAAAATATAATTTTAGAA
Found at i:5665 original size:17 final size:17
Alignment explanation
Indices: 5640--5705 Score: 96
Period size: 17 Copynumber: 3.8 Consensus size: 17
5630 GTTTAAAACC
**
5640 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAAGAA
5658 ATTTAAATTTAAAAGAA
1 ATTTAAATTTAAAAGAA
5675 ATTTAAATTTAAAAAGAA
1 ATTTAAATTT-AAAAGAA
5693 ATTTAAATTTAAA
1 ATTTAAATTTAAA
5706 TTTAAAACCA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 24 0.53
18 21 0.47
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAAGAA
Found at i:5666 original size:6 final size:6
Alignment explanation
Indices: 5640--5711 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
5630 GTTTAAAACC
* **
5640 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-AGAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
***
5687 AAAGAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
5712 ACCAATTTAA
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
5 7 0.14
6 40 0.78
7 4 0.08
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (6 bp):
ATTTAA
Found at i:5691 original size:18 final size:18
Alignment explanation
Indices: 5656--5705 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
5646 AATTTAAACT
5656 AAATTTAAATTT-AAAAG
1 AAATTTAAATTTAAAAAG
5673 AAATTTAAATTTAAAAAG
1 AAATTTAAATTTAAAAAG
5691 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
5706 TTTAAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
AAATTTAAATTTAAAAAG
Found at i:5722 original size:17 final size:17
Alignment explanation
Indices: 5626--5705 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
5616 AATTTTAAAA
* *
5626 TTAAGTTTAAAAC-CAT
1 TTAAATTTAAAACAAAT
5642 TTCAAATTT-AAACTAAAT
1 TT-AAATTTAAAAC-AAAT
*
5660 TTAAATTTAAAAGAAAT
1 TTAAATTTAAAACAAAT
*
5677 TTAAATTTAAAAAGAAAT
1 TTAAATTT-AAAACAAAT
5695 TTAAATTTAAA
1 TTAAATTTAAA
5706 TTTAAAACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
16 6 0.11
17 26 0.46
18 24 0.43
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (17 bp):
TTAAATTTAAAACAAAT
Found at i:9327 original size:17 final size:17
Alignment explanation
Indices: 9299--9345 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
9289 CTCAAACACA
9299 CTTTTGTCTTTTTTTTTT
1 CTTTT-TCTTTTTTTTTT
9317 CTTTTTC-TTTTTTTTT
1 CTTTTTCTTTTTTTTTT
9333 CAATTTTTCTTTT
1 C--TTTTTCTTTT
9346 CAACTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.38
17 2 0.08
18 11 0.42
19 3 0.12
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (17 bp):
CTTTTTCTTTTTTTTTT
Found at i:9370 original size:17 final size:16
Alignment explanation
Indices: 9307--9374 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
9297 CACTTTTGTC
9307 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTCTTTTT
* **
9323 CTTTTTTTTTCAATTT
1 TTTTTTTTTTCTTTTT
* ***
9339 TTCTTTTCAACTTTTT
1 TTTTTTTTTTCTTTTT
*
9355 TTTCTTTTTTCTTTTT
1 TTTTTTTTTTCTTTTT
9371 TTTT
1 TTTT
9375 AACAATAAAA
Statistics
Matches: 36, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTT
Found at i:11560 original size:23 final size:23
Alignment explanation
Indices: 11534--11587 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
11524 TGACTTGGCA
*
11534 TCCAGTCAACAACTTCTAGAAGT
1 TCCAGTCAACAACTTCTAGAAGG
** *
11557 TCCAGTCAGTAGCTTCTAGAAGG
1 TCCAGTCAACAACTTCTAGAAGG
*
11580 TCTAGTCA
1 TCCAGTCA
11588 GCAAGGATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (23 bp):
TCCAGTCAACAACTTCTAGAAGG
Found at i:18518 original size:16 final size:15
Alignment explanation
Indices: 18492--18521 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18482 AATAAAAGAA
18492 ACTCAAAAATAATAC
1 ACTCAAAAATAATAC
18507 ACTCATAAAATAATA
1 ACTCA-AAAATAATA
18522 AAACGCACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (15 bp):
ACTCAAAAATAATAC
Found at i:21830 original size:23 final size:23
Alignment explanation
Indices: 21804--21851 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
21794 ATCCGGTCAA
21804 CAGCTTCTAGAAGGTCCAATCAG
1 CAGCTTCTAGAAGGTCCAATCAG
* *
21827 CAGCTTCTAGAAGGTCTAGTCAG
1 CAGCTTCTAGAAGGTCCAATCAG
21850 CA
1 CA
21852 AGGATGGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
CAGCTTCTAGAAGGTCCAATCAG
Found at i:22620 original size:17 final size:17
Alignment explanation
Indices: 22594--22628 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22584 GCTGATACTT
*
22594 AAATTGATTTTTTTTAA
1 AAATTGATTTGTTTTAA
*
22611 AAATTTATTTGTTTTAA
1 AAATTGATTTGTTTTAA
22628 A
1 A
22629 TTCTTAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
AAATTGATTTGTTTTAA
Found at i:26750 original size:28 final size:28
Alignment explanation
Indices: 26716--26793 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
26706 TTTTGGAGGT
*
26716 TCGAGGGTAAAATAATAATTTTGGACAC
1 TCGAGGGTAAAATAATAATTTTGGACAA
** * *
26744 TTTAGGGGCAAAATGATAATTTTGGACAA
1 TCGA-GGGTAAAATAATAATTTTGGACAA
26773 TCGAGGGTAAAA-AAGTAATTT
1 TCGAGGGTAAAATAA-TAATTT
26794 CGAGAAGCTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 1 0.03
28 15 0.38
29 23 0.59
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (28 bp):
TCGAGGGTAAAATAATAATTTTGGACAA
Found at i:26910 original size:29 final size:30
Alignment explanation
Indices: 26871--27026 Score: 96
Period size: 29 Copynumber: 5.3 Consensus size: 30
26861 TGAGGGTAAT
*
26871 TGGTAATTTTTTGAAAGTTCGAGGTTCATAA
1 TGGTAA-TTTTTGAAAGTTCGAGGTTCAAAA
** * * *
26902 TGG-AATTTTAAAAAATTCAAGGGT-AAAA
1 TGGTAATTTTTGAAAGTTCGAGGTTCAAAA
**
26930 TGGTAATTTTTGGAAA-TTCG-GGAGCAAAA
1 TGGTAATTTTT-GAAAGTTCGAGGTTCAAAA
26959 TGGTAATTTTTGAAATGTTTCG-GGTT-AAGAA
1 TGGTAATTTTTGAAA-G-TTCGAGGTTCAA-AA
* * *
26990 TGAT-ATTTTTGGAAGTTCGACAG-T-AAAA
1 TGGTAATTTTTGAAAGTTCGA-GGTTCAAAA
27018 TGGTAATTT
1 TGGTAATTT
27027 GTACAATAAC
Statistics
Matches: 98, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
28 21 0.21
29 46 0.47
30 17 0.17
31 14 0.14
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (30 bp):
TGGTAATTTTTGAAAGTTCGAGGTTCAAAA
Found at i:48216 original size:23 final size:23
Alignment explanation
Indices: 48181--48230 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
48171 CGTCAATCAT
48181 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
* *
48204 TGCTGGCTGGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
48227 TGCT
1 TGCT
48231 AACTGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:49970 original size:23 final size:21
Alignment explanation
Indices: 49908--49983 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 21
49898 AAATACCAAA
*
49908 AATAAAAAAATAGAAATAAAAT
1 AATAAAAAAATATAAAT-AAAT
* * *
49930 AATTTAAATAACATAAATAAATT
1 AA-TAAAAAAATATAAATAAA-T
49953 AATAAAAAAATATAAAATTAAAT
1 AATAAAAAAATAT-AAA-TAAAT
49976 AATAAAAA
1 AATAAAAA
49984 TACAATAGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
22 13 0.30
23 26 0.60
24 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (21 bp):
AATAAAAAAATATAAATAAAT
Found at i:49974 original size:37 final size:39
Alignment explanation
Indices: 49886--49985 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 39
49876 TTTGAGTCTG
*
49886 AAATA-AAAACTTAAATACCAAAAATAAAAAAATAGAAAT
1 AAATATAAAA-TTAAATAACAAAAATAAAAAAATAGAAAT
* * **
49925 AAA-AT-AATTTAAATAACATAAATAAATTAATA-AAA-
1 AAATATAAAATTAAATAACAAAAATAAAAAAATAGAAAT
*
49960 AAATATAAAATTAAATAATAAAAATA
1 AAATATAAAATTAAATAACAAAAATA
49986 CAATAGGTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
35 3 0.06
36 5 0.10
37 36 0.72
38 3 0.06
39 3 0.06
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (39 bp):
AAATATAAAATTAAATAACAAAAATAAAAAAATAGAAAT
Found at i:54323 original size:23 final size:23
Alignment explanation
Indices: 54289--54344 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
54279 GTCCATCATT
*
54289 GCTGACTAGACCTTCTAGAAACTA
1 GCTGACTGGACCTTCTAGAAAC-A
*
54313 -CTGACTGGACCTTCTAGAAGCA
1 GCTGACTGGACCTTCTAGAAACA
54335 GCTGACTGGA
1 GCTGACTGGA
54345 TGCCAAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
GCTGACTGGACCTTCTAGAAACA
Found at i:55863 original size:23 final size:23
Alignment explanation
Indices: 55829--55873 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55819 AATGTTGAAA
55829 ATAATGGAAAAAGAACAATATTC
1 ATAATGGAAAAAGAACAATATTC
55852 ATAAT-GACAAAAGAACAATATT
1 ATAATGGA-AAAAGAACAATATT
55874 GAGCATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (23 bp):
ATAATGGAAAAAGAACAATATTC
Found at i:72653 original size:13 final size:14
Alignment explanation
Indices: 72635--72664 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
72625 TTTAGAAATT
72635 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
72648 TTTTTATTTTATTA
1 TTTTTATTTTATTA
72662 TTT
1 TTT
72665 GCTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:72677 original size:13 final size:14
Alignment explanation
Indices: 72667--72699 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
72657 TATTATTTGC
72667 TTTTT-TAATTTAA
1 TTTTTCTAATTTAA
72680 TTTTTCTAATTTAAA
1 TTTTTCTAATTT-AA
72695 TTTTT
1 TTTTT
72700 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 6 0.33
15 7 0.39
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCTAATTTAA
Found at i:72684 original size:14 final size:15
Alignment explanation
Indices: 72667--72700 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
72657 TATTATTTGC
72667 TTTTTTAATTT-AAT
1 TTTTTTAATTTAAAT
*
72681 TTTTCTAATTTAAAT
1 TTTTTTAATTTAAAT
72696 TTTTT
1 TTTTT
72701 CCCTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTAATTTAAAT
Found at i:72698 original size:15 final size:13
Alignment explanation
Indices: 72640--72700 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
72630 AAATTTTTTT
* *
72640 ATTTTTTATTTTT
1 ATTTTTTAATTTA
*
72653 ATTTTATT-ATTTG
1 ATTTT-TTAATTTA
*
72666 CTTTTTTAATTTA
1 ATTTTTTAATTTA
72679 ATTTTTCTAATTTAA
1 ATTTTT-TAATTT-A
72694 ATTTTTT
1 ATTTTTT
72701 CCCTTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.05
13 21 0.54
14 9 0.23
15 7 0.18
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (13 bp):
ATTTTTTAATTTA
Done.