Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1024
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: 67947
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:24014 original size:29 final size:29
Alignment explanation
Indices: 23980--24053 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
23970 TAATCAACCG
*
23980 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
24009 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
24038 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
24054 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:38538 original size:19 final size:19
Alignment explanation
Indices: 38514--38555 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
38504 AATACAAGTA
38514 ATATTGATGTATTACTTAC
1 ATATTGATGTATTACTTAC
38533 ATATTGATGTATTACTTAC
1 ATATTGATGTATTACTTAC
38552 ATAT
1 ATAT
38556 AAACTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
ATATTGATGTATTACTTAC
Found at i:44920 original size:40 final size:40
Alignment explanation
Indices: 44827--45084 Score: 337
Period size: 40 Copynumber: 6.5 Consensus size: 40
44817 TGGATGATAA
* *
44827 CCGGGCTAAGTCTCGAAGGCATTT-TGCGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTATA-T
* *
44868 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
44908 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
44948 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
44988 CCGGGCTAAGTCCCGAAGGCATTGGCGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
45028 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
45067 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
45085 TACTTGGCTT
Statistics
Matches: 198, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
38 15 0.08
39 15 0.08
40 141 0.71
41 24 0.12
42 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:53046 original size:40 final size:40
Alignment explanation
Indices: 52946--53243 Score: 372
Period size: 40 Copynumber: 7.5 Consensus size: 40
52936 TGGATGATAA
*
52946 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
52987 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
53027 CCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
53067 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53107 CCGGGCTAAGTCCCGAAGGCATTGGCGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
** * * *
53147 CCGGGCTTTGTCTCGAAGGCATTGGCGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
53187 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
53226 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
53244 TACTTGGCTT
Statistics
Matches: 235, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
38 15 0.06
39 15 0.06
40 177 0.75
41 24 0.10
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:56882 original size:6 final size:6
Alignment explanation
Indices: 56871--56922 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
56861 GGGATCACTA
56871 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTCTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT
56916 ACTAAT A
1 ACTAAT A
56923 GAATAGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 3 0.08
5 13 0.32
6 18 0.45
8 6 0.15
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (6 bp):
ACTAAT
Found at i:56893 original size:20 final size:21
Alignment explanation
Indices: 56867--56921 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
56857 AGCCGGGATC
56867 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
56888 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
56908 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
56922 AGAATAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.33
20 20 0.61
21 2 0.06
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:56901 original size:15 final size:14
Alignment explanation
Indices: 56877--56920 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
56867 ACTAACTAAT
56877 ACTAATCTAATCTA
1 ACTAATCTAATCTA
56891 ACTAATACTAATCTA
1 ACTAAT-CTAATCTA
*
56906 A-TACTCTAATACTA
1 ACTAATCTAAT-CTA
56920 A
1 A
56921 TAGAATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 5 0.19
14 13 0.48
15 9 0.33
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (14 bp):
ACTAATCTAATCTA
Found at i:56936 original size:14 final size:14
Alignment explanation
Indices: 56919--56946 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56909 CTCTAATACT
56919 AATAGAATAGAAAA
1 AATAGAATAGAAAA
56933 AATAGAATAGAAAA
1 AATAGAATAGAAAA
56947 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:65222 original size:18 final size:18
Alignment explanation
Indices: 65187--65224 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
65177 GGTCACGATG
*
65187 AATAGCGTCACTACCATC
1 AATAGCGTCACAACCATC
*
65205 AATAGCGTCACAAGCATC
1 AATAGCGTCACAACCATC
65223 AA
1 AA
65225 ATATCATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.18
Consensus pattern (18 bp):
AATAGCGTCACAACCATC
Found at i:66138 original size:22 final size:21
Alignment explanation
Indices: 66109--66150 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
66099 TGTAGTAACA
*
66109 TAATTGTTGTTTTAAGGAATT
1 TAATTGTTGTGTTAAGGAATT
*
66130 TAATATGTTGTGTTAATGAAT
1 TAAT-TGTTGTGTTAAGGAAT
66151 AGGATGCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (21 bp):
TAATTGTTGTGTTAAGGAATT
Done.