Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3470
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: 8252
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Found at i:68 original size:39 final size:39
Alignment explanation
Indices: 7--296 Score: 464
Period size: 39 Copynumber: 7.5 Consensus size: 39
1 GGAACC
* *
7 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
*
46 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTC-GGACT
*
86 TAG-CCGGATACATCACTAGCACGAATG--CTTCGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
122 TAGCCCGGATATATCA-TAGCCACG-ATGCTCTTCGGGACT
1 TAGCCCGGATATATCACTAG-CACGAATGCTCTTC-GGACT
*
161 TAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
200 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
239 TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCTTC-GGACT
279 TAGCCCGGATATATCACT
1 TAGCCCGGATATATCACT
297 CTCAATTTCT
Statistics
Matches: 236, Mismatches: 6, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
36 14 0.06
37 19 0.08
38 4 0.02
39 156 0.66
40 43 0.18
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCTTCGGACT
Found at i:1602 original size:36 final size:37
Alignment explanation
Indices: 1540--1682 Score: 218
Period size: 38 Copynumber: 3.9 Consensus size: 37
1530 TAGCTCAGAC
* *
1540 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
1577 AAATCTCCACACGTAGTTATC-GGTCTTACCCGTAC-
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1612 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
1649 TATATCTCCACACGTAGTCATCGGGTCTTACCCG
1 -AAATCTCCACACGTAGTCATCGGGTCTTACCCG
1683 AATATATTCC
Statistics
Matches: 98, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
35 20 0.20
36 26 0.27
37 20 0.20
38 32 0.33
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:1663 original size:38 final size:37
Alignment explanation
Indices: 1537--1682 Score: 217
Period size: 36 Copynumber: 4.0 Consensus size: 37
1527 CTTTAGCTCA
* *
1537 GACAA-ATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAATATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
1573 GACAAAATCTCCACACGTAGTTATC-GGTCTTACCCG
1 GACAATATCTCCACACGTAGTCATCGGGTCTTACCCG
*
1609 TACAA-ATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAATATCTCCACACGTAGTCATCGGGTCTTACCCG
1645 GACATATATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACA-ATATCTCCACACGTAGTCATCGGGTCTTACCCG
1683 AATATATTCC
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
35 18 0.18
36 34 0.33
37 19 0.19
38 31 0.30
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.25
Consensus pattern (37 bp):
GACAATATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:1951 original size:48 final size:49
Alignment explanation
Indices: 1827--1963 Score: 215
Period size: 50 Copynumber: 2.8 Consensus size: 49
1817 GCACATCGCC
*
1827 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A
* *
1877 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
1925 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1964 TGCATGTCAT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
48 36 0.45
49 2 0.03
50 42 0.52
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:1965 original size:50 final size:50
Alignment explanation
Indices: 1827--2060 Score: 208
Period size: 50 Copynumber: 4.9 Consensus size: 50
1817 GCACATCGCC
*
1827 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA--CATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTC--A
*
1877 TATATATTTCACATT-GACCATTCGGCTTTACCAC--ATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATATGCATATCTCA
*
1925 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGC--ATGTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
** * * * * *
1973 T--AT-TCACACATTGGCCATTCGGCCTTATCACACATATGCAT-GCTC-
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
* * * *
2018 -ACAT-TCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCAT
2061 GTTCACATTC
Statistics
Matches: 158, Mismatches: 15, Indels: 25
0.80 0.08 0.13
Matches are distributed among these distances:
45 30 0.19
46 7 0.04
47 34 0.22
48 41 0.26
49 2 0.01
50 44 0.28
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (50 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
Found at i:1974 original size:48 final size:48
Alignment explanation
Indices: 1827--2062 Score: 193
Period size: 48 Copynumber: 5.0 Consensus size: 48
1817 GCACATCGCC
* *** *
1827 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTC--A
* *
1877 TATATATTTCACATT-GACCATTCGGCTTTACCAC--ATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATATGC--ATGTCA
1925 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCA
** * * * *
1973 T--AT-TCACACATTGGCCATTCGGCCTTATCACACATATGCATG-C-
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCA
* * * *
2016 TCACAT-TCATCACATTGGCCATTCGGCCTTATCACATATATGCATGT
1 T-ACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCATGT
2063 TCACATTCAT
Statistics
Matches: 159, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 33 0.21
46 5 0.03
47 35 0.22
48 41 0.26
49 2 0.01
50 41 0.26
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.34
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCA
Found at i:1974 original size:98 final size:93
Alignment explanation
Indices: 1826--2094 Score: 278
Period size: 98 Copynumber: 2.8 Consensus size: 93
1816 CGCACATCGC
* *** * *
1826 CTACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACAT
1 CTACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCATAT-T-CA---CACAT
* *
1891 TGACCATTCGGCTTTA-C-CACATATGCATATCT
61 TGACCATTCGGCCTTATCACACATATGCAT-GCT
*
1923 CATACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCATATTCACACATTGGC
1 C-TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCATATTCACACATTGAC
1988 CATTCGGCCTTATCACACATATGCATGCT
65 CATTCGGCCTTATCACACATATGCATGCT
* * * * *
2017 C-ACAT-TCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 CTACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCATG-TCATATTCA-CACATTG
*
2080 GCCATTC-GCCTTATC
63 ACCATTCGGCCTTATC
2095 TCATATATAC
Statistics
Matches: 152, Mismatches: 14, Indels: 16
0.84 0.08 0.09
Matches are distributed among these distances:
91 1 0.01
92 38 0.25
93 35 0.23
94 18 0.12
95 11 0.07
96 1 0.01
97 2 0.01
98 46 0.30
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (93 bp):
CTACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGTCATATTCACACATTGACC
ATTCGGCCTTATCACACATATGCATGCT
Found at i:2112 original size:46 final size:47
Alignment explanation
Indices: 1933--2123 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
1923 CATACATATT
* * * *
1933 TCACATTAGCCATTCGGCTTTACCACATATATGCATG-TCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
1979 -CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
2025 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
2072 TCACATTGGCCATTC-GCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
2118 TCACAT
1 TCACAT
2124 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 32 0.24
46 41 0.31
47 59 0.45
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:2123 original size:93 final size:92
Alignment explanation
Indices: 1933--2123 Score: 267
Period size: 93 Copynumber: 2.1 Consensus size: 92
1923 CATACATATT
* *
1933 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTCATATTCACACATTGGCCATTCGGCCT
1 TCACATTAGCCATTCGGCCTTACCACATATATGCATGTCACATTCACACATTGGCCATTCGGCCT
* **
1998 TATCACACATATGCATGCTCACATTCA
66 TATCACACATATACACACTCACATTCA
* *
2025 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTC-GC
1 TCACATTAGCCATTCGGCCTTACCACATATATGCATG-TCACATTCA-CACATTGGCCATTCGGC
* * *
2089 CTTATCTCATATATACACATTCACATTCA
64 CTTATCACACATATACACACTCACATTCA
2118 TCACAT
1 TCACAT
2124 AAAATCCTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 34 0.39
93 39 0.45
94 14 0.16
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (92 bp):
TCACATTAGCCATTCGGCCTTACCACATATATGCATGTCACATTCACACATTGGCCATTCGGCCT
TATCACACATATACACACTCACATTCA
Found at i:4894 original size:74 final size:73
Alignment explanation
Indices: 4772--4908 Score: 186
Period size: 74 Copynumber: 1.9 Consensus size: 73
4762 CATGTTTCGT
* * * *
4772 TTGGACTAGTTCTTAGGAGCAATTGGCGTGTTATCGGGTGGTTAAGCTCTTATGAGCATTTGGCG
1 TTGGACTAGCTCTTAGAAGCAATTGGCGTGTTATCAGGTGGATAAGCTCTTATGAGCATTTGGCG
4837 TCTTTAGG
66 TCTTTAGG
* * *
4845 TTGGACTAGCTCTTTGAAAGCAATTGGTC-TGTTATCAGGTGGATGAGCTCTTATGTGCATTTGG
1 TTGGACTAGCTCTTAG-AAGCAATTGG-CGTGTTATCAGGTGGATAAGCTCTTATGAGCATTTGG
4909 TGTGTTTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
73 14 0.25
74 40 0.73
75 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (73 bp):
TTGGACTAGCTCTTAGAAGCAATTGGCGTGTTATCAGGTGGATAAGCTCTTATGAGCATTTGGCG
TCTTTAGG
Found at i:5570 original size:23 final size:20
Alignment explanation
Indices: 5527--5571 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
5517 ACCTCTTCTC
*
5527 TTCAATTTTTGATTTGTTAA
1 TTCAATTTTTGATTTGATAA
5547 TTCAATTTTGTGGTATTTGATAA
1 TTCAATTTT-T-G-ATTTGATAA
5570 TT
1 TT
5572 TCGAGTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 1 0.05
22 1 0.05
23 10 0.48
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.58
Consensus pattern (20 bp):
TTCAATTTTTGATTTGATAA
Done.