Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010212.1 Kokia drynarioides strain JFW-HI SEQ_125032, 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: 107316
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:36 original size:23 final size:23
Alignment explanation
Indices: 6--127 Score: 138
Period size: 23 Copynumber: 5.2 Consensus size: 23
1 AGCGC
6 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
29 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
52 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
77 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
100 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
123 ACTCT
1 GCTCT
128 GCTGTGTACT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
22 3 0.04
23 62 0.73
25 17 0.20
26 3 0.04
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:102 original size:48 final size:46
Alignment explanation
Indices: 6--132 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 46
1 AGCGC
6 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
* *
52 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTTAGCAC-TTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
* * * *
100 GCTCTCTGACTAGTACTTTGTGTACTCTGCTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCT-CTGT
133 GTACTCTCTG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
46 24 0.34
47 6 0.08
48 41 0.58
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
Found at i:157 original size:35 final size:34
Alignment explanation
Indices: 95--166 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
85 TTTAGCACTT
* * *
95 TGTGTGCTCTCTGACTAGTACTTTGTGTACTCTGC
1 TGTGTACTCTCTGACTAGCACTGTGTGTACTCT-C
** *
130 TGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTC
1 TGTGTACTCTCTGACTAGCACTGTGTGTACTCTC
164 TGT
1 TGT
167 TGCCCAGCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.44
Consensus pattern (34 bp):
TGTGTACTCTCTGACTAGCACTGTGTGTACTCTC
Found at i:16490 original size:22 final size:22
Alignment explanation
Indices: 16452--16497 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16442 TCGTGGGTTT
*
16452 TTTTAATTAAAATAAAGAATTA
1 TTTTAATTAAAATAAAGAAATA
*
16474 TTTTATATTAGAA-AAAGAAATA
1 TTTTA-ATTAAAATAAAGAAATA
16496 TT
1 TT
16498 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTTAATTAAAATAAAGAAATA
Found at i:24111 original size:20 final size:21
Alignment explanation
Indices: 24075--24121 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
24065 AAAATTACGA
*
24075 AAAATTTTCATAATAATTTTC
1 AAAATTTTCAAAATAATTTTC
*
24096 AAAATTTT-AAAATAATTTTT
1 AAAATTTTCAAAATAATTTTC
24116 AAAATT
1 AAAATT
24122 AAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTTTCAAAATAATTTTC
Found at i:24128 original size:19 final size:20
Alignment explanation
Indices: 24086--24128 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
24076 AAATTTTCAT
*
24086 AATAATTTTCAAAATTTTAA
1 AATAATTTTCAAAATTTAAA
*
24106 AATAATTTTTAAAA-TTAAA
1 AATAATTTTCAAAATTTAAA
24125 AATA
1 AATA
24129 TAAATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAATTTTCAAAATTTAAA
Found at i:24167 original size:9 final size:10
Alignment explanation
Indices: 24144--24186 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
24134 AAGAATTTCA
24144 AAAAAATTTT
1 AAAAAATTTT
24154 AAAAAATTTT
1 AAAAAATTTT
24164 --AAAATTTT
1 AAAAAATTTT
*
24172 GAAAAATTTCT
1 AAAAAATTT-T
24183 AAAA
1 AAAA
24187 TAATAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
10 17 0.59
11 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:24169 original size:18 final size:19
Alignment explanation
Indices: 24146--24187 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
24136 GAATTTCAAA
24146 AAAATTTTAAAAAATTT-T
1 AAAATTTTAAAAAATTTCT
*
24164 AAAATTTTGAAAAATTTCT
1 AAAATTTTAAAAAATTTCT
24183 AAAAT
1 AAAAT
24188 AATAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTTTAAAAAATTTCT
Found at i:25359 original size:15 final size:14
Alignment explanation
Indices: 25332--25373 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
25322 AATATTATTT
*
25332 ATTTAATTTAATTA
1 ATTTTATTTAATTA
25346 ATTTTATTTAAATTA
1 ATTTTATTT-AATTA
25361 A-TTT-TTTAATTA
1 ATTTTATTTAATTA
25373 A
1 A
25374 ATGATTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 11 0.42
15 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTATTTAATTA
Found at i:25373 original size:17 final size:17
Alignment explanation
Indices: 25328--25393 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
25318 CCAAAATATT
*
25328 ATTTATTTAATTTAATTA
1 ATTT-TTTAATTAAATTA
*
25346 A--TTTTATTTAAATTA
1 ATTTTTTAATTAAATTA
*
25361 ATTTTTTAATTAAA-TG
1 ATTTTTTAATTAAATTA
*
25377 ATTTTCTTAATTCAATT
1 ATTTT-TTAATTAAATT
25394 CTAATTCCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
15 12 0.31
16 7 0.18
17 18 0.46
18 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTTTTAATTAAATTA
Found at i:25811 original size:34 final size:32
Alignment explanation
Indices: 25769--25840 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
25759 TATCATTATT
*
25769 TTTAAT-AAAATATTTTATATACTTATAATTTAA
1 TTTAATAAAAATATTTT-TATACATATAA-TTAA
*
25802 TTTACATAAAAATATTTTTTTACATATAATTAA
1 TTTA-ATAAAAATATTTTTATACATATAATTAA
25835 TTTAAT
1 TTTAAT
25841 TTAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 2 0.06
33 12 0.34
34 11 0.31
35 10 0.29
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAATAAAAATATTTTTATACATATAATTAA
Found at i:27889 original size:16 final size:18
Alignment explanation
Indices: 27845--27890 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
27835 TTGTTGATTT
27845 TTTATACAATTTTTCAATTA
1 TTTATA-AATTTTTCAA-TA
*
27865 TTCATAAATTTTT-AA-A
1 TTTATAAATTTTTCAATA
27881 TTTATAAATT
1 TTTATAAATT
27891 AGAGGATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
18 2 0.08
19 7 0.29
20 5 0.21
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATAAATTTTTCAATA
Found at i:31629 original size:5 final size:5
Alignment explanation
Indices: 31619--31647 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31609 ATATACAGAT
31619 GATTA GATTA GATTA GATTA GATTA GATT
1 GATTA GATTA GATTA GATTA GATTA GATT
31648 TTTAACTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
GATTA
Found at i:34091 original size:15 final size:15
Alignment explanation
Indices: 34071--34100 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34061 CAGCTGAGAT
34071 TGTTCACGCAATTAC
1 TGTTCACGCAATTAC
34086 TGTTCACGCAATTAC
1 TGTTCACGCAATTAC
34101 ATACATCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
TGTTCACGCAATTAC
Found at i:35967 original size:19 final size:19
Alignment explanation
Indices: 35943--35980 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35933 GAACCCCTAT
35943 GTGTTGACCGATGATCAAG
1 GTGTTGACCGATGATCAAG
35962 GTGTTGACCGATGATCAAG
1 GTGTTGACCGATGATCAAG
35981 TGTGGTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
GTGTTGACCGATGATCAAG
Found at i:48288 original size:19 final size:19
Alignment explanation
Indices: 48266--48322 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
48256 ATATATATAT
48266 AATTTTTATAATTTTTAAA
1 AATTTTTATAATTTTTAAA
* * *
48285 AATTGTAATTATTATTT-AA
1 AATTTTTATAATT-TTTAAA
*
48304 AATTTCTTATAATTCTTAA
1 AATTT-TTATAATTTTTAA
48323 CCATTTTGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTTATAATTTTTAAA
Found at i:48522 original size:2 final size:2
Alignment explanation
Indices: 48515--48550 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
48505 AAACAATTTG
**
48515 AT AT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48551 TATTTTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48942 original size:29 final size:30
Alignment explanation
Indices: 48909--48980 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
48899 ATCAAAATTA
48909 TTTAATAATTTTAT-TAT-TAAAAAAATAAT
1 TTTAATAATTTTATAT-TCTAAAAAAATAAT
* *
48938 TTTAACAATTTTATATTCTTAAAAAATAAT
1 TTTAATAATTTTATATTCTAAAAAAATAAT
48968 TTTAATAATTTTA
1 TTTAATAATTTTA
48981 AAATAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAATAATTTTATATTCTAAAAAAATAAT
Found at i:49295 original size:4 final size:4
Alignment explanation
Indices: 49286--49313 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
49276 ACAACAACTA
49286 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
49314 TTAAGGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:52916 original size:31 final size:31
Alignment explanation
Indices: 52875--52969 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 31
52865 TTAATATAAC
*
52875 ATTTGGTACCTGAACTTGATTTTTTTTCCTA
1 ATTTGATACCTGAACTTGATTTTTTTTCCTA
* * * *
52906 ATTTGATACCT-TAGTT--TTTTTTTACCCA
1 ATTTGATACCTGAACTTGATTTTTTTTCCTA
***
52934 ATTTGATACCTGAACTTGACACTTTTTCCTA
1 ATTTGATACCTGAACTTGATTTTTTTTCCTA
52965 ATTTG
1 ATTTG
52970 GTAATTAAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
28 21 0.43
29 3 0.06
30 3 0.06
31 22 0.45
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTTGATACCTGAACTTGATTTTTTTTCCTA
Found at i:53018 original size:58 final size:59
Alignment explanation
Indices: 52875--53060 Score: 173
Period size: 58 Copynumber: 3.2 Consensus size: 59
52865 TTAATATAAC
* * * *** **
52875 ATTTGGTACCTGAACTTGATTTTTTTTCCTAATTTGATACCTTAGTTTTTTTTTACCCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACATTAAACTTTTTAGACCCA
* * *
52934 ATTTGATACCTGAACTTGACACTTTTTCCTAATTTGGTA-ATTAAACTTTTTAGACCCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACATTAAACTTTTTAGACCCA
* * * * **
52992 ATTTGGTACTTGAACTTGGTATTTTTT--TAATTTGGTAC-CTAAGCTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACATTAAAC--TTTTTAGACCCA
53050 ATTTGGTACCT
1 ATTTGGTACCT
53061 AAATCTATTA
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
56 14 0.14
58 55 0.53
59 34 0.33
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGATATTTTTTCCTAATTTGGTACATTAAACTTTTTAGACCCA
Found at i:53019 original size:59 final size:60
Alignment explanation
Indices: 52875--53019 Score: 161
Period size: 59 Copynumber: 2.5 Consensus size: 60
52865 TTAATATAAC
* *** **
52875 ATTTGGTACCTGAACTTGAT-TTTTTTTCCTAATTTGATACCTTAGTTTTTTTTTACCCA
1 ATTTGGTACCTGAACTTGATATTTTTTTCCTAATTTGATACATTAAACTTTTTAGACCCA
* * * *
52934 ATTTGATACCTGAACTTGACA-CTTTTTCCTAATTTGGTA-ATTAAACTTTTTAGACCCA
1 ATTTGGTACCTGAACTTGATATTTTTTTCCTAATTTGATACATTAAACTTTTTAGACCCA
* *
52992 ATTTGGTACTTGAACTTGGTATTTTTTT
1 ATTTGGTACCTGAACTTGATATTTTTTT
53020 AATTTGGTAC
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 30 0.43
59 39 0.57
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGATATTTTTTTCCTAATTTGATACATTAAACTTTTTAGACCCA
Found at i:59674 original size:29 final size:29
Alignment explanation
Indices: 59632--59689 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
59622 AAGATGCTTT
59632 CAGTAATTGACGTCTTATGGTGGATTATG
1 CAGTAATTGACGTCTTATGGTGGATTATG
59661 CAGTAATTGACGTCTTATGGTGGATTATG
1 CAGTAATTGACGTCTTATGGTGGATTATG
59690 ATGTTTCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (29 bp):
CAGTAATTGACGTCTTATGGTGGATTATG
Found at i:67695 original size:16 final size:17
Alignment explanation
Indices: 67674--67706 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
67664 CCTTGGTCCC
67674 ATTTTTGCAG-TTTTAA
1 ATTTTTGCAGCTTTTAA
*
67690 ATTTTTGTAGCTTTTAA
1 ATTTTTGCAGCTTTTAA
67707 GAATCAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTTTTGCAGCTTTTAA
Found at i:69519 original size:42 final size:42
Alignment explanation
Indices: 69460--69550 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
69450 AACAGGTTTA
69460 CTGGTTTTATATCTCATATTTTATCTTCATTTTCTCCCTCAT
1 CTGGTTTTATATCTCATATTTTATCTTCATTTTCTCCCTCAT
69502 CTGGTTTTATATCTCATATTTTATCTTCATTTTCTCCCTCAT
1 CTGGTTTTATATCTCATATTTTATCTTCATTTTCTCCCTCAT
69544 CTGGTTT
1 CTGGTTT
69551 CAGGTCTTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (42 bp):
CTGGTTTTATATCTCATATTTTATCTTCATTTTCTCCCTCAT
Found at i:72564 original size:11 final size:10
Alignment explanation
Indices: 72545--72572 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
72535 TCTCATAACC
72545 TTCTTTTTTT
1 TTCTTTTTTT
72555 TTCTTTTTTT
1 TTCTTTTTTT
72565 TTCTTTTT
1 TTCTTTTT
72573 GTAATTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:75019 original size:31 final size:33
Alignment explanation
Indices: 74965--75030 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
74955 CATGTTTTTC
*
74965 TATTTATTTTTAAAATTTTTTAATCATTCATTAA
1 TATTTATTTTT-AAATTTTTTAATCATCCATTAA
*
74999 TATTTATTTTT-AA-TTTTTAATTATCCATTAA
1 TATTTATTTTTAAATTTTTTAATCATCCATTAA
75030 T
1 T
75031 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 17 0.57
32 2 0.07
34 11 0.37
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (33 bp):
TATTTATTTTTAAATTTTTTAATCATCCATTAA
Found at i:78845 original size:2 final size:2
Alignment explanation
Indices: 78840--78866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
78830 TATTATATAA
78840 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
78867 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:78871 original size:4 final size:4
Alignment explanation
Indices: 78864--78889 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
78854 TGTGTGTGTG
78864 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
78890 CATTTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:99430 original size:78 final size:77
Alignment explanation
Indices: 99299--99568 Score: 443
Period size: 77 Copynumber: 3.5 Consensus size: 77
99289 CTAGGGAAAG
* * ** *
99299 CAAGTAGCTGAACAGCCTTGCTTCTGGATTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAATGAG
1 CAAGCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAACGAG
99364 CTGTGTTTAAAC
66 CTGTGTTTAAAC
99376 CAAGCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAACGA
1 CAAGCAGCTTAACAGCCTTGCTTCCAGA-TTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAACGA
99441 GCTGTGTTTAAAC
65 GCTGTGTTTAAAC
* *
99454 CAATCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAGACGAG
1 CAAGCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAACGAG
99519 CTGTGTTTAAAC
66 CTGTGTTTAAAC
* *
99531 CAAACAGCTTAATAGCCTTGCTTCCA-ATTTTTTTTTTG
1 CAAGCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTG
99569 CATAGCATAA
Statistics
Matches: 183, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
76 12 0.07
77 96 0.52
78 75 0.41
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (77 bp):
CAAGCAGCTTAACAGCCTTGCTTCCAGATTTTTTTTTTGTTTTCTCTTTTGTAAGCTCAAACGAG
CTGTGTTTAAAC
Found at i:105388 original size:30 final size:30
Alignment explanation
Indices: 105352--105445 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
105342 AAAAATAATA
*
105352 TTTTAACCTCTAAACTTTGCAAAATTTTAT
1 TTTTAACCTCTAAACTTTCCAAAATTTTAT
* *
105382 TTTTAACCTCCAAACTTTCCATAAATTTGA-
1 TTTTAACCTCTAAACTTTCCA-AAATTTTAT
** * *
105412 TCCTAACCCCTAAACTTTCCAAAATTTTGT
1 TTTTAACCTCTAAACTTTCCAAAATTTTAT
105442 TTTT
1 TTTT
105446 GCCCCCAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 6 0.12
30 38 0.75
31 7 0.14
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTTAACCTCTAAACTTTCCAAAATTTTAT
Found at i:105495 original size:30 final size:29
Alignment explanation
Indices: 105457--105607 Score: 137
Period size: 30 Copynumber: 5.1 Consensus size: 29
105447 CCCCCAATGT
*
105457 TTTC-AAAAATTATATTTTGACCCCTAAAA
1 TTTCTAAAAATTATATTTTGACCCC-AAAC
* ** *
105486 TTTTTAAAAATTATATTTCAAACTCCAAAC
1 TTTCTAAAAATTATATTT-TGACCCCAAAC
*
105516 TTTCTAGAAATTATATTTTGACTCCCAAAC
1 TTTCTAAAAATTATATTTTGAC-CCCAAAC
* * *
105546 TTTCCAAGAATTCA-ATTTTGACCCTTAAAC
1 TTTCTAAAAATT-ATATTTTGACCC-CAAAC
* *
105576 TTTCTAAAAATTACATTTTG-CCCCAAGC
1 TTTCTAAAAATTATATTTTGACCCCAAAC
105604 TTTC
1 TTTC
105608 CAAATTCACC
Statistics
Matches: 98, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
28 7 0.07
29 11 0.11
30 75 0.77
31 5 0.05
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTCTAAAAATTATATTTTGACCCCAAAC
Found at i:106368 original size:31 final size:31
Alignment explanation
Indices: 106328--106393 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
106318 CTTCAAACCT
106328 AAAT-AATCGAACATCCTATTTCAAATTGAA
1 AAATCAATCGAACATCCTATTTCAAATTGAA
106358 AAATCAATCGAACATCCTATTTCAAATTGAA
1 AAATCAATCGAACATCCTATTTCAAATTGAA
106389 AAATC
1 AAATC
106394 GCCATTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (31 bp):
AAATCAATCGAACATCCTATTTCAAATTGAA
Done.