Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2743
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: 21878
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5476 original size:42 final size:43
Alignment explanation
Indices: 5417--5512 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
5407 ACTGGGCAAA
*
5417 TTAGCGGCGTTTTTT-AAAAAGCGCCGCGAAAAGTCCCAGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCAGCGAAAAGTCCCAGTCT
* * * * *
5459 TTAGCGGTGTTTTTTAAAAAAGTGCAGCTAAAAGTCTCGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCAGCGAAAAGTCCCAGTCT
*
5502 TTAGCAGCGTT
1 TTAGCGGCGTT
5513 ACATATAGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 14 0.31
43 31 0.69
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCAGCGAAAAGTCCCAGTCT
Found at i:6997 original size:12 final size:10
Alignment explanation
Indices: 6963--7117 Score: 65
Period size: 10 Copynumber: 15.6 Consensus size: 10
6953 CTTATCAAAC
6963 TATAAAAATA
1 TATAAAAATA
6973 T-TAAAAAATA
1 TAT-AAAAATA
6983 TATAAAAAT-
1 TATAAAAATA
*
6992 TGATATAAATA
1 T-ATAAAAATA
*
7003 T-TATAAATA
1 TATAAAAATA
*
7012 TTATAAAAATC
1 -TATAAAAATA
*
7023 TA-ATAAAT-
1 TATAAAAATA
7031 TATAAAAA-A
1 TATAAAAATA
*
7040 TATATAACATA
1 TATA-AAAATA
* * *
7051 TTTAAAATTT
1 TATAAAAATA
**
7061 TATAAAAACG
1 TATAAAAATA
*
7071 TATGAAAAT-
1 TATAAAAATA
* *
7080 TCTATAAAATT
1 TATA-AAAATA
7091 TATAAAAA-A
1 TATAAAAATA
*
7100 GTATTAAAATTA
1 -TA-TAAAAATA
7112 TATAAA
1 TATAAA
7118 CCTATAAAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
8 2 0.02
9 25 0.23
10 59 0.54
11 22 0.20
12 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (10 bp):
TATAAAAATA
Found at i:7004 original size:30 final size:29
Alignment explanation
Indices: 6968--7046 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
6958 CAAACTATAA
6968 AAATATTAAAAAATATATAAAAAT-TGATAT
1 AAATATTAAAAAATATATAAAAATCT-A-AT
*
6998 AAATATT-ATAAATATTATAAAAATCTAAT
1 AAATATTAAAAAATA-TATAAAAATCTAAT
7027 AAAT-TATAAAAAATATATAA
1 AAATAT-TAAAAAATATATAA
7047 CATATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
28 1 0.02
29 18 0.42
30 23 0.53
31 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
AAATATTAAAAAATATATAAAAATCTAAT
Found at i:7052 original size:48 final size:50
Alignment explanation
Indices: 6963--7068 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 50
6953 CTTATCAAAC
* *
6963 TATAAAAATATTAAAAAATATATAAAAATTGATATAAATA-TTATAAATAT
1 TATAAAAATACTAAAAAATATATAAAAAATGATATAAATATTTA-AAATAT
* *
7013 TATAAAAAT-CTAATAAAT-TATAAAAAAT-ATATAACATATTTAAAATTT
1 TATAAAAATACTAAAAAATATATAAAAAATGATATAA-ATATTTAAAATAT
7061 TATAAAAA
1 TATAAAAA
7069 CGTATGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 6 0.12
48 25 0.50
49 10 0.20
50 9 0.18
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (50 bp):
TATAAAAATACTAAAAAATATATAAAAAATGATATAAATATTTAAAATAT
Found at i:7093 original size:30 final size:31
Alignment explanation
Indices: 7053--7117 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
7043 ATAACATATT
* *
7053 TAAAATTTTATAAAAACGTATGAAAATTCTA
1 TAAAATTTTATAAAAAAGTATGAAAATTATA
*
7084 TAAAA-TTTATAAAAAAGTATTAAAATTATA
1 TAAAATTTTATAAAAAAGTATGAAAATTATA
7114 TAAA
1 TAAA
7118 CCTATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (31 bp):
TAAAATTTTATAAAAAAGTATGAAAATTATA
Found at i:7112 original size:19 final size:19
Alignment explanation
Indices: 7084--7136 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
7074 GAAAATTCTA
*
7084 TAAAATTTATAAAAAAGTAT
1 TAAAA-TTATAAAAAACTAT
* *
7104 TAAAATTATATAAACCTAT
1 TAAAATTATAAAAAACTAT
*
7123 AAAAATTA-AAAAAA
1 TAAAATTATAAAAAA
7137 TCATAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAATTATAAAAAACTAT
Found at i:7713 original size:19 final size:20
Alignment explanation
Indices: 7691--7738 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
7681 ATAAGTGTTT
7691 ATAATTTTTTAT-AATTCTA
1 ATAATTTTTTATAAATTCTA
* * *
7710 ATAAGTTTATATAAATTTTA
1 ATAATTTTTTATAAATTCTA
7730 AT-ATTTTTT
1 ATAATTTTTT
7739 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATAATTTTTTATAAATTCTA
Found at i:12877 original size:20 final size:20
Alignment explanation
Indices: 12854--12898 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12844 ATTTTTATGC
12854 ATTTTATATAAATCTTATAA
1 ATTTTATATAAATCTTATAA
* * * *
12874 ATTTTTTGTAAATTTTATTA
1 ATTTTATATAAATCTTATAA
12894 ATTTT
1 ATTTT
12899 CAATTTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTATATAAATCTTATAA
Found at i:13548 original size:30 final size:30
Alignment explanation
Indices: 13514--13571 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13504 ATTAGAAAAG
* *
13514 TAAAATTATACTTTGACCCTTTAAAAATGA
1 TAAAATTATAATTTAACCCTTTAAAAATGA
* *
13544 TAAAATTTTAATTTAATCCTTTAAAAAT
1 TAAAATTATAATTTAACCCTTTAAAAAT
13572 TTAAAGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (30 bp):
TAAAATTATAATTTAACCCTTTAAAAATGA
Found at i:14847 original size:24 final size:26
Alignment explanation
Indices: 14820--14879 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
14810 TAAAATCTTA
14820 TAATATTTTTAAT-TTCAT-T-ATTTT
1 TAATATTTTTAATCTT-ATATAATTTT
*
14844 TAATACTTTTAATCTTATATAATTTT
1 TAATATTTTTAATCTTATATAATTTT
*
14870 AAATATTTTT
1 TAATATTTTT
14880 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.47
25 3 0.10
26 13 0.43
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TAATATTTTTAATCTTATATAATTTT
Found at i:14902 original size:20 final size:21
Alignment explanation
Indices: 14879--14935 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
14869 TAAATATTTT
*
14879 TTTATTTTTTTTTTTCATA-A
1 TTTATTTTTTTATTTCATATA
* *
14899 TTTATATTTTTATTTCATATT
1 TTTATTTTTTTATTTCATATA
14920 TTTATTTTTTGTATTT
1 TTTATTTTTT-TATTT
14936 TTTCTAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.55
21 9 0.29
22 5 0.16
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTATTTTTTTATTTCATATA
Done.