Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1913
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: 33798
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7118 original size:82 final size:81
Alignment explanation
Indices: 7002--7157 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
6992 AAATTGTACA
* * * *
7002 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
7066 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
7083 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
7148 TGCGAGTTGA
65 TGCGAATTGA
7158 TGTATAGCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:7125 original size:55 final size:52
Alignment explanation
Indices: 7001--7177 Score: 178
Period size: 55 Copynumber: 3.3 Consensus size: 52
6991 TAAATTGTAC
* *
7001 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
7054 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * * *
7109 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGTTGATGTAT-
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAG-TGA-ATATG
*
7163 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
7178 GGCTCAATAT
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
53 17 0.16
54 36 0.35
55 49 0.47
56 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:7158 original size:27 final size:27
Alignment explanation
Indices: 7002--7157 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
6992 AAATTGTACA
*
7002 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
7029 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
7056 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
7083 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
7111 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
7138 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
7158 TGTATAGCAC
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:7174 original size:26 final size:26
Alignment explanation
Indices: 7083--7177 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
7073 TGACCATGCG
* * *
7083 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAGT-TGATTA-CTA
* *
7111 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTAC-TA
7138 GCACTAAGTGTGCGAGTTGATGTA-TA
1 GCACTAAGTGTGCGAGTTGAT-TACTA
*
7164 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
7178 GGCTCAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
26 14 0.25
27 25 0.44
28 18 0.32
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGAGTTGATTACTA
Found at i:11299 original size:4 final size:4
Alignment explanation
Indices: 11290--11317 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
11280 AAGTTTTATT
11290 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
11318 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:21880 original size:14 final size:14
Alignment explanation
Indices: 21863--21910 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
21853 TCAATTTCAA
21863 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
* **
21877 TTTTTTTAATTCTGA
1 TTTTTTT-CTTCTTC
21892 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
21906 TTTTT
1 TTTTT
21911 CTTCAATACT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:21971 original size:10 final size:10
Alignment explanation
Indices: 21956--22001 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
21946 AATACAAACT
21956 TTTTTTTGAA
1 TTTTTTTGAA
21966 TTTTTTTTGAA
1 -TTTTTTTGAA
21977 TTTTTTTGAA
1 TTTTTTTGAA
21987 TTTTTTT--A
1 TTTTTTTGAA
21995 TTTTTTT
1 TTTTTTT
22002 TACAATACCG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.23
10 17 0.49
11 10 0.29
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:21971 original size:11 final size:11
Alignment explanation
Indices: 21955--21993 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
21945 GAATACAAAC
21955 TTTTTTTTGAA
1 TTTTTTTTGAA
21966 TTTTTTTTGAA
1 TTTTTTTTGAA
21977 -TTTTTTTGAA
1 TTTTTTTTGAA
21987 TTTTTTT
1 TTTTTTT
21994 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:22001 original size:21 final size:21
Alignment explanation
Indices: 21955--22002 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
21945 GAATACAAAC
21955 TTTTTTTTGAATTTTTTTTGA
1 TTTTTTTTGAATTTTTTTTGA
*
21976 ATTTTTTTGAA-TTTTTTT-A
1 TTTTTTTTGAATTTTTTTTGA
21995 TTTTTTTT
1 TTTTTTTT
22003 ACAATACCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 7 0.28
21 10 0.40
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTTTTTGAATTTTTTTTGA
Found at i:25587 original size:22 final size:22
Alignment explanation
Indices: 25557--25600 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25547 TTTGGTATTT
25557 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
25579 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
25601 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Done.