Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009681.1 Kokia drynarioides strain JFW-HI SEQ_124399, 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, 933
Length: 1556
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Found at i:86 original size:29 final size:28
Alignment explanation
Indices: 10--130 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 28
1 AATGGTATT
* * * *
10 TTTTGGAAAAATTGAGGTTAAAAAAGGAA
1 TTTTGG-AAAGTTGAGGGTAAAAATGTAA
* *
39 TTTGGGAAAGTTTGGGGGTAAAAATGTAA
1 TTTTGGAAAG-TTGAGGGTAAAAATGTAA
* *
68 TTTTGGAAAGTTCGAGGGTTAAAATATAA
1 TTTTGGAAAGTT-GAGGGTAAAAATGTAA
* * *
97 TTTTGGAGAAGTTTAGGGGTCAAAATATAA
1 TTTTGGA-AAGTTGA-GGGTAAAAATGTAA
127 TTTT
1 TTTT
131 TGGACAATTT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
28 5 0.07
29 49 0.64
30 22 0.29
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (28 bp):
TTTTGGAAAGTTGAGGGTAAAAATGTAA
Found at i:122 original size:30 final size:29
Alignment explanation
Indices: 37--144 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
27 TTAAAAAAGG
* * *
37 AATTTGGGAAAGTTTGGGGGTAAAAATGT
1 AATTTTGGAAAGTTTAGGGGTAAAAATAT
* *
66 AATTTTGGAAAG-TTCGAGGGTTAAAATAT
1 AATTTTGGAAAGTTTAG-GGGTAAAAATAT
*
95 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTGGA-AAGTTTAGGGGTAAAAATAT
125 AATTTTTGGACAA-TTTAGGG
1 AA-TTTTGGA-AAGTTTAGGG
145 ACCTTCGAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.04
29 30 0.44
30 23 0.34
31 12 0.18
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAAGTTTAGGGGTAAAAATAT
Found at i:988 original size:34 final size:34
Alignment explanation
Indices: 950--1016 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
940 ATTTTAATTT
*
950 AAAAT-AATCTTAAATTTAAAGTAAATTCAAACTC
1 AAAATGAAT-TTAAATTTAAAATAAATTCAAACTC
*
984 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATGAATTTAAATTTAAAATAAATTCAAACT
1017 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATGAATTTAAATTTAAAATAAATTCAAACTC
Found at i:1004 original size:17 final size:17
Alignment explanation
Indices: 939--1010 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
929 CTTTTAATTT
*
939 AATTTTAATTTAAAAT-
1 AATTTAAATTTAAAATA
*
955 AATCTTAAATTTAAAGTA
1 AAT-TTAAATTTAAAATA
* * * *
973 AATTCAAACTCAAAATG
1 AATTTAAATTTAAAATA
*
990 AATTTGAATTTAAAATA
1 AATTTAAATTTAAAATA
1007 AATT
1 AATT
1011 CAAACTTATT
Statistics
Matches: 42, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
16 3 0.07
17 36 0.86
18 3 0.07
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:1498 original size:39 final size:39
Alignment explanation
Indices: 1439--1554 Score: 126
Period size: 39 Copynumber: 3.0 Consensus size: 39
1429 TGGATAACTA
*
1439 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGACGG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGATGACGG
** * * * * * *
1478 TGATTTGCCCCATGCTCGGGGTAA-AAAGTCGGATGGCTG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGA-TTGGATGACGG
*
1517 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGACG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGATGACG
1555 AT
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
38 2 0.04
39 53 0.93
40 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.22
Consensus pattern (39 bp):
CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGATGACGG
Done.