Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009544.1 Kokia drynarioides strain JFW-HI SEQ_124256, 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: 13909
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1236 original size:20 final size:20
Alignment explanation
Indices: 1211--1277 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1201 GATGATGATT
1211 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
*
1231 ATAATTTT---ATATTTTTAAAA
1 ATAATTTTAAAATAATTTT---A
*
1251 ATAATTTTAAATTAATTTTA
1 ATAATTTTAAAATAATTTTA
*
1271 AAAATTT
1 ATAATTT
1278 ATATTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 7 0.19
20 24 0.65
23 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:1290 original size:39 final size:40
Alignment explanation
Indices: 1211--1308 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 40
1201 GATGATGATT
* **
1211 ATAATTTTAAAATAATTTTAATAATTTTATATTTTTAAAA
1 ATAATTTTAAAATAATTTTAATAAATTTATATTTAAAAAA
*
1251 ATAATTTTAAATTAATTTTAA-AAATTTATATTTAAAAAA
1 ATAATTTTAAAATAATTTTAATAAATTTATATTTAAAAAA
*
1290 ATAATTTTAAAATCATTTT
1 ATAATTTTAAAATAATTTT
1309 TTGACATGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 32 0.62
40 20 0.38
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
ATAATTTTAAAATAATTTTAATAAATTTATATTTAAAAAA
Found at i:1298 original size:14 final size:13
Alignment explanation
Indices: 1211--1301 Score: 55
Period size: 11 Copynumber: 6.9 Consensus size: 13
1201 GATGATGATT
1211 ATAATTTT--AAA
1 ATAATTTTAAAAA
*
1222 ATAATTTTAATAATT
1 ATAATTTTAA-AA-A
* *
1237 TTATATTTTTAAAA
1 ATA-ATTTTAAAAA
1251 ATAATTTT--AAA
1 ATAATTTTAAAAA
*
1262 TTAATTTTAAAAA
1 ATAATTTTAAAAA
* *
1275 TTTATATTTAAAAAA
1 -ATA-ATTTTAAAAA
1290 ATAATTTTAAAA
1 ATAATTTTAAAA
1302 TCATTTTTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
11 18 0.29
13 16 0.26
14 9 0.15
15 13 0.21
16 6 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:1298 original size:20 final size:20
Alignment explanation
Indices: 1230--1298 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1220 AAATAATTTT
**
1230 AATAATTTTATATTTTTAAA
1 AATAATTTTATATTTAAAAA
* **
1250 AATAATTTTA-AATTAATTTTA
1 AATAATTTTATATTTAA--AAA
1271 AA-AA-TTTATATTTAAAAA
1 AATAATTTTATATTTAAAAA
1289 AATAATTTTA
1 AATAATTTTA
1299 AAATCATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 3 0.08
19 9 0.25
20 21 0.58
21 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTATATTTAAAAA
Found at i:1308 original size:11 final size:11
Alignment explanation
Indices: 1211--1273 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
1201 GATGATGATT
1211 ATAATTTTAAA
1 ATAATTTTAAA
1222 ATAATTTT--A
1 ATAATTTTAAA
1231 ATAATTTT---
1 ATAATTTTAAA
*
1239 ATATTTTTAAAA
1 ATAATTTT-AAA
1251 ATAATTTTAAA
1 ATAATTTTAAA
*
1262 TTAATTTTAAA
1 ATAATTTTAAA
1273 A
1 A
1274 ATTTATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.16
9 9 0.20
11 21 0.48
12 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:1684 original size:17 final size:18
Alignment explanation
Indices: 1650--1686 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1640 ATGAATATAT
1650 AAAAATTTTCAATAAATA
1 AAAAATTTTCAATAAATA
1668 AAAAATTATT-AAT-AATA
1 AAAAATT-TTCAATAAATA
1685 AA
1 AA
1687 TAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 10 0.56
19 2 0.11
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTTTCAATAAATA
Found at i:2118 original size:13 final size:14
Alignment explanation
Indices: 2095--2124 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2085 TAGGGATTTA
2095 CAATATTACATAAT
1 CAATATTACATAAT
2109 CAAT-TTACATAAT
1 CAATATTACATAAT
2122 CAA
1 CAA
2125 ATCAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
CAATATTACATAAT
Found at i:2560 original size:182 final size:182
Alignment explanation
Indices: 2231--2603 Score: 606
Period size: 182 Copynumber: 2.0 Consensus size: 182
2221 GACCATCCAG
* * * *
2231 ATTTCAATCTAGCATCCTTCTCCAACAACTCTTTGAATCGTGTTAGCTCTCGTGGGTCAAATGAG
1 ATTT-AATCTAACAACCTTCTCCAACAACTCTTTGAATCGTGTTACCTCTCGTGAGTCAAATGAG
2296 CCCCCATCTAACTGATAGACCTTATTGGGACACATTTTATGCAATGGTCATGGGCTTTGAACTAC
65 CCCCCATCTAACTGATAGACCTTATTGGGACACATTTTATGCAATGGTCATGGGCTTTGAACTAC
2361 GCCCATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATT
130 GCCCATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATT
* *
2414 ATTTAATCTAACAACCTTCTTCAACAACTCTTTGAATCAG-GTTACCTCTCGTTAGTCAAATGAG
1 ATTTAATCTAACAACCTTCTCCAACAACTCTTTGAATC-GTGTTACCTCTCGTGAGTCAAATGAG
* * * * *
2478 -CCCCATCTAATTGATAGACCTTCTTGGGACACATTTTGTGCAATTGTCATGGGCTTTGAACTGC
65 CCCCCATCTAACTGATAGACCTTATTGGGACACATTTTATGCAATGGTCATGGGCTTTGAACTAC
2542 TGCCCATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATT
130 -GCCCATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATT
2596 ATTTAATC
1 ATTTAATC
2604 CAAACAAGGT
Statistics
Matches: 177, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
181 59 0.33
182 113 0.64
183 5 0.03
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (182 bp):
ATTTAATCTAACAACCTTCTCCAACAACTCTTTGAATCGTGTTACCTCTCGTGAGTCAAATGAGC
CCCCATCTAACTGATAGACCTTATTGGGACACATTTTATGCAATGGTCATGGGCTTTGAACTACG
CCCATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATT
Found at i:5725 original size:13 final size:13
Alignment explanation
Indices: 5707--5736 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5697 TACCCAAATA
5707 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
5720 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
5733 TTTT
1 TTTT
5737 AAGACACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Done.