Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001404.1 Kokia drynarioides strain JFW-HI SEQ_112892, 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: 2259
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Found at i:994 original size:6 final size:6
Alignment explanation
Indices: 980--1043 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
970 ATTTGGAAAA
* *
980 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
1026 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
1044 CTACACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:1020 original size:34 final size:34
Alignment explanation
Indices: 977--1042 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
967 TAAATTTGGA
977 AAATAAATTTAAACTTAAAT-TAAATTTAAATTCG
1 AAATAAATTTAAA-TTAAATATAAATTTAAATTCG
*
1011 AAATAAATTTAAATTTAATATAAATTTAAATT
1 AAATAAATTTAAATTAAATATAAATTTAAATT
1043 TCTACACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (34 bp):
AAATAAATTTAAATTAAATATAAATTTAAATTCG
Found at i:1043 original size:17 final size:16
Alignment explanation
Indices: 948--1043 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 16
938 CCTTATTTAT
948 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
964 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
984 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
1001 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
1018 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
1035 TTTAAATTT
1 TTTAAATTT
1044 CTACACAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 6 0.09
17 45 0.66
18 3 0.04
19 10 0.15
20 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:1869 original size:203 final size:203
Alignment explanation
Indices: 1483--2041 Score: 795
Period size: 203 Copynumber: 2.7 Consensus size: 203
1473 TTTCATCAGG
** * ** * * *
1483 ATTTGGTTCACTTCTCGGTATCTCATCAGGGGGCTAACCACTTTATGGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACC-TTTTATTGCTTCGACCTGCTTCTCA
** ** * * *
1548 GCATCTCATCAGGAAGCTGGGGTTAGAAGA-TTTGCTCGTTTTGAGCCTCGTTTGGGTATTTTTT
65 GTGTCTCATCAGGAAGCTGGGGTTA-AAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
* *
1612 TCAGTGCCTCATCAGGAAGATGATTACATCGCTGTTTTTTTCAATTCGCTCCTCCGTATATCA-T
129 TCAGTGTCTCATCAGGAAGATGATTACATCACTGTTTTTTTCAATTCGCTCCTCCGTATATCATT
*
1676 CTGGAAGACGA
194 C-GAAAGACGA
*
1687 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGTTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCAG
* *
1752 TGTCTCATCAGGAAGCTAGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGATCTTCTTCT
66 TGTCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* *
1817 CAGTGTCTCATCAGG-AGATGATTACATTACTGTTTGTTTT-AATTCGCTCCTCCGTATCTCATT
130 CAGTGTCTCATCAGGAAGATGATTACATCACTGTTT-TTTTCAATTCGCTCCTCCGTATATCATT
1880 CGAAAGACGA
194 CGAAAGACGA
*
1890 ATTTGGTTCACTTCTCAA-TACCTCATCAGGAAGTTAACCTTATATTGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCT-AAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCA
*
1954 GTGTCTCATCAGGAAGCTGGGGTTGAAAGACTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTTC
65 GTGTCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
2019 TCAGTGTCTCATCAGGAAGATGA
129 TCAGTGTCTCATCAGGAAGATGA
2042 CCGCGTCGTT
Statistics
Matches: 320, Mismatches: 29, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
203 229 0.72
204 91 0.28
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (203 bp):
ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAGGAAGCTGGGGTTAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGATTACATCACTGTTTTTTTCAATTCGCTCCTCCGTATATCATTCG
AAAGACGA
Found at i:2112 original size:37 final size:37
Alignment explanation
Indices: 2061--2209 Score: 127
Period size: 37 Copynumber: 3.7 Consensus size: 37
2051 TCGTTTCAAC
* *
2061 TCACTTCTCTGTATCTTATCAGGAAGGCGGATTTGGT
1 TCACTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
* *
2098 TCACTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTT
1 TCACTTCTCAGTATCTCATCAGGAAG--G-C-G-G--ATTTGGT
* * *
2142 TCAACTCGCTTCTCTGTATCTCCTCAGGAAGGCGAATTTGGT
1 TC-A----CTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
2184 TCACTTCTCAGTATCTCATCAGGAAG
1 TCACTTCTCAGTATCTCATCAGGAAG
2210 CTAACCTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
37 45 0.51
39 1 0.01
40 1 0.01
41 2 0.02
42 8 0.09
44 7 0.08
45 2 0.02
46 1 0.01
47 1 0.01
49 21 0.24
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (37 bp):
TCACTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
Found at i:2160 original size:86 final size:86
Alignment explanation
Indices: 2015--2209 Score: 327
Period size: 86 Copynumber: 2.3 Consensus size: 86
2005 TTTGGGTCTT
* *
2015 CTTCTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTTAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
*
2080 CAGGAAGGCGGATTTGGTTCA
66 CAGGAAGGCGAATTTGGTTCA
* * * *
2101 CTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
2166 CAGGAAGGCGAATTTGGTTCA
66 CAGGAAGGCGAATTTGGTTCA
2187 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
2210 CTAACCTTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (86 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
CAGGAAGGCGAATTTGGTTCA
Found at i:2172 original size:203 final size:198
Alignment explanation
Indices: 1483--2123 Score: 741
Period size: 203 Copynumber: 3.2 Consensus size: 198
1473 TTTCATCAGG
* * ** * * *
1483 ATTTGGTTCACTTCTCGGTATCTCATCAGGGGGCTAACCACTT-TATGGCTTCGACCTGCTTCTC
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAA-C-CTTATATTGTTTCGACCTGCTTCTC
* ** * *
1547 AGCATCTCATCAGGAAGCTGGGGTTAGAAGA-TTTGCTCGTTTTGAGCCTCGTTTGGGTATTTTT
64 AGTATCTCATCAGGAAGCTGGGGTTA-AAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTT
* * * *
1611 TTCAGTGCCTCATCAGGAAGATGATTACATCGCT-GTTTTTTTCAATTCGCTCCTCCGTATATCA
128 CTCAGTGTCTCATCAGGAAGATG---AC--CGCTCGTTTGTTTCAATTCGCTCCTCCGTATCTCA
1675 TCTGGAAGACGA
188 TC-GGAAGACGA
* *
1687 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGTTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
* * *
1752 TGTCTCATCAGGAAGCTAGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGATCTTCTTCT
66 TATCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* ** *
1817 CAGTGTCTCATCAGG-AGATGATTACATTACTGTTTGTTTTAATTCGCTCCTCCGTATCTCATTC
130 CAGTGTCTCATCAGGAAGATGA--CCGCT-C-GTTTGTTTCAATTCGCTCCTCCGTATCTCA-TC
*
1881 GAAAGACGA
190 GGAAGACGA
* *
1890 ATTTGGTTCACTTCTCAATACCTCATCAGGAAGTTAACCTTATATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
* *
1955 TGTCTCATCAGGAAGCTGGGGTTGAAAGACTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTTCT
66 TATCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* * * * * *
2020 CAGTGTCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTTATCAGGA
130 CAGTGTCTCATCAGGAAGATGACCGC-TCGTTTGTTTCAATTCGCTCCTCCGTATCTCATC-GGA
* *
2085 AGGCGG
193 AGACGA
*
2091 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAG
2124 ATGACTGCGT
Statistics
Matches: 377, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
200 5 0.01
201 60 0.16
202 5 0.01
203 224 0.59
204 83 0.22
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (198 bp):
ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
TATCTCATCAGGAAGCTGGGGTTAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGACCGCTCGTTTGTTTCAATTCGCTCCTCCGTATCTCATCGGAAGA
CGA
Done.