Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: COLO4_26428
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: 3792
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Found at i:1609 original size:21 final size:21
Alignment explanation
Indices: 1561--1610 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1551 TCCTGTGCAA
*
1561 TCTCCACCACCTCCCATACAC
1 TCTCCACCACCGCCCATACAC
* * * *
1582 TCCCCACCACCGCCCGTATAT
1 TCTCCACCACCGCCCATACAC
1603 TCTCCACC
1 TCTCCACC
1611 CCCACCACCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.56, G:0.04, T:0.20
Consensus pattern (21 bp):
TCTCCACCACCGCCCATACAC
Found at i:2215 original size:198 final size:199
Alignment explanation
Indices: 1706--2222 Score: 631
Period size: 198 Copynumber: 2.6 Consensus size: 199
1696 CCACCACCTA
* * *
1706 CATTAAAACCTTCGGCCCCAGCACCATTAGACGA-TCCGCATAAGGAATCACCCATGACAAGGCT
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCC-CATAAGGAATCACCAATAACAAGGCA
* ** * **
1770 ACGGTCGCCTCCTCCTGTACAATCTCCAC-CAC-C-TGTCTATTCTTCACCACCACCATTACCAG
65 ACGATCGCCTCCTCCTGTACAATCTCCACAC-CTCATGTCTATTCCCCTCCACCACCAACACCAG
* *
1832 TAAATTCTCCGCCACCTCCAGTTCAGTCACCACCACCATCACCTGTATACTCTCCTCCACCAATG
129 TAAATTCTCCGCCACCTCCAGTTCACTCACCACCACCA-CACCTGTAAACTCTCCTCCACCAATG
1897 CACCCTC
193 CACCCTC
* * * * * ** *
1904 CATCAAAACCATT-GACCCCAGAACCATTGGACGATTCACATAAGGAATCACCCAATATGAA-CC
1 CATTAAAACC-TTCGGCCCCAGCACCATTAGACGATTCCCATAAGGAATCA-CCAATAACAAGGC
* * *
1967 AAAGATCGCCTCCTCCTGTACAATCCTCGC-CACCTCCA-ATCCATTCCCCTCCACCACCAACAC
64 AACGATCGCCTCCTCCTGTACAAT-CTC-CACACCT-CATGTCTATTCCCCTCCACCACCAACAC
* *
2030 CAGTAAATTCTCCTCCACCTCCAGTTTACTCACCACCA-C-CACCTGTAAACTCTCCTCCACCAA
126 CAGTAAATTCTCCGCCACCTCCAGTTCACTCACCACCACCACACCTGTAAACTCTCCTCCACCAA
*
2093 TGGACCCTC
191 TGCACCCTC
*
2102 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCCCATAAGGAATCACCTATAACAAGGCAA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCCCATAAGGAATCACCAATAACAAGGCAA
* *
2167 CGATTGCCTCCTCCTGTACAATCTCCATCACCTCATGTCTACTCCCCTCCACCACC
66 CGATCGCCTCCTCCTGTACAATCTCCA-CACCTCATGTCTATTCCCCTCCACCACC
2223 TGTCTATTCT
Statistics
Matches: 266, Mismatches: 39, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
196 1 0.00
197 14 0.05
198 179 0.67
199 15 0.06
200 3 0.01
201 54 0.20
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.21
Consensus pattern (199 bp):
CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCCCATAAGGAATCACCAATAACAAGGCAA
CGATCGCCTCCTCCTGTACAATCTCCACACCTCATGTCTATTCCCCTCCACCACCAACACCAGTA
AATTCTCCGCCACCTCCAGTTCACTCACCACCACCACACCTGTAAACTCTCCTCCACCAATGCAC
CCTC
Done.