Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1751
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: 35191
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:5235 original size:16 final size:17
Alignment explanation
Indices: 5204--5243 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5194 TAAATTTAAT
5204 TTTTAATTCATAAAATA
1 TTTTAATTCATAAAATA
*
5221 TTTTAATT-TTAAAATA
1 TTTTAATTCATAAAATA
5237 TATTTAA
1 T-TTTAA
5244 ATACATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAATTCATAAAATA
Found at i:5985 original size:24 final size:24
Alignment explanation
Indices: 5922--5987 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
5912 TGTAAAAAAA
* *
5922 AAAAAAATTATTTAA-ATTAAATT
1 AAAATAATTTTTTAATATTAAATT
* * *
5945 ATAAAT-ATTTATAAATATTAATTT
1 A-AAATAATTTTTTAATATTAAATT
5969 AAAATAATTTTTTAATATT
1 AAAATAATTTTTTAATATT
5988 TTTTTGGTAG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
23 11 0.33
24 22 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATAATTTTTTAATATTAAATT
Found at i:7929 original size:25 final size:25
Alignment explanation
Indices: 7883--7931 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
7873 ATATCTGAAA
* *
7883 ATTTATTCAAAAATATATAAGTTTG
1 ATTTAATCAAAAAGATATAAGTTTG
7908 ATTTAATCAAAAAAGATA-AAGTTT
1 ATTTAATC-AAAAAGATATAAGTTT
7932 TTTGGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTAATCAAAAAGATATAAGTTTG
Found at i:9189 original size:26 final size:27
Alignment explanation
Indices: 9133--9198 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
9123 GTTACCATTT
* * * * *
9133 TTGTTTGTAAAAAATGGTGATTTTTTT
1 TTGTTTGTCAAAAATAGTGAGTTCTTG
9160 TTGTTTGTCAAAAATAGTG-GTTCTTG
1 TTGTTTGTCAAAAATAGTGAGTTCTTG
*
9186 TTGTTTATCAAAA
1 TTGTTTGTCAAAA
9199 TTGGTGGCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (27 bp):
TTGTTTGTCAAAAATAGTGAGTTCTTG
Found at i:13569 original size:26 final size:26
Alignment explanation
Indices: 13540--13602 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
13530 AAAGCCACCA
* * * *
13540 TTTTTGTTTGTTAAAAATGGTGGTTT
1 TTTTTGTTTGTAAAAAATGATGATTC
13566 TTTTTGTTTGTAAAAAATGATGATTC
1 TTTTTGTTTGTAAAAAATGATGATTC
*
13592 TTGTTGTTTGT
1 TTTTTGTTTGT
13603 CAATATTGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.57
Consensus pattern (26 bp):
TTTTTGTTTGTAAAAAATGATGATTC
Found at i:14183 original size:13 final size:14
Alignment explanation
Indices: 14167--14196 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14157 ATTTATATTT
14167 TTTCTTTTT-CCAA
1 TTTCTTTTTACCAA
14180 TTTCTTTTTACCAA
1 TTTCTTTTTACCAA
14194 TTT
1 TTT
14197 ATTAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTCTTTTTACCAA
Found at i:16099 original size:23 final size:20
Alignment explanation
Indices: 16062--16103 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
16052 AAAGATGTAT
16062 TTGGATGAAATTATATATTTG
1 TTGGATGAAATTATA-ATTTG
16083 TTGGATGAAAAATTATAATTT
1 TTGGATG--AAATTATAATTT
16104 TTACAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (20 bp):
TTGGATGAAATTATAATTTG
Found at i:17023 original size:36 final size:35
Alignment explanation
Indices: 16955--17030 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
16945 ATGCAAACAT
* *
16955 AGATTATATATTATATTTATATGCAATAGATTAAAA
1 AGATTATATATGATATCTATATGCAATAGATT-AAA
* * * *
16991 AGATTTTATATGATATCTATGTGTAATTGATTAAA
1 AGATTATATATGATATCTATATGCAATAGATTAAA
17026 AGATT
1 AGATT
17031 GAACAAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 8 0.24
36 26 0.76
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (35 bp):
AGATTATATATGATATCTATATGCAATAGATTAAA
Found at i:21332 original size:22 final size:24
Alignment explanation
Indices: 21307--21351 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
21297 TTTTTCAAGT
*
21307 AAAA-AAATTAAATATTA-ATATA
1 AAAAGAAATTAAAAATTATATATA
*
21329 AAAAGAATTTAAAAATTATATAT
1 AAAAGAAATTAAAAATTATATAT
21352 CTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAGAAATTAAAAATTATATATA
Done.