Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007682.1 Kokia drynarioides strain JFW-HI SEQ_122313, 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: 4352
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:1947 original size:30 final size:30
Alignment explanation
Indices: 1911--1972 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1901 CCCAAAAGGT
1911 CCCTGAACCGTCCAAAAATCAC-ATTTTGAC
1 CCCTGAA-CGTCCAAAAATCACAATTTTGAC
* * *
1941 CCCTGAACTTCCTAAAATTACAATTTTGAC
1 CCCTGAACGTCCAAAAATCACAATTTTGAC
1971 CC
1 CC
1973 TAAACATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.27
Consensus pattern (30 bp):
CCCTGAACGTCCAAAAATCACAATTTTGAC
Found at i:1973 original size:29 final size:29
Alignment explanation
Indices: 1932--2075 Score: 118
Period size: 29 Copynumber: 4.9 Consensus size: 29
1922 CCAAAAATCA
1932 CATTTTGACCCCTGAACTTCCTAAAATTAC
1 CATTTTGA-CCCTGAACTTCCTAAAATTAC
* *
1962 AATTTTGACCCTAAACATT-CTAAAATTAC
1 CATTTTGACCCTGAAC-TTCCTAAAATTAC
** *
1991 CATTTT-ACCCCCAAAC-TCAC-AAAAATAC
1 CATTTTGA-CCCTGAACTTC-CTAAAATTAC
*
2019 CATTTTCGACCCTGAACTTTCTAAAAATTAC
1 CATTTT-GACCCTGAACTTCCT-AAAATTAC
* * *
2050 CATTTT-ACCCTTAAATTTCTAAAATT
1 CATTTTGACCCTGAACTTCCTAAAATT
2076 TCATTTTTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
27 1 0.01
28 20 0.21
29 49 0.52
30 11 0.12
31 13 0.14
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CATTTTGACCCTGAACTTCCTAAAATTAC
Found at i:2016 original size:58 final size:58
Alignment explanation
Indices: 1954--2123 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 58
1944 TGAACTTCCT
*
1954 AAAATTACAATTTTGACCCTAAACATTCT-AAAATTACCATTTTACCCCCAAACTCACA
1 AAAATTACAATTTTGACCCTAAACTTTCTAAAAATTACCATTTTACCCCCAAA-TCACA
* * ** ** *
2012 AAAA-TACCATTTTCGACCCTGAACTTTCTAAAAATTACCATTTTACCCTTAAATTTCT
1 AAAATTACAATTTT-GACCCTAAACTTTCTAAAAATTACCATTTTACCCCCAAATCACA
* * * * * *
2070 AAAATTTCATTTTTAACCCCAAATTTTCTAAAAATTACCATTTTACCCCTAAAT
1 AAAATTACAATTTTGACCCTAAACTTTCTAAAAATTACCATTTTACCCCCAAAT
2124 GTCTAAAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
57 8 0.09
58 58 0.62
59 27 0.29
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACAATTTTGACCCTAAACTTTCTAAAAATTACCATTTTACCCCCAAATCACA
Found at i:2036 original size:87 final size:87
Alignment explanation
Indices: 1923--2092 Score: 215
Period size: 87 Copynumber: 2.0 Consensus size: 87
1913 CTGAACCGTC
1923 CAAAAATCACATTTTGACCCCTGAACTTCCT-AAAATTACAATTTTGACCC-TAAACATTCTAAA
1 CAAAAATCACATTTTGACCCCTGAACTTCCTAAAAATTACAATTTT-ACCCTTAAA-ATTCTAAA
*
1986 ATTACCA-TTTTACCCCCAAACTCA
64 ATT-CCATTTTTAACCCCAAACTCA
* * *
2010 CAAAAAT-ACCATTTTCGA-CCCTGAACTTTCTAAAAATTACCATTTTACCCTTAAATTTCTAAA
1 CAAAAATCA-CATTTT-GACCCCTGAACTTCCTAAAAATTACAATTTTACCCTTAAAATTCTAAA
*
2073 ATTTCATTTTTAACCCCAAA
64 ATTCCATTTTTAACCCCAAA
2093 TTTTCTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
86 3 0.04
87 51 0.70
88 19 0.26
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (87 bp):
CAAAAATCACATTTTGACCCCTGAACTTCCTAAAAATTACAATTTTACCCTTAAAATTCTAAAAT
TCCATTTTTAACCCCAAACTCA
Found at i:2088 original size:29 final size:28
Alignment explanation
Indices: 2011--2169 Score: 119
Period size: 29 Copynumber: 5.4 Consensus size: 28
2001 CCAAACTCAC
* * *
2011 AAAAATACCATTTTCGACCCTGAACTTTCT
1 AAAAATTCCATTTT-TACCCT-AAATTTCT
2041 AAAAATTACCA-TTTTACCCTTAAATTTCT
1 AAAAATT-CCATTTTTACCC-TAAATTTCT
* *
2070 -AAAATTTCATTTTTAACCCCAAATTTTCT
1 AAAAATTCCATTTTT-ACCCTAAA-TTTCT
*
2099 AAAAATTACCA-TTTTACCCCTAAATGTCT
1 AAAAATT-CCATTTTTA-CCCTAAATTTCT
* *
2128 AAAAATTCCATTTTTTTCCC-AAATTTTT
1 AAAAATTCCA-TTTTTACCCTAAATTTCT
2156 CAAAAATTACCATT
1 -AAAAATT-CCATT
2170 GTACCTCGAA
Statistics
Matches: 106, Mismatches: 11, Indels: 25
0.75 0.08 0.18
Matches are distributed among these distances:
27 2 0.02
28 22 0.21
29 44 0.42
30 33 0.31
31 5 0.05
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTAAATTTCT
Found at i:2129 original size:58 final size:58
Alignment explanation
Indices: 1979--2174 Score: 202
Period size: 58 Copynumber: 3.4 Consensus size: 58
1969 ACCCTAAACA
* * * * * ** *
1979 TTCT-AAAATTACCATTTTACCCCCAAA-CTCACAAAAATACCATTTTCGACCCTGAACT
1 TTCTAAAAATTACCATTTTACCCCTAAATGTC-TAAAAATTCCATTTT-TACCCCAAATT
* * *
2037 TTCTAAAAATTACCATTTTACCCTTAAATTTCT-AAAATTTCATTTTTAACCCCAAATT
1 TTCTAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTT-ACCCCAAATT
**
2095 TTCTAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTTTCCCAAATT
1 TTCTAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTACCCCAAATT
*
2153 TT-TCAAAAATTACCATTGTACC
1 TTCT-AAAAATTACCATTTTACC
2175 TCGAAACTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 80 0.68
59 34 0.29
60 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (58 bp):
TTCTAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTACCCCAAATT
Done.