Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3100
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: 15662
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Found at i:524 original size:16 final size:16
Alignment explanation
Indices: 505--538 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
495 ATTCGGCCAC
505 TGGTCTATTCTTTACA
1 TGGTCTATTCTTTACA
521 TGGTCTATTCTTTACA
1 TGGTCTATTCTTTACA
537 TG
1 TG
539 CCATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (16 bp):
TGGTCTATTCTTTACA
Found at i:1152 original size:37 final size:37
Alignment explanation
Indices: 1099--1201 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
1089 CGAATAGTCC
*
1099 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
1136 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
1173 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
1202 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:1400 original size:48 final size:48
Alignment explanation
Indices: 1342--1835 Score: 837
Period size: 48 Copynumber: 10.3 Consensus size: 48
1332 ATATACACAC
*
1342 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
1390 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACGTATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
1438 ATCTCATTCATATTTCACACTAGCCATTCGGTTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
1486 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* **
1534 ATCTCATATATATTTCACGTTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
**
1582 ATCTCATACATATTTCACGTTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
1630 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
1678 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
1726 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCATATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
1774 ATCTCATACATA-TTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1821 ATCTCATACATATTT
1 ATCTCATACATATTT
1836 ATCTTGTACA
Statistics
Matches: 425, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
47 45 0.11
48 380 0.89
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:2248 original size:21 final size:21
Alignment explanation
Indices: 2222--2263 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2212 AAATTTTATC
*
2222 TTATAACCATTTTTGTAAAAA
1 TTATAACCATTTTTCTAAAAA
**
2243 TTATAATGATTTTTCTAAAAA
1 TTATAACCATTTTTCTAAAAA
2264 CAAAACAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (21 bp):
TTATAACCATTTTTCTAAAAA
Found at i:5398 original size:40 final size:40
Alignment explanation
Indices: 5331--5458 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
5321 CCTTCGGAGT
* *
5331 TTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* *
5370 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCAGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
5410 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
5450 TTAGCCCGG
1 TTAGCCCGG
5459 GTATCAATCC
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 5 0.06
40 76 0.94
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:13588 original size:39 final size:39
Alignment explanation
Indices: 13559--13703 Score: 274
Period size: 39 Copynumber: 3.7 Consensus size: 39
13549 GCTACTAGCT
13559 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
13598 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
13637 CAAATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
13676 CAAATGCCTTCGGGACTTAGCCCGGTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTAT
13704 CAATCCGAAT
Statistics
Matches: 104, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
38 13 0.12
39 78 0.75
40 13 0.12
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:14370 original size:21 final size:21
Alignment explanation
Indices: 14344--14386 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
14334 ATACCACATA
*
14344 TAATGCA-TACATTTTACTAAC
1 TAATGCATTACATATTA-TAAC
14365 TAATGCATTACATATTATAAC
1 TAATGCATTACATATTATAAC
14386 T
1 T
14387 CAATACGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (21 bp):
TAATGCATTACATATTATAAC
Done.