Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004652.1 Kokia drynarioides strain JFW-HI SEQ_118183, 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: 8804
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:254 original size:123 final size:122
Alignment explanation
Indices: 20--446 Score: 545
Period size: 123 Copynumber: 3.5 Consensus size: 122
10 ACACGAAGAA
* * *
20 TAAAAAAACGAATGACTTAATTGTATTAATCGGATCCGATATGTTATTACTTAAAAAAAAAAAAA
1 TAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTT--AAAAAAAAAAA
* * * *
85 TGC-CTTTAAAAAAATAACTTGAAACCCTGAACATGAGCTATGAAATAAATATGAACAG
64 TGCTTTTTAAAAAATTAACTTGAAACCCTGAACATGAACTATAAAATAAATATGAACAG
* * *
143 TAGAAAAATGAACGAGTTAATTATATTAATCGGATCCGATATGTAATTACTTAAAAAAAGAAAAT
1 TAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTTAAAAAAA-AAAAT
* * * * * *
208 GTCTTTTTTAAAAATTGACTCGAAACCCTGAA-ATGAACTATAAAATAAACATGAAGAA
65 G-CTTTTTAAAAAATTAACTTGAAACCCTGAACATGAACTATAAAATAAATATGAACAG
* * * *
266 TAAAAAAATAAATGAGTTAATTGTATTAATCGGATCCGATATTTAATTACTTAAAAAAAAATA-C
1 TAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTTAAAAAAAAAAATG
* * * *
330 CTTTTAAAAAAATTAACTTGAAACTCTGAACATGAACTATAATATAAATATAAACAG
66 CTTTTTAAAAAATTAACTTGAAACCCTGAACATGAACTATAAAATAAATATGAACAG
* * * *
387 TAAAAAAATGAATGAATTAATTTTATTAATCAGATCCGATATATAATTACTTAAAAAAAA
1 TAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTTAAAAAAAA
447 TACCTTCTTA
Statistics
Matches: 262, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
120 25 0.10
121 83 0.32
122 9 0.03
123 122 0.47
124 23 0.09
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.30
Consensus pattern (122 bp):
TAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTTAAAAAAAAAAATG
CTTTTTAAAAAATTAACTTGAAACCCTGAACATGAACTATAAAATAAATATGAACAG
Found at i:436 original size:244 final size:243
Alignment explanation
Indices: 1--445 Score: 671
Period size: 244 Copynumber: 1.8 Consensus size: 243
* *
1 ATAAAATAGACACGAAGAATAAAAAAACGAATGACTTAATTGTATTAATCGGATCCGATATGTTA
1 ATAAAATAAACACGAAGAATAAAAAAACAAATGACTTAATTGTATTAATCGGATCCGATATGTTA
* *
66 TTACTTAAAAAAAAAAAAATGCCTTTAAAAAAATAACTTGAAACCCTGAACATGAGCTATGAAAT
66 TTACTT---AAAAAAAAAATACCTTTAAAAAAATAACTTGAAACCCTGAACATGAACTATGAAAT
* * * * *
131 AAATATGAACAGTAGAAAAATGAACGAGTTAATTATATTAATCGGATCCGATATGTAATTACTTA
128 AAATATAAACAGTAAAAAAATGAACGAATTAATTATATTAATCAGATCCGATATATAATTACTTA
196 AAAAAAGAAAATGTCTTTTTTAAAAATTGACTCGAAACCCTGAAATGAACT
193 AAAAAAGAAAATGTCTTTTTTAAAAATTGACTCGAAACCCTGAAATGAACT
* * *
247 ATAAAATAAACATGAAGAATAAAAAAATAAATGAGTTAATTGTATTAATCGGATCCGATAT-TTA
1 ATAAAATAAACACGAAGAATAAAAAAACAAATGACTTAATTGTATTAATCGGATCCGATATGTT-
*
311 ATTACTT-AAAAAAAAATACCTTTTAAAAAAATTAACTTGAAACTCTGAACATGAACTAT-AATA
65 ATTACTTAAAAAAAAAATACC-TTTAAAAAAA-TAACTTGAAACCCTGAACATGAACTATGAA-A
* *
374 TAAATATAAACAGTAAAAAAATGAATGAATTAATTTTATTAATCAGATCCGATATATAATTACTT
127 TAAATATAAACAGTAAAAAAATGAACGAATTAATTATATTAATCAGATCCGATATATAATTACTT
439 AAAAAAA
192 AAAAAAA
446 ATACCTTCTT
Statistics
Matches: 180, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
242 12 0.07
243 12 0.07
244 91 0.51
245 2 0.01
246 63 0.35
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (243 bp):
ATAAAATAAACACGAAGAATAAAAAAACAAATGACTTAATTGTATTAATCGGATCCGATATGTTA
TTACTTAAAAAAAAAATACCTTTAAAAAAATAACTTGAAACCCTGAACATGAACTATGAAATAAA
TATAAACAGTAAAAAAATGAACGAATTAATTATATTAATCAGATCCGATATATAATTACTTAAAA
AAAGAAAATGTCTTTTTTAAAAATTGACTCGAAACCCTGAAATGAACT
Found at i:5381 original size:19 final size:20
Alignment explanation
Indices: 5357--5400 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5347 AGGAACTTGC
5357 CTTGTGGA-AAAGCTAACCA
1 CTTGTGGAGAAAGCTAACCA
**
5376 CTTGT-GAGATCGCTAACCA
1 CTTGTGGAGAAAGCTAACCA
5395 CTTGTG
1 CTTGTG
5401 AGATCTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (20 bp):
CTTGTGGAGAAAGCTAACCA
Found at i:5401 original size:19 final size:19
Alignment explanation
Indices: 5368--5405 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5358 TTGTGGAAAA
5368 GCTAACCACTTGTGAGATC
1 GCTAACCACTTGTGAGATC
5387 GCTAACCACTTGTGAGATC
1 GCTAACCACTTGTGAGATC
5406 TATTCCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
GCTAACCACTTGTGAGATC
Found at i:6602 original size:19 final size:19
Alignment explanation
Indices: 6570--6607 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6560 ATTTTTATTT
* *
6570 TAAATTTAATTATAAAATA
1 TAAATATAAATATAAAATA
6589 TAAATATAAATATAAAATA
1 TAAATATAAATATAAAATA
6608 ATATAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATATAAATATAAAATA
Done.