Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3412
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: 28506
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1926 original size:79 final size:82
Alignment explanation
Indices: 1815--1999 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
1805 GCTACTCGTT
* *
1815 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
1878 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
1895 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
1958 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
1975 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2000 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:1999 original size:40 final size:40
Alignment explanation
Indices: 1796--1999 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
1786 CGGAATTTAA
** *
1796 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1836 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1876 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1915 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1955 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1995 CCGGA
1 CCGGA
2000 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:14858 original size:13 final size:12
Alignment explanation
Indices: 14838--14896 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
14828 ATAGAAACTA
*
14838 AATTTTTTTTCG
1 AATTTTTTTTTG
14850 AATTTTTTTTTG
1 AATTTTTTTTTG
*
14862 AATTTTTTTTTTCA
1 AA-TTTTTTTTT-G
14876 AATTTTTTTTTG
1 AATTTTTTTTTG
14888 AATTTTTTT
1 AATTTTTTT
14897 CAAAGAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 22 0.52
13 18 0.43
14 2 0.05
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:14879 original size:26 final size:26
Alignment explanation
Indices: 14840--14896 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
14830 AGAAACTAAA
*
14840 TTTTTTTTCGAATTTTTTTTTGAATT
1 TTTTTTTTCAAATTTTTTTTTGAATT
14866 TTTTTTTTCAAATTTTTTTTTGAATT
1 TTTTTTTTCAAATTTTTTTTTGAATT
14892 TTTTT
1 TTTTT
14897 CAAAGAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (26 bp):
TTTTTTTTCAAATTTTTTTTTGAATT
Found at i:20085 original size:12 final size:12
Alignment explanation
Indices: 20068--20124 Score: 87
Period size: 12 Copynumber: 4.8 Consensus size: 12
20058 ATAGAAACTA
20068 AATTTTTTTTCG
1 AATTTTTTTTCG
*
20080 AATTTTTTTTTG
1 AATTTTTTTTCG
*
20092 AATTTTTTTTCA
1 AATTTTTTTTCG
*
20104 AATTTTTTTTTG
1 AATTTTTTTTCG
20116 AATTTTTTT
1 AATTTTTTT
20125 CAAAGAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTCG
Found at i:20126 original size:23 final size:24
Alignment explanation
Indices: 20068--20128 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
20058 ATAGAAACTA
*
20068 AATTTTTTTTCGAATTTTTTTTTG
1 AATTTTTTTTCAAATTTTTTTTTG
20092 AATTTTTTTTCAAATTTTTTTTTG
1 AATTTTTTTTCAAATTTTTTTTTG
20116 AA-TTTTTTTCAAA
1 AATTTTTTTTCAAA
20129 GAAACTACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (24 bp):
AATTTTTTTTCAAATTTTTTTTTG
Found at i:24726 original size:11 final size:11
Alignment explanation
Indices: 24710--24743 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
24700 ATAGTAGTTT
24710 TTCAAAAAAAA
1 TTCAAAAAAAA
24721 TTCAAAAAAAAA
1 TTC-AAAAAAAA
24733 TTCAAAAAAAA
1 TTCAAAAAAAA
24744 AATTTTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:24747 original size:13 final size:12
Alignment explanation
Indices: 24713--24744 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
24703 GTAGTTTTTC
24713 AAAAAAAATTCA
1 AAAAAAAATTCA
24725 AAAAAAAATTCA
1 AAAAAAAATTCA
24737 AAAAAAAA
1 AAAAAAAA
24745 ATTTTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:24803 original size:14 final size:15
Alignment explanation
Indices: 24781--24819 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
24771 GATATCAAGT
24781 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
24796 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
24811 TGAAAAAAA
1 TGAAAAAAA
24820 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Done.