Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009773.1 Kokia drynarioides strain JFW-HI SEQ_124494, 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: 6713
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1807 original size:28 final size:28
Alignment explanation
Indices: 1774--1948 Score: 117
Period size: 28 Copynumber: 6.2 Consensus size: 28
1764 ATTTTGAATT
1774 TGGCTCGGATAGAGCGTTACTCTATTTC
1 TGGCTCGGATAGAGCGTTACTCTATTTC
* * * * *
1802 TAGCTC-GAGTAAAGCATTATTCTATTTT
1 TGGCTCGGA-TAGAGCGTTACTCTATTTC
* * *
1830 TGGCTC-GAGTAAAGCATTACTCCATTTC
1 TGGCTCGGA-TAGAGCGTTACTCTATTTC
* * *
1858 TGGCTCAGG-TAGAGCGTTATTCTGTTTT
1 TGGCTC-GGATAGAGCGTTACTCTATTTC
* * *
1886 TGGCTTGGGTAGAGCGTTAAT-T-TGTTC
1 TGGCTCGGATAGAGCGTTACTCTAT-TTC
* * *
1913 TAGCTCGGAAAGAGCGTTACTCTATATC
1 TGGCTCGGATAGAGCGTTACTCTATTTC
1941 TGGGCTCG
1 T-GGCTCG
1949 AATGAACTAT
Statistics
Matches: 114, Mismatches: 25, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
26 1 0.01
27 23 0.20
28 83 0.73
29 6 0.05
30 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (28 bp):
TGGCTCGGATAGAGCGTTACTCTATTTC
Found at i:1857 original size:56 final size:56
Alignment explanation
Indices: 1772--1890 Score: 143
Period size: 56 Copynumber: 2.1 Consensus size: 56
1762 ATATTTTGAA
* * *
1772 TTTGGCTCGGATAGAGCGTTACTCTATTTCTAGCTC-GAGTAAAGCATTATTCTATT
1 TTTGGCTCGGATAAAGCATTACTCCATTTCTAGCTCAG-GTAAAGCATTATTCTATT
* * * *
1828 TTTGGCTC-GAGTAAAGCATTACTCCATTTCTGGCTCAGGTAGAGCGTTATTCTGTT
1 TTTGGCTCGGA-TAAAGCATTACTCCATTTCTAGCTCAGGTAAAGCATTATTCTATT
1884 TTTGGCT
1 TTTGGCT
1891 TGGGTAGAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 2 0.04
56 51 0.94
57 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (56 bp):
TTTGGCTCGGATAAAGCATTACTCCATTTCTAGCTCAGGTAAAGCATTATTCTATT
Found at i:4311 original size:42 final size:42
Alignment explanation
Indices: 4175--4361 Score: 189
Period size: 43 Copynumber: 4.4 Consensus size: 42
4165 AATCGCGACG
4175 CTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCA
1 CTTTTCCCACAAACG-CGCTAAAGAACATGGTCTTTAGCGGCA
* *
4218 C-TTACCTCACAAACGCTGCTGAAGAACATGGTCTTTAGCGGCA
1 CTTTTCC-CACAAACGC-GCTAAAGAACATGGTCTTTAGCGGCA
* * * *
4261 CTTATCCCACAAATGTCGCTAAAGAATA-GGTCTTTAGCGGCG
1 CTTTTCCCACAAACG-CGCTAAAGAACATGGTCTTTAGCGGCA
* * * * * * *
4303 CTTTTCCCACAAACACCGCAAAAGAACATGATTTTTAGTGACG
1 CTTTTCCCACAAAC-GCGCTAAAGAACATGGTCTTTAGCGGCA
*
4346 TTTTTCCCACAAACGC
1 CTTTTCCCACAAACGC
4362 CACTAAAACT
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
42 41 0.34
43 74 0.62
44 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
CTTTTCCCACAAACGCGCTAAAGAACATGGTCTTTAGCGGCA
Found at i:4340 original size:85 final size:86
Alignment explanation
Indices: 4179--4368 Score: 204
Period size: 85 Copynumber: 2.2 Consensus size: 86
4169 GCGACGCTTT
* * **
4179 TCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTACCTCACAAACGCTGCTGAAGAA
1 TCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTACCTCACAAACACCGCAAAAGAA
*
4244 CATGGTCTTTAGCGGCACTTA
66 CATGATCTTTAGCGGCACTTA
* * * * *
4265 TCCCACAAATGTCGCTAAAGAATA-GGTCTTTAGCGGCGCTTTTCC-CACAAACACCGCAAAAGA
1 TCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCAC-TTACCTCACAAACACCGCAAAAGA
* * * ** *
4328 ACATGATTTTTAGTGACGTTTT
65 ACATGATCTTTAGCGGCACTTA
*
4350 TCCCACAAACGCCACTAAA
1 TCCCACAAACGCCGCTAAA
4369 ACTTGAATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
85 59 0.70
86 25 0.30
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (86 bp):
TCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTACCTCACAAACACCGCAAAAGAA
CATGATCTTTAGCGGCACTTA
Found at i:4876 original size:164 final size:166
Alignment explanation
Indices: 4599--4929 Score: 607
Period size: 164 Copynumber: 2.0 Consensus size: 166
4589 ACACTCGAAT
4599 TACCAAAAAAAAACAAATATTCTTAACAAAATTGAAACAAAATAAAAAATAAAAAACATCATCAA
1 TACCAAAAAAAAACAAATATTCTTAACAAAATTGAAACAAAATAAAAAATAAAAAACATCATCAA
*
4664 TTATTCCTAATGCTTAATTGCAAGGTCCTTCTTATAGCACATAATTGAAGATCATCTCCACAAGT
66 TTATTCCTAATGCTTAATTGCAAGGTCCTTCTTATAGCACAGAATTGAAGATCATCTCCACAAGT
4729 TCCTGCAACAACAAAAACAATATAATCATTTTCAAA
131 TCCTGCAACAACAAAAACAATATAATCATTTTCAAA
4765 TACCAAAAAAAAAACAAATATTCTTAACAAAATTGAAACAAAA-AGAAAAAT-AAAAA-A-CATC
1 TACC-AAAAAAAAACAAATATTCTTAACAAAATTGAAACAAAATA-AAAAATAAAAAACATCATC
4826 AATTATTCCTAATGCTTAATTGCAAGGTCCTTCTTATAGCACAGAATTGAAGATCATCTCCACAA
64 AATTATTCCTAATGCTTAATTGCAAGGTCCTTCTTATAGCACAGAATTGAAGATCATCTCCACAA
4891 GTTCCTGCAACAACAAAAACAATATAATCATTTTCAAA
129 GTTCCTGCAACAACAAAAACAATATAATCATTTTCAAA
4929 T
1 T
4930 TTGATTTGGG
Statistics
Matches: 162, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
164 107 0.66
165 1 0.01
166 10 0.06
167 44 0.27
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (166 bp):
TACCAAAAAAAAACAAATATTCTTAACAAAATTGAAACAAAATAAAAAATAAAAAACATCATCAA
TTATTCCTAATGCTTAATTGCAAGGTCCTTCTTATAGCACAGAATTGAAGATCATCTCCACAAGT
TCCTGCAACAACAAAAACAATATAATCATTTTCAAA
Done.