Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004239.1 Kokia drynarioides strain JFW-HI SEQ_117507, 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: 23137
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:2037 original size:17 final size:17
Alignment explanation
Indices: 2015--2047 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2005 ACATGTATTG
2015 AAACTA-AAAACAAAATA
1 AAACTACAAAA-AAAATA
2032 AAACTACAAAAAAAAT
1 AAACTACAAAAAAAAT
2048 GTTGAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAACTACAAAAAAAATA
Found at i:2519 original size:35 final size:36
Alignment explanation
Indices: 2445--2531 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
2435 AAAAAATCAG
*
2445 AAAAAAATCTAAAAATATATAAATATTATTAAATATT
1 AAAAAAAT-TAAAAATATAGAAATATTATTAAATATT
* * *
2482 AAAAAAATTAAGAATAT-GAAATTTTATATAAA-CTT
1 AAAAAAATTAAAAATATAGAAATATTAT-TAAATATT
2517 AAAAAAATTATAAAA
1 AAAAAAATTA-AAAA
2532 ATTCTAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 20 0.47
36 15 0.35
37 8 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (36 bp):
AAAAAAATTAAAAATATAGAAATATTATTAAATATT
Found at i:8727 original size:2 final size:2
Alignment explanation
Indices: 8720--8753 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8710 TAGTAAGGGG
8720 AT AT AT AT AT 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
8754 CAAAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12418 original size:87 final size:87
Alignment explanation
Indices: 12263--12428 Score: 237
Period size: 87 Copynumber: 1.9 Consensus size: 87
12253 TACATGCATA
* * *
12263 AGGTTGAGTTTATTACTCTTAATGAATTCATAACCTAGAGTTTGGGTGGTCCTATTGAGACGAAC
1 AGGTTGAGTTTATTACTCTTAATGAATTCATAACCTAGAGTTTGGGTGATCCTATTAAGAAGAAC
12328 TTGATGAATTCACCAACATGTG
66 TTGATGAATTCACCAACATGTG
* * *
12350 AGGTTGCA-TTTATTACTTTTAATGAATTTATATCCTAGAGTTTGGGTGATCCTATTAAGATAG-
1 AGGTTG-AGTTTATTACTCTTAATGAATTCATAACCTAGAGTTTGGGTGATCCTATTAAGA-AGA
*
12413 GCTTGATGAATTCACC
64 ACTTGATGAATTCACC
12429 GAATTTAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 68 0.97
88 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (87 bp):
AGGTTGAGTTTATTACTCTTAATGAATTCATAACCTAGAGTTTGGGTGATCCTATTAAGAAGAAC
TTGATGAATTCACCAACATGTG
Found at i:13917 original size:19 final size:19
Alignment explanation
Indices: 13895--13936 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
13885 AAATTACAAC
*
13895 AAAATTTAAAATAA-TTTTT
1 AAAATTTAAAA-AAGTTTCT
13914 AAAA-TTAAAAAAGTTTCT
1 AAAATTTAAAAAAGTTTCT
13932 AAAAT
1 AAAAT
13937 AATAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.10
18 14 0.70
19 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATTTAAAAAAGTTTCT
Found at i:17648 original size:12 final size:12
Alignment explanation
Indices: 17633--17658 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17623 ATAAAATTAG
17633 AATTATAAATAT
1 AATTATAAATAT
17645 AATTATAAATAT
1 AATTATAAATAT
17657 AA
1 AA
17659 ATAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTATAAATAT
Found at i:17648 original size:18 final size:18
Alignment explanation
Indices: 17615--17664 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
17605 GTGCATAATA
*
17615 AAATAGAAATAAAATTAG
1 AAATATAAATAAAATTAG
* * *
17633 AATTATAAATATAATTAT
1 AAATATAAATAAAATTAG
17651 AAATATAAATAAAA
1 AAATATAAATAAAA
17665 AATAACATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
AAATATAAATAAAATTAG
Found at i:19752 original size:20 final size:20
Alignment explanation
Indices: 19723--19766 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19713 AACTAAATGT
*
19723 AAAA-ATTAAATTAAAAACA
1 AAAATATTAAAATAAAAACA
*
19742 AAAATATTAAAATAAAAATA
1 AAAATATTAAAATAAAAACA
19762 AAAAT
1 AAAAT
19767 TGGTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:21256 original size:16 final size:15
Alignment explanation
Indices: 21233--21275 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
21223 ATTTTTTAAA
21233 AATATTTTTATATTAT
1 AATATTTTTATATT-T
* *
21249 ATTATTTTAATATTT
1 AATATTTTTATATTT
*
21264 AATAATTTTATA
1 AATATTTTTATA
21276 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATATTTTTATATTT
Found at i:21405 original size:18 final size:18
Alignment explanation
Indices: 21384--21418 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21374 AATGTGTTTT
*
21384 AAATTACATAATATATAA
1 AAATAACATAATATATAA
21402 AAATAACATAATATATA
1 AAATAACATAATATATA
21419 GTATCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAACATAATATATAA
Done.