Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: XM_021431553.1
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: 2370
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Found at i:1672 original size:21 final size:21
Alignment explanation
Indices: 1643--1938 Score: 120
Period size: 21 Copynumber: 13.5 Consensus size: 21
1633 GATGTCCGCT
*
1643 CACCTCCACCAGTCTACTCAC
1 CACCCCCACCAGTCTACTCAC
*
1664 CACCCCCACCCGTGC-ACTCAC
1 CACCCCCACCAGT-CTACTCAC
* *
1685 C-CCCGCCACCAGTCCATTCAC
1 CACCC-CCACCAGTCTACTCAC
*
1706 CACCGCCACCACCAGTCCATTCTCCAC
1 CA-C-CC-CCACCAGT-C-TACT-CAC
* *
1733 CACCACCTCCACCTGTCT--TC-T
1 CA-C-CC-CCACCAGTCTACTCAC
*
1754 CACCCCCACCAAT-TCACTCAC
1 CACCCCCACCAGTCT-ACTCAC
*
1775 CACCTCCACCAGTCTACTCACCCC
1 CACCCCCACCAGTCTACTCA---C
* * *
1799 CACCACCGCCACCTGTGTATTCAC
1 CA-C-CC-CCACCAGTCTACTCAC
* * *
1823 CACCTCCACCAGTCCATTCAC
1 CACCCCCACCAGTCTACTCAC
* * *
1844 CACCACCTCCTGTCTACTC-C
1 CACCCCCACCAGTCTACTCAC
* *
1864 CACCACCACCAAGTCTACTCCC
1 CACCCCCACC-AGTCTACTCAC
* * * * *
1886 CTCCACCACCTGTCCATTCAC
1 CACCCCCACCAGTCTACTCAC
* *
1907 CACCCCCACCCGTCTACTCTC
1 CACCCCCACCAGTCTACTCAC
*
1928 CACCACCACCA
1 CACCCCCACCA
1939 CCACCACCTG
Statistics
Matches: 208, Mismatches: 45, Indels: 44
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.00
18 6 0.03
19 2 0.01
20 17 0.08
21 115 0.55
22 14 0.07
23 3 0.01
24 16 0.08
25 3 0.01
26 3 0.01
27 28 0.13
ACGTcount: A:0.21, C:0.55, G:0.06, T:0.18
Consensus pattern (21 bp):
CACCCCCACCAGTCTACTCAC
Found at i:1717 original size:24 final size:24
Alignment explanation
Indices: 1690--1739 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1680 CTCACCCCCG
*
1690 CCACCAGTCCATTCACCACCGCCA
1 CCACCAGTCCATTCACCACCACCA
*
1714 CCACCAGTCCATTCTCCACCACCA
1 CCACCAGTCCATTCACCACCACCA
1738 CC
1 CC
1740 TCCACCTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.14
Consensus pattern (24 bp):
CCACCAGTCCATTCACCACCACCA
Found at i:1757 original size:24 final size:26
Alignment explanation
Indices: 1690--1764 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 26
1680 CTCACCCCCG
*
1690 CCACCAGTCCA-T-TCACCACCGCCA
1 CCACCAGTCCATTCTCACCACCACCA
*
1714 CCACCAGTCCATTCTCCACCACCACCT
1 CCACCAGTCCATTCT-CACCACCACCA
* *
1741 CCACCTGT-C-TTCTCACCCCCACCA
1 CCACCAGTCCATTCTCACCACCACCA
1765 ATTCACTCAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 20 0.47
25 5 0.12
26 2 0.05
27 16 0.37
ACGTcount: A:0.21, C:0.56, G:0.05, T:0.17
Consensus pattern (26 bp):
CCACCAGTCCATTCTCACCACCACCA
Found at i:1805 original size:42 final size:43
Alignment explanation
Indices: 1643--2031 Score: 160
Period size: 42 Copynumber: 8.7 Consensus size: 43
1633 GATGTCCGCT
**
1643 CACCTCCACCAGTCTACTCACCACCC-CCACCCGTG-CACTCAC
1 CACCTCCACCAGTCTACTCACC-CCCACCACCAATGTCACTCAC
* * * * *
1685 CCCCGCCACCAGTCCATTCACCACCGCCACCACCAGTCCATTCTCCAC-CAC
1 CACCTCCACCAGTCTACTCA-C-CC-CCACCACCA----A-TGT-CACTCAC
* *
1736 CACCTCCACCTGTCTTCTCA--CCC-CCACCAAT-TCACTCAC
1 CACCTCCACCAGTCTACTCACCCCCACCACCAATGTCACTCAC
* * *
1775 CACCTCCACCAGTCTACTCACCCCCACCACCGCCACCTGTGTATTCAC
1 CACCTCCACCAGTCTACTCACCCCCACCA---CCA-ATGT-CACTCAC
* * * *
1823 CACCTCCACCAGTCCATTCACCACCACCTCC--TGTCTACTC-C
1 CACCTCCACCAGTCTACTCACCCCCACCACCAATGTC-ACTCAC
* *
1864 CACCACCACCAAGTCTACTC-CCCTCCACCACC--TGTCCATTCAC
1 CACCTCCACC-AGTCTACTCACCC-CCACCACCAATGT-CACTCAC
* * * *
1907 CACCCCCACCCGTCTACTCTCCACCACCACCACCACCACCTGTCCACTCTC
1 CACCTCCACCAGTCTA--CT-CA-C-CC-CCACCACCA-ATGT-CACTCAC
* * * *
1958 CACCTCCACCAGTTTACTCACCACCACCACC--TGTACAATCCC
1 CACCTCCACCAGTCTACTCACCCCCACCACCAATGT-CACTCAC
* * *
2000 CACCTCCACCGGTTTACTCACCACCACCACCA
1 CACCTCCACCAGTCTACTCACCCCCACCACCA
2032 CCAGTTCCAA
Statistics
Matches: 268, Mismatches: 43, Indels: 71
0.70 0.11 0.19
Matches are distributed among these distances:
38 3 0.01
39 22 0.08
40 1 0.00
41 16 0.06
42 88 0.33
43 13 0.05
44 5 0.02
45 25 0.09
46 4 0.01
47 4 0.01
48 42 0.16
49 2 0.01
50 1 0.00
51 39 0.15
52 3 0.01
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.18
Consensus pattern (43 bp):
CACCTCCACCAGTCTACTCACCCCCACCACCAATGTCACTCAC
Found at i:1811 original size:48 final size:48
Alignment explanation
Indices: 1754--1850 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
1744 CCTGTCTTCT
* *
1754 CACCCCCACCAAT-TCACTCACCACCTCCACCAGTCTACTCACCCCCAC
1 CACCCCCACCAATGT-ACTCACCACCTCCACCAGTCCACTCACCACCAC
* ** * *
1802 CACCGCCACCTGTGTATTCACCACCTCCACCAGTCCATTCACCACCAC
1 CACCCCCACCAATGTACTCACCACCTCCACCAGTCCACTCACCACCAC
1850 C
1 C
1851 TCCTGTCTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.24, C:0.55, G:0.05, T:0.16
Consensus pattern (48 bp):
CACCCCCACCAATGTACTCACCACCTCCACCAGTCCACTCACCACCAC
Found at i:1822 original size:27 final size:27
Alignment explanation
Indices: 1772--1832 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1762 CCAATTCACT
* *
1772 CACCACCTCCACCAGTCTACTCACCCC
1 CACCACCGCCACCAGTCTACTCACCAC
* * *
1799 CACCACCGCCACCTGTGTATTCACCAC
1 CACCACCGCCACCAGTCTACTCACCAC
*
1826 CTCCACC
1 CACCACC
1833 AGTCCATTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.56, G:0.07, T:0.16
Consensus pattern (27 bp):
CACCACCGCCACCAGTCTACTCACCAC
Found at i:1832 original size:69 final size:65
Alignment explanation
Indices: 1700--1873 Score: 172
Period size: 66 Copynumber: 2.6 Consensus size: 65
1690 CCACCAGTCC
* * * *
1700 ATTCAC-CACCGCCACCACCAGTCCATTCTCCACCACCACCTCCACCTGTCTTCTCACCCCCACC
1 ATTCACTCACCACCACCACCAGTCTACTC-CCACCACCACCGCCACCTGTCTTCTCACCCCCACC
1764 A
65 A
* * *
1765 ATTCACTCACCACCTCCACCAGTCTACTCACCCCCACCACCGCCACCTGTGTAT-TCACCACCTC
1 ATTCACTCACCACCACCACCAGTCTACTC-CCACCACCACCGCCACCTGTCT-TCTCA-C-CC-C
1829 CACCA
61 CACCA
* * * * *
1834 GTCCATTCACCACCACCTCCTGTCTACTCCCACCACCACC
1 ATTCACTCACCACCACCACCAGTCTACTCCCACCACCACC
1874 AAGTCTACTC
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
65 6 0.07
66 40 0.45
67 2 0.02
68 12 0.13
69 29 0.33
ACGTcount: A:0.22, C:0.54, G:0.05, T:0.19
Consensus pattern (65 bp):
ATTCACTCACCACCACCACCAGTCTACTCCCACCACCACCGCCACCTGTCTTCTCACCCCCACCA
Found at i:1940 original size:30 final size:30
Alignment explanation
Indices: 1904--1968 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1894 CCTGTCCATT
* *
1904 CACCACCCCCACCCGTCTACTCTCCACCAC
1 CACCACCACCACCCGTCCACTCTCCACCAC
* *
1934 CACCACCACCACCTGTCCACTCTCCACCTC
1 CACCACCACCACCCGTCCACTCTCCACCAC
1964 CACCA
1 CACCA
1969 GTTTACTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.62, G:0.03, T:0.14
Consensus pattern (30 bp):
CACCACCACCACCCGTCCACTCTCCACCAC
Found at i:1946 original size:51 final size:51
Alignment explanation
Indices: 1888--1988 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
1878 CTACTCCCCT
* * *
1888 CCACCACCTGTCCATTCACCACCCCCACCCGTCTACTCTCCACCACCACCA
1 CCACCACCTGTCCACTCACCACCCCCACCAGTCTACTCACCACCACCACCA
* * *
1939 CCACCACCTGTCCACTCTCCACCTCCACCAGTTTACTCACCACCACCACC
1 CCACCACCTGTCCACTCACCACCCCCACCAGTCTACTCACCACCACCACC
1989 TGTACAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.22, C:0.57, G:0.04, T:0.17
Consensus pattern (51 bp):
CCACCACCTGTCCACTCACCACCCCCACCAGTCTACTCACCACCACCACCA
Found at i:1966 original size:21 final size:21
Alignment explanation
Indices: 1934--2030 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
1924 TCTCCACCAC
*
1934 CACCACCACCACCTGTCCACT
1 CACCACCACCACCTGTACACT
* * * **
1955 CTCCACCTCCACCAGTTTACT
1 CACCACCACCACCTGTACACT
*
1976 CACCACCACCACCTGTACAAT
1 CACCACCACCACCTGTACACT
* * * **
1997 CCCCACCTCCACCGGTTTACT
1 CACCACCACCACCTGTACACT
2018 CACCACCACCACC
1 CACCACCACCACC
2031 ACCAGTTCCA
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.24, C:0.54, G:0.05, T:0.18
Consensus pattern (21 bp):
CACCACCACCACCTGTACACT
Found at i:1976 original size:93 final size:93
Alignment explanation
Indices: 1841--2034 Score: 255
Period size: 93 Copynumber: 2.1 Consensus size: 93
1831 CCAGTCCATT
* * * * * *
1841 CACCACCACCTCCTGTCTACTCCCACCACCACCAAGTCTACTCCCCTCCACCACCTGTCCATTCA
1 CACCACCACCACCTGTCCACTCCCACCACCACCAAGTCTACTCACCACCACCACCTGTACAATCA
*
1906 CCACCCCCACCCGTCTACTCTCCACCAC
66 CCACCCCCACCCGTCTACTCACCACCAC
* *
1934 CACCACCACCACCTGTCCACTCTCCACCTCCACC-AGTTTACTCACCACCACCACCTGTACAATC
1 CACCACCACCACCTGTCCACTC-CCACCACCACCAAGTCTACTCACCACCACCACCTGTACAATC
* * * *
1998 CCCACCTCCACCGGTTTACTCACCACCAC
65 ACCACCCCCACCCGTCTACTCACCACCAC
2027 CACCACCA
1 CACCACCA
2035 GTTCCAACTC
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 77 0.89
94 10 0.11
ACGTcount: A:0.23, C:0.55, G:0.05, T:0.18
Consensus pattern (93 bp):
CACCACCACCACCTGTCCACTCCCACCACCACCAAGTCTACTCACCACCACCACCTGTACAATCA
CCACCCCCACCCGTCTACTCACCACCAC
Done.