Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1566
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: 25383
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Found at i:1984 original size:26 final size:28
Alignment explanation
Indices: 1896--2044 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
1886 GAGATTGGCG
* * * *
1896 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
1925 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
1953 CTAAGTGTGCGAGTTTGA-T-TATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
1979 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
2007 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
2034 CTGAGTGTGCG
1 CTAAGTGTGCG
2045 GACTTAATAT
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
26 24 0.22
27 26 0.23
28 46 0.41
29 15 0.14
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:1985 original size:54 final size:55
Alignment explanation
Indices: 1921--2044 Score: 207
Period size: 54 Copynumber: 2.3 Consensus size: 55
1911 TAAATTGTAC
*
1921 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGA-T-TAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATAT
1975 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
*
2030 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2045 GACTTAATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
53 4 0.06
54 45 0.68
55 17 0.26
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
Found at i:10207 original size:31 final size:28
Alignment explanation
Indices: 10120--10245 Score: 155
Period size: 28 Copynumber: 4.4 Consensus size: 28
10110 GAGATTGGCG
* * * *
10120 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
10149 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
10177 CTAAGTGTGCGAGTTTGATTATTATATAGCA
1 CTAAGTGTGCGAGTTTG---ATTATATAGCA
10208 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
10235 CTGAGTGTGCG
1 CTAAGTGTGCG
10246 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
27 21 0.24
28 25 0.29
29 15 0.17
30 3 0.03
31 23 0.26
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:10214 original size:59 final size:56
Alignment explanation
Indices: 10120--10245 Score: 171
Period size: 58 Copynumber: 2.2 Consensus size: 56
10110 GAGATTGGCG
* * *
10120 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
10177 CTAAGTGTGCGAGTTTGATTATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTT-A-AATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
10235 CTGAGTGTGCG
1 CTAAGTGTGCG
10246 GACTTAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 15 0.25
58 24 0.39
59 22 0.36
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:10256 original size:27 final size:27
Alignment explanation
Indices: 10145--10258 Score: 104
Period size: 28 Copynumber: 4.0 Consensus size: 27
10135 TAAATTGTAC
* * *
10145 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
*
10173 AGCACTAAGTGTGCGAGTTTGATTATTATAT
1 AGCACTAAGTGTGCGA-CTTGA--A-TATAT
* *
10204 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
10231 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
10258 A
1 A
10259 CTTTTGAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
27 25 0.33
28 26 0.35
30 4 0.05
31 20 0.27
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:18416 original size:56 final size:56
Alignment explanation
Indices: 18325--18447 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
18315 GAGATTGGCG
* * *
18325 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
18382 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
18437 CTGAGTGTGCG
1 CTAAGTGTGCG
18448 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:18434 original size:27 final size:28
Alignment explanation
Indices: 18325--18447 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
18315 GAGATTGGCG
* * * *
18325 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
18354 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
18382 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
18410 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
18437 CTGAGTGTGCG
1 CTAAGTGTGCG
18448 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:18458 original size:27 final size:27
Alignment explanation
Indices: 18350--18460 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
18340 TAAATTGTAC
* * *
18350 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18378 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18406 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
18433 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
18460 A
1 A
18461 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:19990 original size:22 final size:22
Alignment explanation
Indices: 19962--20005 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19952 TCCGGCGACG
* *
19962 GTCTCGGGTTCGGGGTGTTACA
1 GTCTCGGGCTCGGGGCGTTACA
19984 GTCTCGGGCTCGGGGCGTTACA
1 GTCTCGGGCTCGGGGCGTTACA
20006 AACCAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.41, T:0.27
Consensus pattern (22 bp):
GTCTCGGGCTCGGGGCGTTACA
Done.