Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014684.1 Kokia drynarioides strain JFW-HI SEQ_129723, 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: 10703
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2321 original size:25 final size:25
Alignment explanation
Indices: 2274--2321 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2264 AAATATTAAT
**
2274 TAATTAAAAATTAAGTTTTTTAACA
1 TAATTAAAAATTAAGTTAATTAACA
2299 TAATT-AAAATTAAGTTAAATTAA
1 TAATTAAAAATTAAGTT-AATTAA
2322 TTATTAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TAATTAAAAATTAAGTTAATTAACA
Found at i:2650 original size:27 final size:28
Alignment explanation
Indices: 2610--2666 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
2600 TTGCTATGTG
*
2610 TTTAACTTTAATATA-AGACTTTTTAAT
1 TTTAAATTTAATATATAGACTTTTTAAT
* * *
2637 TTTAAATTTGATATATATATTTTTTAAT
1 TTTAAATTTAATATATAGACTTTTTAAT
2665 TT
1 TT
2667 CAAAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTAAATTTAATATATAGACTTTTTAAT
Found at i:3603 original size:7 final size:7
Alignment explanation
Indices: 3591--3726 Score: 59
Period size: 7 Copynumber: 19.9 Consensus size: 7
3581 TGAATTTGAC
3591 GGGTTTA
1 GGGTTTA
3598 GGGTTTA
1 GGGTTTA
*
3605 GGTTTTA
1 GGGTTTA
*
3612 -TGTTTA
1 GGGTTTA
*
3618 GAGTTTA
1 GGGTTTA
3625 GGGTTTA
1 GGGTTTA
*
3632 -TGTTTA
1 GGGTTTA
3638 GGGTTTTA
1 GGG-TTTA
*
3646 -TGTTTA
1 GGGTTTA
*
3652 -TGTTTA
1 GGGTTTA
*
3658 GGATTTA
1 GGGTTTA
**
3665 ATGTTTA
1 GGGTTTA
*
3672 GAGTTTA
1 GGGTTTA
*
3679 AGGTTTA
1 GGGTTTA
*
3686 GGATTTTA
1 GG-GTTTA
* *
3694 -TGTTTT
1 GGGTTTA
3700 GGGTTTAA
1 GGGTTT-A
*
3708 GGTTTTA
1 GGGTTTA
*
3715 -TGTTTA
1 GGGTTTA
3721 GGGTTT
1 GGGTTT
3727 TATATTTGGG
Statistics
Matches: 93, Mismatches: 28, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
6 26 0.28
7 54 0.58
8 13 0.14
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (7 bp):
GGGTTTA
Found at i:3618 original size:20 final size:20
Alignment explanation
Indices: 3593--3726 Score: 137
Period size: 20 Copynumber: 6.5 Consensus size: 20
3583 AATTTGACGG
3593 GTTTAGGGTTTAGGTTTTAT
1 GTTTAGGGTTTAGGTTTTAT
* *
3613 GTTTAGAGTTTAGGGTTTAT
1 GTTTAGGGTTTAGGTTTTAT
*
3633 GTTTAGGGTTTTATG-TTTAT
1 GTTTAGGG-TTTAGGTTTTAT
* * *
3653 GTTTAGGATTTA-ATGTTTAGA
1 GTTTAGGGTTTAGGT-TTTA-T
*
3674 GTTTAAGGTTTAGGATTTTAT
1 GTTTAGGGTTTAGG-TTTTAT
*
3695 GTTTTGGGTTTAAGGTTTTAT
1 GTTTAGGGTTT-AGGTTTTAT
3716 GTTTAGGGTTT
1 GTTTAGGGTTT
3727 TATATTTGGG
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.04
20 41 0.44
21 40 0.43
22 7 0.08
23 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.54
Consensus pattern (20 bp):
GTTTAGGGTTTAGGTTTTAT
Found at i:3630 original size:14 final size:13
Alignment explanation
Indices: 3592--3726 Score: 76
Period size: 14 Copynumber: 9.9 Consensus size: 13
3582 GAATTTGACG
3592 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
*
3605 GGTTTTA-TGTTTA
1 GG-TTTAGGGTTTA
3618 GAGTTTAGGGTTTA
1 G-GTTTAGGGTTTA
*
3632 TGTTTAGGGTTTTA
1 GGTTTAGGG-TTTA
* *
3646 TGTTTA-TGTTTA
1 GGTTTAGGGTTTA
**
3658 GGATTTAATGTTTA
1 GG-TTTAGGGTTTA
*
3672 GAGTTTAAGGTTTA
1 G-GTTTAGGGTTTA
* * *
3686 GGATTTTATGTTTTG
1 GG--TTTAGGGTTTA
*
3701 GGTTTAAGGTTTTA
1 GGTTT-AGGGTTTA
*
3715 TGTTTAGGGTTT
1 GGTTTAGGGTTT
3727 TATATTTGGG
Statistics
Matches: 99, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
12 5 0.05
13 35 0.35
14 48 0.48
15 11 0.11
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:3727 original size:14 final size:14
Alignment explanation
Indices: 3702--3739 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3692 TATGTTTTGG
*
3702 GTTTAAGGTTTTAT
1 GTTTAGGGTTTTAT
3716 GTTTAGGGTTTTAT
1 GTTTAGGGTTTTAT
*
3730 ATTT-GGGTTT
1 GTTTAGGGTTT
3740 CATTTTTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTTAGGGTTTTAT
Found at i:6421 original size:20 final size:20
Alignment explanation
Indices: 6383--6421 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6373 ACTCAATTTA
*
6383 AAAAAATTTCGAATTGAGTC
1 AAAAAATTTCGAATCGAGTC
* *
6403 AAAAAATTTTGAGTCGAGT
1 AAAAAATTTCGAATCGAGT
6422 TAACGGATCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (20 bp):
AAAAAATTTCGAATCGAGTC
Done.