Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3456
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: 23520
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2013 original size:39 final size:40
Alignment explanation
Indices: 1899--2079 Score: 226
Period size: 40 Copynumber: 4.5 Consensus size: 40
1889 GCTACTCGTT
*
1899 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
1939 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
1979 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
2018 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
2059 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
2080 GGACATCATT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 75 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:2043 original size:79 final size:80
Alignment explanation
Indices: 1901--2079 Score: 222
Period size: 79 Copynumber: 2.2 Consensus size: 80
1891 TACTCGTTCA
* *
1901 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
1966 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
**
1981 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
2043 ATATGGTCACTTAGCAC
64 ATATAGTAACTTAGCAC
*
2060 AAAGCCTTCGGGACTTAGCC
1 AATGCCTTCGGGACTTAGCC
2080 GGACATCATT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 4 0.05
79 59 0.69
80 23 0.27
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:4207 original size:93 final size:93
Alignment explanation
Indices: 4094--4265 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
4084 CGCCCATAAG
*
4094 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
4158 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
4187 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
4252 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
4266 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:4260 original size:46 final size:46
Alignment explanation
Indices: 4087--4262 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
4077 TGTAACCCGC
* *
4087 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
4133 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
4183 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
4226 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
4263 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:7680 original size:28 final size:28
Alignment explanation
Indices: 7648--7775 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
7638 ATAGTAAGTC
*
7648 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
7676 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
7705 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
7733 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
7762 CGCACACTTAGTGC
1 CGCACACTTAGTGC
7776 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:7738 original size:57 final size:57
Alignment explanation
Indices: 7647--7775 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
7637 TATAGTAAGT
*
7647 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
7704 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
7761 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
7776 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:12967 original size:46 final size:46
Alignment explanation
Indices: 12917--13089 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
12907 TGGTTGAGCA
12917 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12963 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
13008 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
13056 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
13090 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13073 original size:93 final size:93
Alignment explanation
Indices: 12914--13084 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
12904 GGATGGTTGA
* *
12914 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12979 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
13007 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
13072 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
13085 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20541 original size:46 final size:46
Alignment explanation
Indices: 20491--20663 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
20481 TGGTTGAGCA
20491 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20537 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
20582 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
20630 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
20664 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20647 original size:93 final size:93
Alignment explanation
Indices: 20488--20658 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
20478 GGATGGTTGA
* *
20488 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20553 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
20581 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20646 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20659 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.