Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008634.1 Kokia drynarioides strain JFW-HI SEQ_123314, whole genome shotgun sequence
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: 10334
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:37 original size:15 final size:15
Alignment explanation
Indices: 19--67 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
9 CGACCACCAC
19 CACCTCCAAGTACAA
1 CACCTCCAAGTACAA
* ** *
34 CACCACCACCTACAC
1 CACCTCCAAGTACAA
*
49 CATCTCCAAGTACAA
1 CACCTCCAAGTACAA
64 CACC
1 CACC
68 ACCACCACCA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.47, G:0.04, T:0.12
Consensus pattern (15 bp):
CACCTCCAAGTACAA
Found at i:37 original size:30 final size:30
Alignment explanation
Indices: 1--77 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
*
1 CAACACCACGACCACCACCACCTCCAAGTA
1 CAACACCACCACCACCACCACCTCCAAGTA
*
31 CAACACCACCACCTA-CACCATCTCCAAGTA
1 CAACACCACCACC-ACCACCACCTCCAAGTA
61 CAACACCACCACCACCA
1 CAACACCACCACCACCA
78 TGTACACCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.38, C:0.51, G:0.04, T:0.08
Consensus pattern (30 bp):
CAACACCACCACCACCACCACCTCCAAGTA
Found at i:101 original size:33 final size:33
Alignment explanation
Indices: 64--142 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
54 CCAAGTACAA
* *
64 CACCACCACCACCATGTACACCTCTGAGGGGAC
1 CACCACCACCACCAAGTACACCTCCGAGGGGAC
97 CACCACCACCACCAAGTACACCTCCGAGGGGAC
1 CACCACCACCACCAAGTACACCTCCGAGGGGAC
*
130 CACCACCTCCACC
1 CACCACCACCACC
143 TCCACCTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.28, C:0.48, G:0.15, T:0.09
Consensus pattern (33 bp):
CACCACCACCACCAAGTACACCTCCGAGGGGAC
Found at i:143 original size:6 final size:6
Alignment explanation
Indices: 132--156 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
122 GAGGGGACCA
132 CCACCT CCACCT CCACCT CCACCT C
1 CCACCT CCACCT CCACCT CCACCT C
157 GGTCATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCACCT
Found at i:6510 original size:13 final size:13
Alignment explanation
Indices: 6492--6527 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
6482 AAAAGATTCA
6492 TGTCCGACACCTG
1 TGTCCGACACCTG
6505 TGTCCGACACCTG
1 TGTCCGACACCTG
6518 TGTCCGACAC
1 TGTCCGACAC
6528 ATATCAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (13 bp):
TGTCCGACACCTG
Found at i:8456 original size:7 final size:7
Alignment explanation
Indices: 8443--8480 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
8433 CGCAACCCCG
8443 AACCCTTA
1 AACCC-TA
*
8451 AACCTTA
1 AACCCTA
8458 AA-CCTA
1 AACCCTA
8464 AACCCTA
1 AACCCTA
8471 AACCCTA
1 AACCCTA
8478 AAC
1 AAC
8481 TTCACATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 18 0.67
8 4 0.15
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:8479 original size:14 final size:14
Alignment explanation
Indices: 8443--8480 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
8433 CGCAACCCCG
*
8443 AACCCTTAAACCTTA
1 AACCC-TAAACCCTA
8458 AA-CCTAAACCCTA
1 AACCCTAAACCCTA
8471 AACCCTAAAC
1 AACCCTAAAC
8481 TTCACATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 9 0.43
15 2 0.10
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCCTA
Done.