Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2879
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: 6777
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:185 original size:30 final size:30
Alignment explanation
Indices: 151--247 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
141 AGCTCACTCC
151 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
181 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
211 CAGCTCAACTTTAGCTCACGGGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
241 TAGCTCA
1 TAGCTCA
248 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:1969 original size:12 final size:11
Alignment explanation
Indices: 1952--1995 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
1942 GGAAATTCGA
1952 AAAAAAAAATTT
1 AAAAAAAAA-TT
*
1964 AAAAAAAAATCG
1 AAAAAAAAAT-T
1976 AAAAAAAAA-T
1 AAAAAAAAATT
1986 AAAAAAAAAT
1 AAAAAAAAAT
1996 CGAAGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.32
11 1 0.04
12 18 0.64
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:2014 original size:22 final size:22
Alignment explanation
Indices: 1919--1999 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
1909 ATTGTAATTG
*
1919 AAAAAAATC-AAAAAAAAAGAA
1 AAAAAAATCGAAAAAAAAATAA
** *
1940 GAGGAAATTCGAAAAAAAAAATTTAA
1 -AAAAAAATCG-AAAAAAAAA--TAA
1966 AAAAAAATCGAAAAAAAAATAA
1 AAAAAAATCGAAAAAAAAATAA
1988 AAAAAAATCGAA
1 AAAAAAATCGAA
2000 GTATATAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
22 21 0.44
24 18 0.38
25 7 0.15
26 2 0.04
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAAAATCGAAAAAAAAATAA
Found at i:2925 original size:5 final size:5
Alignment explanation
Indices: 2915--2976 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
2905 AAGAGAAAAT
* *
2915 AAAGA AAAGA AAAGA AAAGA AAA-A GCAAGA TAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA -AAAGA AAAG-A AAAGA AAA-GA
2962 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
2977 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 36 0.75
6 9 0.19
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:3054 original size:11 final size:12
Alignment explanation
Indices: 3024--3054 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3014 TTGAGAGAAC
3024 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
3036 TTGAAAAATCCT
1 TTGAAAAAGCCT
3048 TTGAAAA
1 TTGAAAA
3055 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:3065 original size:12 final size:13
Alignment explanation
Indices: 3050--3084 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3040 AAAATCCTTT
3050 GAAAA-GAAAAAA
1 GAAAATGAAAAAA
3062 GAAAATG-AAAAA
1 GAAAATGAAAAAA
3074 GAAAATGAAAA
1 GAAAATGAAAA
3085 GAAATTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (13 bp):
GAAAATGAAAAAA
Found at i:3072 original size:11 final size:12
Alignment explanation
Indices: 3057--3088 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3047 TTTGAAAAGA
3057 AAAAAGAAAATG
1 AAAAAGAAAATG
3069 AAAAAGAAAATG
1 AAAAAGAAAATG
3081 -AAAAGAAA
1 AAAAAGAAA
3089 TTTGAGAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:5264 original size:30 final size:30
Alignment explanation
Indices: 5168--5265 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
5158 AGCTCACTCC
* *
5168 TAGCTCATA-TTTAGCTCACACAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCAC-GAGCTAAAGCT
* * * **
5199 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
5229 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
5259 TAGCTCA
1 TAGCTCA
5266 TTTTAGTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
29 2 0.04
30 31 0.62
31 17 0.34
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Done.