Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001391.1 Kokia drynarioides strain JFW-HI SEQ_112874, 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: 12480
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:879 original size:17 final size:18
Alignment explanation
Indices: 859--901 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
849 GGCTTTATTT
**
859 ATTTTAAATTT-ATGATA
1 ATTTTAAATTTGAAAATA
876 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
894 ATTTTAAA
1 ATTTTAAA
902 CTTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:929 original size:17 final size:17
Alignment explanation
Indices: 859--918 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
849 GGCTTTATTT
**
859 ATTTTAAATTTATGATA
1 ATTTTAAATTTAAAATA
876 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
* *
894 ATTTTAAACTTAAATTA
1 ATTTTAAATTTAAAATA
*
911 AATTTAAA
1 ATTTTAAA
919 ATAAATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:2770 original size:24 final size:24
Alignment explanation
Indices: 2754--2805 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2744 AATCAATGTA
2754 AAATATATTATGTTAATAAATGCT
1 AAATATATTATGTTAATAAATGCT
** *
2778 AAATATATTATACTAATAAATACT
1 AAATATATTATGTTAATAAATGCT
2802 AAAT
1 AAAT
2806 CTTCTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGTTAATAAATGCT
Found at i:5299 original size:18 final size:18
Alignment explanation
Indices: 5272--5307 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5262 CTTTATATTT
*
5272 TTTTAGAATTTTTTAAAA
1 TTTTAGAATTTTTGAAAA
*
5290 TTTTATAATTTTTGAAAA
1 TTTTAGAATTTTTGAAAA
5308 ATATAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTAGAATTTTTGAAAA
Found at i:5666 original size:14 final size:14
Alignment explanation
Indices: 5642--5668 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5632 ATGATACACA
5642 AATTATGATATATT
1 AATTATGATATATT
5656 AATTATGATATAT
1 AATTATGATATAT
5669 ATTAGTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AATTATGATATATT
Found at i:9792 original size:29 final size:29
Alignment explanation
Indices: 9757--9824 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
9747 TCAACTACAG
* *
9757 ATATAATACGGATACAGTTACAAATGCAA
1 ATATAATACAGATACAATTACAAATGCAA
* * *
9786 ATGTAATACAGATACAATTACAGATGCAG
1 ATATAATACAGATACAATTACAAATGCAA
9815 ATATAATACA
1 ATATAATACA
9825 AATATAATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (29 bp):
ATATAATACAGATACAATTACAAATGCAA
Found at i:9827 original size:40 final size:40
Alignment explanation
Indices: 9783--9858 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
9773 GTTACAAATG
*
9783 CAAATGTAATACAGATACAATTACAGATGCAGATATAATA
1 CAAATATAATACAGATACAATTACAGATGCAGATATAATA
* *
9823 CAAATATAATACAGATACAGTTACAGATGCATATAT
1 CAAATATAATACAGATACAATTACAGATGCAGATAT
9859 GATATCCCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (40 bp):
CAAATATAATACAGATACAATTACAGATGCAGATATAATA
Done.