Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2208
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: 16294
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:269 original size:2 final size:2
Alignment explanation
Indices: 262--291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
252 AGTATTTTAT
262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
292 CACTAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1817 original size:30 final size:31
Alignment explanation
Indices: 1783--1849 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
1773 AATATATATA
*
1783 AAGAAAAAATTAA-AATTTTCAGTAAAATTC
1 AAGAAAAAAATAACAATTTTCAGTAAAATTC
*
1813 AAGAAAAAAATAACATTTTTCAGTAAAATTC
1 AAGAAAAAAATAACAATTTTCAGTAAAATTC
1844 AAGAAA
1 AAGAAA
1850 GCATTATCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.27
Consensus pattern (31 bp):
AAGAAAAAAATAACAATTTTCAGTAAAATTC
Found at i:4182 original size:2 final size:2
Alignment explanation
Indices: 4175--4216 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4165 TTACAGTTAC
4175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4217 TTCCATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5324 original size:20 final size:20
Alignment explanation
Indices: 5288--5325 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5278 AAAATCTCTT
*
5288 AATTTTATGTTTATTTTAAA
1 AATTTTATGTTAATTTTAAA
5308 AATTTTAT-TTAAGTTTTA
1 AATTTTATGTTAA-TTTTA
5326 TCTTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTTATGTTAATTTTAAA
Found at i:6546 original size:11 final size:11
Alignment explanation
Indices: 6530--6554 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6520 AATGTAACGT
6530 ATTAACTATTA
1 ATTAACTATTA
6541 ATTAACTATTA
1 ATTAACTATTA
6552 ATT
1 ATT
6555 CAGTTTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAACTATTA
Found at i:9831 original size:3 final size:3
Alignment explanation
Indices: 9823--9859 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9813 CCGTCAATGG
9823 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
9860 ATCATCATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:9864 original size:3 final size:3
Alignment explanation
Indices: 9858--9908 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
9848 TTCTTCTTCT
9858 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
9906 TCA
1 TCA
9909 ATGGCTTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:11881 original size:17 final size:18
Alignment explanation
Indices: 11854--11891 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11844 TTTTCTAAGC
*
11854 TAAAGAAAATTAAAATAA
1 TAAAGAAAATTAAAAAAA
11872 TAAA-AAAATTAAAAAAA
1 TAAAGAAAATTAAAAAAA
11889 TAA
1 TAA
11892 TGTGACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAGAAAATTAAAAAAA
Found at i:15119 original size:14 final size:15
Alignment explanation
Indices: 15088--15121 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
15078 TTTATCTTTC
15088 ATTTTTTTAAAATCAA
1 ATTTTTTTAAAA-CAA
15104 ATTTTTTTAAAA-AA
1 ATTTTTTTAAAACAA
15118 ATTT
1 ATTT
15122 AAATTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
16 12 0.67
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTTTAAAACAA
Found at i:15837 original size:14 final size:14
Alignment explanation
Indices: 15799--15860 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
15789 TTGGATTTTG
* *
15799 ATATATATATATAT
1 ATATATATATTTAA
15813 ATATATATATTTAA
1 ATATATATATTTAA
*
15827 ATATACATA-TTAA
1 ATATATATATTTAA
15840 ATATA-ATTATTTAA
1 ATATATA-TATTTAA
15854 ATATATA
1 ATATATA
15861 AAAAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.02
13 11 0.26
14 29 0.69
15 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATATATTTAA
Done.