Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001502.1 Kokia drynarioides strain JFW-HI SEQ_113041, 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: 36689
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1950 original size:24 final size:24
Alignment explanation
Indices: 1914--1959 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1904 AAAAATAATT
*
1914 AAAAATTAGATAA-TTTTTTTTGA
1 AAAAATTAAATAAGTTTTTTTTGA
1937 AAAAAGTTAAATAAGTTTTTTTT
1 AAAAA-TTAAATAAGTTTTTTTT
1960 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
AAAAATTAAATAAGTTTTTTTTGA
Found at i:6740 original size:26 final size:26
Alignment explanation
Indices: 6711--6760 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6701 TTCAAATTTT
*
6711 TCAAAATAAATAAATATGTTTAAAAA
1 TCAAAATAAATAAATATGGTTAAAAA
* *
6737 TCAATATAAATAAATTTGGTTAAA
1 TCAAAATAAATAAATATGGTTAAA
6761 TTTTTAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (26 bp):
TCAAAATAAATAAATATGGTTAAAAA
Found at i:6992 original size:23 final size:23
Alignment explanation
Indices: 6962--7008 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
6952 CACTTAAATA
6962 ATTTTTATATATTTTTA-ATTTT
1 ATTTTTATATATTTTTAGATTTT
6984 ATTTGTTATATATTTTTAGATTTT
1 ATTT-TTATATATTTTTAGATTTT
7008 A
1 A
7009 AAAAATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
ATTTTTATATATTTTTAGATTTT
Found at i:11033 original size:22 final size:22
Alignment explanation
Indices: 11005--11051 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
10995 AGCTGAATCA
11005 ATGCAATGGCATAATAGCTTGT
1 ATGCAATGGCATAATAGCTTGT
11027 ATGCAATGGCATAATAGCTTGT
1 ATGCAATGGCATAATAGCTTGT
11049 ATG
1 ATG
11052 AAAGTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (22 bp):
ATGCAATGGCATAATAGCTTGT
Found at i:16221 original size:3 final size:3
Alignment explanation
Indices: 16213--16242 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16203 CTGTTAGCCG
*
16213 ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16243 TTTTATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:23101 original size:17 final size:16
Alignment explanation
Indices: 23074--23107 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23064 GTTATGCCTC
*
23074 TATTTTCTTTAATATT
1 TATTTTCTTTAACATT
23090 TATTTATCTTTAACATT
1 TATTT-TCTTTAACATT
23107 T
1 T
23108 TATTATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTCTTTAACATT
Found at i:31235 original size:9 final size:9
Alignment explanation
Indices: 31223--31295 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
31213 TATTTTTTGA
31223 AAAAAATTT
1 AAAAAATTT
*
31232 AAAAAATTC
1 AAAAAATTT
31241 AAAAAATATAT
1 AAAAAAT-T-T
*
31252 AAAATTATTT
1 AAAA-AATTT
*
31262 TAAAAATATT
1 AAAAAAT-TT
**
31272 AAAATTTTT
1 AAAAAATTT
31281 AAAAAA--T
1 AAAAAATTT
31288 AAAAAATT
1 AAAAAATT
31296 AATTGATTGC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.15
9 23 0.48
10 11 0.23
11 5 0.10
12 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAAATTT
Found at i:31270 original size:19 final size:19
Alignment explanation
Indices: 31242--31296 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
31232 AAAAAATTCA
31242 AAAAATATATAAAATTATTT
1 AAAAA-ATATAAAATTATTT
*
31262 TAAAAATATTAAAATT-TTT
1 AAAAAATA-TAAAATTATTT
*
31281 AAAAAATAAAAAATTA
1 AAAAAATATAAAATTA
31297 ATTGATTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 11 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATATAAAATTATTT
Found at i:31292 original size:17 final size:18
Alignment explanation
Indices: 31242--31292 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
31232 AAAAAATTCA
31242 AAAAATATATAAAATTATTTT
1 AAAAATATA-AAAA-T-TTTT
*
31263 AAAAATATTAAAATTTTT
1 AAAAATATAAAAATTTTT
31281 AAAAA-ATAAAAA
1 AAAAATATAAAAA
31293 ATTAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 1 0.04
20 4 0.14
21 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATATAAAAATTTTT
Done.