Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010372.1 Kokia drynarioides strain JFW-HI SEQ_125245, 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: 2762
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.22
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:1685 original size:199 final size:204
Alignment explanation
Indices: 1296--1975 Score: 792
Period size: 199 Copynumber: 3.4 Consensus size: 204
1286 TCCTGACCAT
* * * * * ** *
1296 CTTCCCGATGAGGTACAGAGAAGTGGACCAGATTCGTTTTCCTGATGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * * * * * *
1361 TGGAGCAGACGACGCGGTCGTCTTCCTGATGAGATATTGAGAAGAAGACC---CCAAA-CAAGGC
66 TGAAACAAACGGCGCGG--ATCTTACTGATGAGATACTGAGAAAAAGACCAAACCAAACCCACGC
* * * * * * *
1422 T-TAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGACACACCGAGAAGCAGGTGGAAGCA
129 TCGACA-TGAGCAAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
*
1486 ATAAATGGTTAG
193 ATAAAAGGTTAG
**
1498 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATGTAGAGAAGC-GAG
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGA-
*
1562 TTGAAACAAAC-G-GC-G-TCTTACTGATGAGATACTGAGAAAAAGACCAAACTAAACCCACGCT
65 TTGAAACAAACGGCGCGGATCTTACTGATGAGATACTGAGAAAAAGACCAAACCAAACCCACGCT
** * * * *
1623 CGATC-TGAGC-AGGTCTTCGGATCCTAGCTTCCGGATGACACACCAAGAAGCAGATCGAAGCAA
130 CGA-CATGAGCAAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCAA
*
1686 TAAACGGTTAG
194 TAAAAGGTTAG
* *
1697 CTTCCTGATGAGATACGGAGAAGT-ATACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
1 CTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGA
* * *
1761 TTGAAACAAACGGCGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATG
65 TTGAAACAAACGGCGCGG--ATCTTACTGATGAGATACTGAGAAAAAGACCAAACCAAACCCACG
* *
1826 CTCGACATTAGCAAAATCTTTGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
128 CTCGACATGAGCAAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
1891 ATAAAAGGTTAG
193 ATAAAAGGTTAG
* *
1903 CTTCCTGATGAGATACTAAGAATTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
1968 TGAAACAA
66 TGAAACAA
1976 TAATGGGATC
Statistics
Matches: 406, Mismatches: 54, Indels: 32
0.83 0.11 0.07
Matches are distributed among these distances:
196 27 0.07
198 1 0.00
199 124 0.31
200 15 0.04
201 4 0.01
202 61 0.15
204 1 0.00
205 49 0.12
206 123 0.30
207 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (204 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAACGGCGCGGATCTTACTGATGAGATACTGAGAAAAAGACCAAACCAAACCCACGCTC
GACATGAGCAAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCAATA
AAAGGTTAG
Found at i:1911 original size:206 final size:204
Alignment explanation
Indices: 1296--2021 Score: 850
Period size: 206 Copynumber: 3.6 Consensus size: 204
1286 TCCTGACCAT
* * * * * ** *
1296 CTTCCCGATGAGGTACAGAGAAGTGGACCAGATTCGTTTTCCTGATGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * * * *
1361 TGGAGCAGACGACGCGGTCGTCTTCCTGATGAGATATTGAGAAGAAGACC---CCAAA-CAAGGC
66 TGAAACAAACG-GGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGC
* * * * * *
1422 T-TAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGACACACCGAGAAGCAGGTGGAAGCA
130 TCGACA-TGAGC-AAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
*
1486 ATAAATGGTTAG
193 ATAAAAGGTTAG
**
1498 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATGTAGAGAAGC-GAG
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGA-
* * *
1562 TTGAAACAAAC-GGC-G---TCTTACTGATGAGATACTGAGAAAAAGACCAAACTAAACCCACGC
65 TTGAAACAAACGGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGC
** * * * *
1622 TCGATC-TGAGCAGGTCTTCGGATCCTAGCTTCCGGATGACACACCAAGAAGCAGATCGAAGCAA
130 TCGA-CATGAGCAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCAA
*
1686 TAAACGGTTAG
194 TAAAAGGTTAG
* *
1697 CTTCCTGATGAGATACGGAGAAGT-ATACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
1 CTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGA
*
1761 TTGAAACAAACGGCGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATG
65 TTGAAACAAACGG-GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACG
* *
1826 CTCGACATTAGCAAAATCTTTGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
129 CTCGACATGAGC-AAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCA
1891 ATAAAAGGTTAG
193 ATAAAAGGTTAG
* *
1903 CTTCCTGATGAGATACTAAGAATTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
** * *
1968 TGAAACAATAATGG-GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC
66 TGAAACAA-ACGGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA-CCAAAC
2022 GAGGCTCGAA
Statistics
Matches: 446, Mismatches: 58, Indels: 36
0.83 0.11 0.07
Matches are distributed among these distances:
196 27 0.06
198 1 0.00
199 124 0.28
200 15 0.03
201 4 0.01
202 61 0.14
204 1 0.00
205 80 0.18
206 130 0.29
207 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (204 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAACGGGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCT
CGACATGAGCAAATCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGAAGCAATA
AAAGGTTAG
Found at i:2103 original size:139 final size:139
Alignment explanation
Indices: 1903--2342 Score: 718
Period size: 139 Copynumber: 3.2 Consensus size: 139
1893 AAAAGGTTAG
* * *
1903 CTTCCTGATGAGATACTAAGAATTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
*
1968 TGAAACAATAATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
66 TGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
2033 CGAGCAAAT
131 CGAGCAAAT
* * * *
2042 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATACACCTTCCTGATGAGATACAGAAAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
* * *
2107 TGGAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCAAAA
66 TGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
*
2172 CGAGCGAAT
131 CGAGCAAAT
* *
2181 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGCCTTCCCGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
* * *
2246 TGAAACAGTGATGGGATCATCTTCCTGGTGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
66 TGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
2311 CGAGCAAAT
131 CGAGCAAAT
*
2320 CTTCCAGATGAGACACTGAGAAG
1 CTTCCAGATGAGATACTGAGAAG
2343 CAGGTCGAAG
Statistics
Matches: 276, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
139 276 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (139 bp):
CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
CGAGCAAAT
Done.