Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009888.1 Kokia drynarioides strain JFW-HI SEQ_124624, 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: 6231
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Found at i:793 original size:23 final size:24
Alignment explanation
Indices: 762--814 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
752 AGCTTTGGAC
*
762 ATTTTATTTGTAATTT-AACTTTG
1 ATTTAATTTGTAATTTGAACTTTG
*
785 ATTTAATTTGTAATTTGGACTTTG
1 ATTTAATTTGTAATTTGAACTTTG
809 ATTTAA
1 ATTTAA
815 ATAGATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (24 bp):
ATTTAATTTGTAATTTGAACTTTG
Found at i:847 original size:17 final size:17
Alignment explanation
Indices: 822--883 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
812 TAAATAGATT
*
822 TAAACTTAAATTTATAA
1 TAAATTTAAATTTATAA
839 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
855 GTAAATTTAATTTTAAAA
1 -TAAATTTAAATTTATAA
873 TAAATTTAAAT
1 TAAATTTAAAT
884 CCTGTTGGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.08
17 34 0.87
18 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:1299 original size:37 final size:37
Alignment explanation
Indices: 1249--1319 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1239 CATATCACTT
* * *
1249 GTTTTGATCCACTTCTCTGTGTTTCATCAGGAAGATG
1 GTTTTGATCCACTTCACCGTATTTCATCAGGAAGATG
* *
1286 GTTTTGGTTCACTTCACCGTATTTCATCAGGAAG
1 GTTTTGATCCACTTCACCGTATTTCATCAGGAAG
1320 CTAACCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (37 bp):
GTTTTGATCCACTTCACCGTATTTCATCAGGAAGATG
Found at i:1846 original size:205 final size:206
Alignment explanation
Indices: 1208--2072 Score: 1184
Period size: 205 Copynumber: 4.2 Consensus size: 206
1198 TTGACTTGAC
* *** * ** * * *
1208 CTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTCTCTGTGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGTATCT
* * ** * * * *
1273 CATCAGGAAGATGGTTTTGGTTCACTTCACCGTATTTCATCAGGAAGCTAACCATTTTATTACTT
66 CATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
*
1338 CGACCTGCTTCTTAGTATCTAATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
131 CGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
1403 TTTGATTTGGT
196 TTTGATTTGGT
* * *
1414 CTTCTCTACTC--TGTCTCATCAGGAAGATGATCGCGTCATTTGTTTCAATCCGCTTCTCTGTAC
1 CTTCT-T-CTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGTAT
* * * * *
1477 CTCAACAGGAAGACGAATTTGGTTCACTTCTCACTATCTCGTCAGGAAGCTAACCATTTTATTAC
64 CTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTAC
* * * * * * *
1542 TTCAAACTGCTTCTCAGTATCTTATCAAGAAGCTGGGGTTCGAGGATTTGCTCACATCGAGCGTA
129 TTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG
1607 GGTTTGATTTGGT
194 GGTTTGATTTGGT
* * *
1620 CTTCTTCTAAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGTATTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGTATCT
*
1685 CATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTT
66 CATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
* *
1749 CGACCTGCTTCTTAGTGTTTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
131 CGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
1814 TTTGATTTGGT
196 TTTGATTTGGT
* * *
1825 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTATATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGTATCT
* *
1890 CATCA-AGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCT
66 CATCAGA-AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT
* *
1953 TCGACCTGCTT-TTCAATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG
130 TCGACCTGCTTCTT-AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG
*
2017 GGTTTGATTAGGT
194 GGTTTGATTTGGT
* * * *
2030 CTTATTCTCAATATCTCATCAGGAAGATGACCGCTTCGTTTGT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGT
2073 GGATAATCGC
Statistics
Matches: 592, Mismatches: 61, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
204 5 0.01
205 310 0.52
206 273 0.46
207 1 0.00
208 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTTCTCTGTATCT
CATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
CGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
TTTGATTTGGT
Done.