Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008346.1 Kokia drynarioides strain JFW-HI SEQ_123013, 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: 7019
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:1364 original size:21 final size:19
Alignment explanation
Indices: 1340--1380 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
1330 GAATATGATA
1340 TTTTTCATTTCTTTTCTCTTTT
1 TTTTTC-TTT-TTTT-TCTTTT
1362 TTTTTCTTTTTTTTCTTTT
1 TTTTTCTTTTTTTTCTTTT
1381 CTTCCAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 3 0.16
22 6 0.32
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTTTT
Found at i:2045 original size:74 final size:74
Alignment explanation
Indices: 1919--2068 Score: 255
Period size: 74 Copynumber: 2.0 Consensus size: 74
1909 GCTTTACAAA
* * * *
1919 TGAAAGTGAACAGCCATCATTCATCATTCATAATTGAATGTGTTGATTCATTTAAAAAGTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATATGTTGATTCATTTAAAAACTCTTGA
1984 ATGAAACAT
66 ATGAAACAT
*
1993 TGAATGTGAACAACCATCATTCATCATTCATAAATGAATATGTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATATGTTGATTCATTTAAAAACTCTTGA
2058 ATGAAACAT
66 ATGAAACAT
2067 TG
1 TG
2069 TATCCCTTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (74 bp):
TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATATGTTGATTCATTTAAAAACTCTTGA
ATGAAACAT
Found at i:2954 original size:24 final size:24
Alignment explanation
Indices: 2927--2976 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2917 TTGTGAGAGC
2927 TTCTAGTGAGCGAGATGATACTAG
1 TTCTAGTGAGCGAGATGATACTAG
2951 TTCTAGTGAGCGAGATGATACTAG
1 TTCTAGTGAGCGAGATGATACTAG
2975 TT
1 TT
2977 ATTTTGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (24 bp):
TTCTAGTGAGCGAGATGATACTAG
Found at i:3623 original size:6 final size:6
Alignment explanation
Indices: 3607--3648 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3597 TAAAAATTTT
* * *
3607 GAAAAA AAAAAA GAAAAA G-AAAA GGAAAA GGAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
3649 GAATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:3635 original size:18 final size:19
Alignment explanation
Indices: 3614--3651 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
3604 TTTGAAAAAA
3614 AAAAAGAAAAAG-AAAAGG
1 AAAAAGAAAAAGAAAAAGG
*
3632 -AAAAGGAAAAGAAAAAGG
1 AAAAAGAAAAAGAAAAAGG
3650 AA
1 AA
3652 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
17 10 0.59
18 6 0.35
19 1 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAGG
Found at i:3676 original size:21 final size:22
Alignment explanation
Indices: 3644--3685 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3634 AAGGAAAAGA
3644 AAAAGGAA-TTTTAAAAAAATT
1 AAAAGGAATTTTTAAAAAAATT
*
3665 AAAA-GAATTTTTTTAAAAAAT
1 AAAAGGAA-TTTTTAAAAAAAT
3686 AGTCCACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 4 0.22
22 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAGGAATTTTTAAAAAAATT
Found at i:4076 original size:17 final size:16
Alignment explanation
Indices: 4049--4095 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
4039 AACCAAAGTG
*
4049 ATTTCATTTAATTTTA
1 ATTTTATTTAATTTTA
*
4065 TTTTTTATTTAATTTTA
1 -ATTTTATTTAATTTTA
4082 ATTTTATTTTAATT
1 ATTTTA-TTTAATT
4096 ATCAGTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTATTTAATTTTA
Found at i:4122 original size:10 final size:10
Alignment explanation
Indices: 4067--4128 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 10
4057 TAATTTTATT
*
4067 TTTTATTTAA
1 TTTTATTTTA
4077 TTTTAATTTTA
1 TTTT-ATTTTA
*
4088 TTTTAATTATCA
1 TTTT-ATT-TTA
*
4100 GTGTTTTTTTTA
1 -T-TTTATTTTA
4112 TTTTATTTTA
1 TTTTATTTTA
4122 TTTTATT
1 TTTTATT
4129 ATGCACTGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 19 0.44
11 14 0.33
12 4 0.09
13 3 0.07
14 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTTATTTTA
Done.