Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003255.1 Kokia drynarioides strain JFW-HI SEQ_115907, 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: 8197
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:1260 original size:21 final size:22
Alignment explanation
Indices: 1212--1276 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
1202 AATTGAAAAA
1212 AAAAT-TTATT-AAAAATTTGT
1 AAAATATTATTAAAAAATTTGT
* *
1232 ACATTATTATTAAAAAATTT-T
1 AAAATATTATTAAAAAATTTGT
*
1253 AAAATATT-TCTTAAAAA-TTGT
1 AAAATATTAT-TAAAAAATTTGT
1274 AAA
1 AAA
1277 TAGATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
20 6 0.17
21 22 0.61
22 8 0.22
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (22 bp):
AAAATATTATTAAAAAATTTGT
Found at i:1296 original size:10 final size:10
Alignment explanation
Indices: 1237--1402 Score: 56
Period size: 10 Copynumber: 16.4 Consensus size: 10
1227 TTTGTACATT
1237 ATTATTAAAAA
1 ATTATT-AAAA
1248 ATT-TTAAAA
1 ATTATTAAAA
*
1257 TATTTCTTAAAA
1 -A-TTATTAAAA
* *
1269 ATT-GTAAAT
1 ATTATTAAAA
*
1278 A-GATT-AAA
1 ATTATTAAAA
1286 ATTATTAAAA
1 ATTATTAAAA
*
1296 A-AATTTAAAA
1 ATTA-TTAAAA
*
1306 ATTATTTAAA
1 ATTATTAAAA
* *
1316 GTTATAAAAA
1 ATTATTAAAA
* *
1326 ATAAATAAATTTAA
1 AT-TATTAA---AA
* *
1340 ATAATAAAAA
1 ATTATTAAAA
*
1350 ATTAATAAAA
1 ATTATTAAAA
*
1360 ATTA-CAAAA
1 ATTATTAAAA
*
1369 ATAATTAAAA
1 ATTATTAAAA
* **
1379 ATTATGACTA
1 ATTATTAAAA
1389 ATTATTAAAA
1 ATTATTAAAA
1399 ATTA
1 ATTA
1403 CAAAAATTCA
Statistics
Matches: 115, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
8 3 0.03
9 21 0.18
10 63 0.55
11 12 0.10
12 6 0.05
13 6 0.05
14 4 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:1346 original size:24 final size:25
Alignment explanation
Indices: 1309--1358 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1299 TTTAAAAATT
*
1309 ATTTAAAGTTATAAAAAATAAATAA
1 ATTTAAAGTAATAAAAAATAAATAA
*
1334 ATTTAAA-TAATAAAAAATTAATAA
1 ATTTAAAGTAATAAAAAATAAATAA
1358 A
1 A
1359 AATTACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
ATTTAAAGTAATAAAAAATAAATAA
Found at i:1357 original size:14 final size:17
Alignment explanation
Indices: 1320--1352 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1310 TTTAAAGTTA
*
1320 TAAAAAATAAATAAATT
1 TAAATAATAAATAAATT
1337 TAAATAATAAA-AAATT
1 TAAATAATAAATAAATT
1353 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATAATAAATAAATT
Found at i:1665 original size:17 final size:17
Alignment explanation
Indices: 1645--1679 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1635 AAATAAATAT
*
1645 TAAAAAATTTAAAATTA
1 TAAAAAATTAAAAATTA
*
1662 TAAAAACTTAAAAATTA
1 TAAAAAATTAAAAATTA
1679 T
1 T
1680 TTTTTAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAAATTAAAAATTA
Found at i:4873 original size:18 final size:18
Alignment explanation
Indices: 4852--4887 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4842 GCAATTTTTT
*
4852 ATTATTTTATTAATTATA
1 ATTATTTAATTAATTATA
*
4870 ATTATTTAATTATTTATA
1 ATTATTTAATTAATTATA
4888 TTTTAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTTAATTAATTATA
Found at i:8134 original size:27 final size:27
Alignment explanation
Indices: 8104--8175 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
8094 ACCTGTGAGC
8104 AAAGAGAGAGGAGAGAGAAAG-GAGGAA-
1 AAAGAGAGAGGAGAGAGAAAGTGA--AAG
* * *
8131 AAAGA-ACTATGACAGAGAAAGTGAAAG
1 AAAGAGA-GAGGAGAGAGAAAGTGAAAG
8158 AAAGAGAGAGGAGAGAGA
1 AAAGAGAGAGGAGAGAGA
8176 GAAAAGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.38, T:0.04
Consensus pattern (27 bp):
AAAGAGAGAGGAGAGAGAAAGTGAAAG
Done.