Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006323.1 Kokia drynarioides strain JFW-HI SEQ_120898, 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: 74955
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:13054 original size:24 final size:24
Alignment explanation
Indices: 13027--13081 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
13017 ACAATCAATT
*
13027 CATTTTATGTTACATTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
*
13051 CATTTTATATTACTTTTGCACTGA
1 CATTTTATATTACATTTGCACTGA
13075 CAATTTT
1 C-ATTTT
13082 TACTCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.49
Consensus pattern (24 bp):
CATTTTATATTACATTTGCACTGA
Found at i:29992 original size:25 final size:26
Alignment explanation
Indices: 29964--30015 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
29954 TAAGAACTTA
29964 TAAAATAAAAAATAA-AAAATAA-AAG
1 TAAAA-AAAAAATAAGAAAATAACAAG
*
29989 TAAAACAAAAATAAGAAAATAACAAG
1 TAAAAAAAAAATAAGAAAATAACAAG
30015 T
1 T
30016 TTTGACTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 12 0.50
26 4 0.17
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (26 bp):
TAAAAAAAAAATAAGAAAATAACAAG
Found at i:31397 original size:19 final size:19
Alignment explanation
Indices: 31373--31413 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
31363 TAAAAATGAC
31373 ACATGAAATGGATTAAACG
1 ACATGAAATGGATTAAACG
31392 ACATGAAATGGATTAAACG
1 ACATGAAATGGATTAAACG
31411 ACA
1 ACA
31414 ATCTTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (19 bp):
ACATGAAATGGATTAAACG
Found at i:37019 original size:17 final size:18
Alignment explanation
Indices: 36999--37035 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
36989 GGATGGTGAA
36999 TTTAAAGGTTA-TGGGTC
1 TTTAAAGGTTATTGGGTC
*
37016 TTTAATGGTTATTGGGTC
1 TTTAAAGGTTATTGGGTC
37034 TT
1 TT
37036 CTTGTAGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.27, T:0.49
Consensus pattern (18 bp):
TTTAAAGGTTATTGGGTC
Found at i:37157 original size:16 final size:14
Alignment explanation
Indices: 37131--37177 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
37121 TAAATTTTTA
*
37131 GGAAATGGGTATTT
1 GGAACTGGGTATTT
37145 GGAACATTGGGTATTTT
1 GGAAC--TGGGTA-TTT
37162 GGAACTGGGTATTT
1 GGAACTGGGTATTT
37176 GG
1 GG
37178 GTATTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 6 0.21
17 8 0.28
ACGTcount: A:0.23, C:0.04, G:0.36, T:0.36
Consensus pattern (14 bp):
GGAACTGGGTATTT
Found at i:37172 original size:15 final size:15
Alignment explanation
Indices: 37126--37175 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
37116 TGGGTTAAAT
*
37126 TTTTAGGAAATGGGTA
1 TTTT-GGAACTGGGTA
37142 -TTTGGAACATTGGGTA
1 TTTTGGAAC--TGGGTA
37158 TTTTGGAACTGGGTA
1 TTTTGGAACTGGGTA
37173 TTT
1 TTT
37176 GGGTATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.13
15 12 0.40
16 6 0.20
17 8 0.27
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.42
Consensus pattern (15 bp):
TTTTGGAACTGGGTA
Found at i:43827 original size:22 final size:23
Alignment explanation
Indices: 43801--43853 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
43791 CCTATTTGCT
* *
43801 AAAAATAAATAATTTATTAAA-A
1 AAAAATAAATAACTTATCAAATA
*
43823 GAAAAT-AATAACTTATCAAATA
1 AAAAATAAATAACTTATCAAATA
43845 AAAAATAAA
1 AAAAATAAA
43854 AAATAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 12 0.48
22 11 0.44
23 2 0.08
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAATAAATAACTTATCAAATA
Found at i:43838 original size:21 final size:22
Alignment explanation
Indices: 43801--43852 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
43791 CCTATTTGCT
* *
43801 AAAAATAAATAATTTATTAAA-A
1 AAAAAT-AATAACTTATCAAATA
*
43823 GAAAATAATAACTTATCAAATA
1 AAAAATAATAACTTATCAAATA
43845 AAAAATAA
1 AAAAATAA
43853 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATAATAACTTATCAAATA
Found at i:50900 original size:35 final size:34
Alignment explanation
Indices: 50854--50970 Score: 144
Period size: 34 Copynumber: 3.4 Consensus size: 34
50844 TCTAATCTGG
50854 TATGACATTCTGATCTGATATATGTTTTTAAAAAA
1 TATGACATTCTGATCTGATATATGTTTTT-AAAAA
* * *
50889 TATGACATTCTGATCTAATATGTATTTTTAAAAA
1 TATGACATTCTGATCTGATATATGTTTTTAAAAA
* * * ***
50923 TATAACATTTTGATATGATATATGTTTTTGGTAA
1 TATGACATTCTGATCTGATATATGTTTTTAAAAA
50957 TATGACATTCTGAT
1 TATGACATTCTGAT
50971 TTATTATTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
34 42 0.62
35 26 0.38
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (34 bp):
TATGACATTCTGATCTGATATATGTTTTTAAAAA
Found at i:59668 original size:14 final size:14
Alignment explanation
Indices: 59631--59669 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
59621 AACTATAGTA
*
59631 AAATTTAATCTATC
1 AAATTTAATTTATC
59645 AAATTTAATTTATC
1 AAATTTAATTTATC
59659 AAATTTAATTT
1 AAATTTAATTT
59670 CTTTTTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTAATTTATC
Found at i:73896 original size:20 final size:21
Alignment explanation
Indices: 73871--73937 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
73861 AGAGGCATCG
73871 AAGTGCAAAT-AGAGACA-CA
1 AAGTGCAAATCAGAGACACCA
73890 AATGTGC-AATCAGAGACACCA
1 AA-GTGCAAATCAGAGACACCA
* * *
73911 AAGTGCAAA-CAAAGGCACAA
1 AAGTGCAAATCAGAGACACCA
73931 AAGTGCA
1 AAGTGCA
73938 GTCCCATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.12
20 30 0.73
21 6 0.15
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.10
Consensus pattern (21 bp):
AAGTGCAAATCAGAGACACCA
Done.