Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001662.1 Kokia drynarioides strain JFW-HI SEQ_113316, 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: 9742
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:1132 original size:17 final size:17
Alignment explanation
Indices: 1103--1135 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1093 ATGTATTTTG
1103 AAATTAAAGAATATATT
1 AAATTAAAGAATATATT
1120 AAATGTAAA-AATATAT
1 AAAT-TAAAGAATATAT
1136 ATTTTTTAAT
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:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAATTAAAGAATATATT
Found at i:5070 original size:12 final size:12
Alignment explanation
Indices: 5053--5239 Score: 90
Period size: 12 Copynumber: 16.4 Consensus size: 12
5043 AAACATTATA
5053 TTGTTGTTTTTG
1 TTGTTGTTTTTG
*
5065 TTGTTGTTTCTG
1 TTGTTGTTTTTG
* * *
5077 GTG-TGTGTGTG
1 TTGTTGTTTTTG
*
5088 -TG-TGTTTTTT
1 TTGTTGTTTTTG
5098 TTGTTG-TTTT-
1 TTGTTGTTTTTG
*
5108 TTGGTG-TTTTG
1 TTGTTGTTTTTG
* *
5119 GTATT-TTTTT-
1 TTGTTGTTTTTG
**
5129 TTACTG-TTTTG
1 TTGTTGTTTTTG
* *
5140 GTGTTGCTTTTG
1 TTGTTGTTTTTG
*
5152 TTGTTATTTTTTG
1 TTGTT-GTTTTTG
5165 TTGTTGTTTTTG
1 TTGTTGTTTTTG
* *
5177 TTGCTATTTTTG
1 TTGTTGTTTTTG
5189 TTGTTG-TTTTG
1 TTGTTGTTTTTG
* * *
5200 CTATTATTTTTG
1 TTGTTGTTTTTG
* ** *
5212 CTACTG-TTTAG
1 TTGTTGTTTTTG
5223 TTGTTGTTTTTG
1 TTGTTGTTTTTG
5235 TTGTT
1 TTGTT
5240 TGGATTTTAT
Statistics
Matches: 131, Mismatches: 34, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
10 23 0.18
11 36 0.27
12 62 0.47
13 10 0.08
ACGTcount: A:0.04, C:0.04, G:0.24, T:0.68
Consensus pattern (12 bp):
TTGTTGTTTTTG
Found at i:5126 original size:30 final size:33
Alignment explanation
Indices: 5057--5169 Score: 85
Period size: 33 Copynumber: 3.5 Consensus size: 33
5047 ATTATATTGT
* * *
5057 TGTTTTTGTTGTTGTTTCTGGTGTGTGTGTGTG
1 TGTTTTTTTTGTTGTTTTTGGTGTGTGTGTGTA
*
5090 TGTTTTTTTTGTTGTTTTTTGGTGT-TTTG-GTA
1 TGTTTTTTTTGTTG-TTTTTGGTGTGTGTGTGTA
** *
5122 T-TTTTTTTTACTG-TTTTGGTGT-TGCTTTTGT-
1 TGTTTTTTTTGTTGTTTTTGGTGTGTG--TGTGTA
5153 TGTTATTTTTTGTTGTT
1 TGTT-TTTTTTGTTGTT
5170 GTTTTTGTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
29 10 0.16
31 12 0.19
32 7 0.11
33 24 0.38
34 10 0.16
ACGTcount: A:0.03, C:0.03, G:0.26, T:0.69
Consensus pattern (33 bp):
TGTTTTTTTTGTTGTTTTTGGTGTGTGTGTGTA
Found at i:5163 original size:25 final size:24
Alignment explanation
Indices: 5135--5210 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 24
5125 TTTTTTACTG
*
5135 TTTTGGTGTTGCTTTTGTTGTTATT
1 TTTTGTTGTTG-TTTTGTTGTTATT
*
5160 TTTTGTTGTTGTTTTTGTTGCTA-T
1 TTTTGTTGTTG-TTTTGTTGTTATT
* *
5184 TTTTGTTGTTGTTTTGCTATTATT
1 TTTTGTTGTTGTTTTGTTGTTATT
5208 TTT
1 TTT
5211 GCTACTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.18
24 16 0.36
25 20 0.45
ACGTcount: A:0.05, C:0.04, G:0.20, T:0.71
Consensus pattern (24 bp):
TTTTGTTGTTGTTTTGTTGTTATT
Found at i:5179 original size:34 final size:35
Alignment explanation
Indices: 5141--5239 Score: 87
Period size: 35 Copynumber: 2.9 Consensus size: 35
5131 ACTGTTTTGG
5141 TGTTGCT-TTTGTTGTTATTTTTTGTTGTTGTTTT
1 TGTTGCTATTTGTTGTTATTTTTTGTTGTTGTTTT
* * * *
5175 TGTTGCTATTT-TTGTTGTTGTTTTGCTATTATTTT
1 TGTTGCTATTTGTTGTTATT-TTTTGTTGTTGTTTT
* * * *
5210 TGCTACTGTTTAGTTGTT-GTTTTTGTTGTT
1 TGTTGCTATTT-GTTGTTATTTTTTGTTGTT
5240 TGGATTTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
34 14 0.27
35 31 0.61
36 1 0.02
37 5 0.10
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (35 bp):
TGTTGCTATTTGTTGTTATTTTTTGTTGTTGTTTT
Found at i:7641 original size:22 final size:22
Alignment explanation
Indices: 7585--7641 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
7575 ATAAAAATGT
*
7585 ATAAAATT-ATTAAATATTAAA
1 ATAAAATTAAATAAATATTAAA
*
7606 ATAAAA-CAATATAAATATTTAAA
1 ATAAAATTAA-ATAAATA-TTAAA
7629 A-AAAATTAAATAA
1 ATAAAATTAAATAA
7642 TAATATTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 7 0.24
22 14 0.48
23 8 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAATTAAATAAATATTAAA
Done.