Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015055.1 Kokia drynarioides strain JFW-HI SEQ_130099, 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: 16424
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 167 characters in sequence are not A, C, G, or T
Found at i:9042 original size:60 final size:62
Alignment explanation
Indices: 8907--9223 Score: 273
Period size: 60 Copynumber: 5.3 Consensus size: 62
8897 GCCAACACCT
* * ** * * * *
8907 TTTTTTGTCAGATAAAAAATA-CATTTTTTTTTGTGTTGGCCATACAATGGCCGACA--CTC
1 TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
* * * * *
8966 TTATTTATCTGATAAAAAAAATCAAATTTTTT-GTGTTGGTCATGCAAT-GTCGACACCCGC
1 TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
* ** ** * * *
9026 TTTTTTATCAG-T-TAAAATTTTTAATTTTTTGGTGTTAACCATGCAATGGTCGACACCCCC
1 TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
* * ** *
9086 TTTTTTATCAG-T-TAAAAATTTTAATTTTTTGGTGTTAGCCATGCAATGGCCAACACCC-C
1 TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
* *
9145 -TATTTATCTGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACA-CCGC
1 TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
* *
9205 -CTTTTCTCAGATAAAAAAA
1 TTTTTTATCAGATAAAAAAA
9224 TTTCATGGCC
Statistics
Matches: 214, Mismatches: 36, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
58 27 0.13
59 49 0.23
60 138 0.64
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (62 bp):
TTTTTTATCAGATAAAAAAAATCAAATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCGC
Found at i:9338 original size:59 final size:61
Alignment explanation
Indices: 9227--9378 Score: 182
Period size: 59 Copynumber: 2.5 Consensus size: 61
9217 AAAAAAATTT
** * * * *
9227 CATGGCCAACACCCAAAAATTTGATTTTTTTTTTATCAGATAAATAGAGGTGTCAGTCATTG
1 CATGGCCAACACAAAAAAAATTG-TATTTTTTTTATCAAATAAATAGAGGTGTCAGCCATTG
* * *
9289 CATGGCCAACA-GAAAAAAATTG-ATTTTTTTTATCAAATAAATAGGGGTGTCGGCCATTG
1 CATGGCCAACACAAAAAAAATTGTATTTTTTTTATCAAATAAATAGAGGTGTCAGCCATTG
* *
9348 TATGTCCAACACAAAAAAAATTGTATTTTTT
1 CATGGCCAACACAAAAAAAATTGTATTTTTT
9379 ATCTGACAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 41 0.53
60 10 0.13
61 15 0.19
62 11 0.14
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (61 bp):
CATGGCCAACACAAAAAAAATTGTATTTTTTTTATCAAATAAATAGAGGTGTCAGCCATTG
Found at i:9379 original size:59 final size:59
Alignment explanation
Indices: 9255--9404 Score: 185
Period size: 59 Copynumber: 2.5 Consensus size: 59
9245 ATTTGATTTT
* * * * *
9255 TTTTTTATCAGATAAATAGAGGTGTCAGTCATTGCATGGCCAACAGAAAAAAATTGATT
1 TTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCCAACAAAAAAAAATTGATA
* * *
9314 TTTTTTATCAAATAAATAGGGGTGTCGGCCATTGTATGTCCAACACAAAAAAAATTG-TA
1 TTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCCAACA-AAAAAAAATTGATA
* * *
9373 TTTTTTATCTGACAAAAAGGGGTGTCGGCCAT
1 TTTTTTATCAGATAAATAGGGGTGTCGGCCAT
9405 GCAAATTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 68 0.87
60 10 0.13
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (59 bp):
TTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCCAACAAAAAAAAATTGATA
Found at i:10401 original size:15 final size:16
Alignment explanation
Indices: 10375--10404 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10365 TAAATTTTTT
10375 TAAAATTTTAAATTAG
1 TAAAATTTTAAATTAG
10391 TAAAA-TTTAAATTA
1 TAAAATTTTAAATTA
10405 TACTTTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAATTTTAAATTAG
Found at i:13413 original size:228 final size:229
Alignment explanation
Indices: 12973--13426 Score: 709
Period size: 228 Copynumber: 2.0 Consensus size: 229
12963 TAACTAAGAG
* *
12973 TTAGTAGTTTTAATAAAGCAGCAGTAAAGTAAACAAGGCAATATTCTTCTCAAATTCTATCCATA
1 TTAGTAGTTTTAATAAAGCACCAGTAAACTAAACAAGGCAATATTCTTCTCAAATTCTATCCATA
* *
13038 ATTAGCAAATTGCATAGATTTCATGCATAAAGTAAAGAGAAGATCCCTGGAGAAAATAAAAACAT
66 ATTAGCAAATTACATAGATTTCATGCATAAAGTAAAGAGAAGAACCCTGGAGAAAATAAAAACAT
13103 GTGCCTTTCTTCTCAATGCCTTTGTATTATTGAGTTGATTACACTGTGATTTTCTCTAATTAATA
131 GTGCCTTTCTTCTCAATGCCTTTGTATTATTGAGTTGATTACACTGTGATTTTCTCTAATTAATA
13168 TAATCATGCCAAATATAAGCAACCTTACATTTTC
196 TAATCATGCCAAATATAAGCAACCTTACATTTTC
* *
13202 TTAGTAGTTTTAATAAAGCACCAGTGAACTAAAGAA-G-ATATATTCTTCTCAAATTCTATCCAT
1 TTAGTAGTTTTAATAAAGCACCAGTAAACTAAACAAGGCA-ATATTCTTCTCAAATTCTATCCAT
* * * * *
13265 ACTTAGCAAATTACATATATTTCATGCATGAAGTGATAAGA-AA-AACTCTGGAGAAAATAAATA
65 AATTAGCAAATTACATAGATTTCATGCATAAAGT-A-AAGAGAAGAACCCTGGAGAAAATAAAAA
** *
13328 CATGTGCCTTTCTTCTCAATGTTTTTGTATTATTGAGTTGATTAGACTGTGATTTTCTCTAATTA
128 CATGTGCCTTTCTTCTCAATGCCTTTGTATTATTGAGTTGATTACACTGTGATTTTCTCTAATTA
* *
13393 ATTTAATCATGCCCAATATAAGCAACCTTACATT
193 ATATAATCATGCCAAATATAAGCAACCTTACATT
13427 AATTCTATGA
Statistics
Matches: 206, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
227 1 0.00
228 166 0.81
229 35 0.17
230 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (229 bp):
TTAGTAGTTTTAATAAAGCACCAGTAAACTAAACAAGGCAATATTCTTCTCAAATTCTATCCATA
ATTAGCAAATTACATAGATTTCATGCATAAAGTAAAGAGAAGAACCCTGGAGAAAATAAAAACAT
GTGCCTTTCTTCTCAATGCCTTTGTATTATTGAGTTGATTACACTGTGATTTTCTCTAATTAATA
TAATCATGCCAAATATAAGCAACCTTACATTTTC
Done.