Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007528.1 Kokia drynarioides strain JFW-HI SEQ_122153, 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: 12633
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:1706 original size:21 final size:21
Alignment explanation
Indices: 1682--1735 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1672 AAGGGAAGTT
*
1682 CTACTGATACAAGTATAGGTA
1 CTACAGATACAAGTATAGGTA
*
1703 CTACCGATACAAGTATAGGTA
1 CTACAGATACAAGTATAGGTA
1724 CTACAGATACAA
1 CTACAGATACAA
1736 CCTATATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (21 bp):
CTACAGATACAAGTATAGGTA
Found at i:5841 original size:83 final size:83
Alignment explanation
Indices: 5696--5965 Score: 445
Period size: 83 Copynumber: 3.3 Consensus size: 83
5686 AACTCAATAT
*
5696 TTAAATGGAAGACTCATGTCTCGGGATGCGAATGAGATTATATTAAAAGGAAGACTCATGTCTTA
1 TTAAA-GGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTTA
5761 GGATGAGAATGAGATTATA
65 GGATGAGAATGAGATTATA
* **
5780 TTAAAGGAAGACTCATGTCTCGGGATGAGAATAAGATTATATTAAAAGGAAGACTCATGTCTCGG
1 TTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTTAG
5845 GATGAGAATGAGATTATA
66 GATGAGAATGAGATTATA
* *
5863 TTAAAGGAAGACTCATGTCTCAGGATGAGAATGCGATTATATT-AAAGGAAGACTCATGTCTCTA
1 TTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCT-TA
5927 -GATGAGAATGAGATTATA
65 GGATGAGAATGAGATTATA
*
5945 TTAAAGGAAGACCCATGTCTC
1 TTAAAGGAAGACTCATGTCTC
5966 AAAATGAGCA
Statistics
Matches: 175, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
82 56 0.32
83 114 0.65
84 5 0.03
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (83 bp):
TTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTTAG
GATGAGAATGAGATTATA
Found at i:5917 original size:124 final size:125
Alignment explanation
Indices: 5696--5965 Score: 454
Period size: 124 Copynumber: 2.2 Consensus size: 125
5686 AACTCAATAT
* * *
5696 TTAAATGGAAGACTCATGTCTCGGGATGCGAATGAGATTATATTAAAAGGAAGACTCATGTCTTA
1 TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTCA
*
5761 GGATGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCGGGATGAGAATAAGATTATA
66 GGATGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCGAGATGAGAATAAGATTATA
5821 TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATT-AAAGGAAGACTCATGTCTCA
1 TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTCA
* * *
5885 GGATGAGAATGCGATTATATTAAAGGAAGACTCATGTCTCTAGATGAGAATGAGATTATA
66 GGATGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCGAGATGAGAATAAGATTATA
*
5945 TT-AAAGGAAGACCCATGTCTC
1 TTAAAAGGAAGACTCATGTCTC
5966 AAAATGAGCA
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
123 18 0.13
124 77 0.56
125 42 0.31
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (125 bp):
TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATATTAAAAGGAAGACTCATGTCTCA
GGATGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCGAGATGAGAATAAGATTATA
Found at i:5979 original size:41 final size:41
Alignment explanation
Indices: 5696--5966 Score: 427
Period size: 41 Copynumber: 6.5 Consensus size: 41
5686 AACTCAATAT
* *
5696 TTAAATGGAAGACTCATGTCTCGGGATGCGAATGAGATTATA
1 TTAAA-GGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
*
5738 TTAAAAGGAAGACTCATGTCTTAGGATGAGAATGAGATTATA
1 TT-AAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
* *
5780 TTAAAGGAAGACTCATGTCTCGGGATGAGAATAAGATTATA
1 TTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
*
5821 TTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATA
1 TT-AAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
*
5863 TTAAAGGAAGACTCATGTCTCAGGATGAGAATGCGATTATA
1 TTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
5904 TTAAAGGAAGACTCATGTCTCTA-GATGAGAATGAGATTATA
1 TTAAAGGAAGACTCATGTCTC-AGGATGAGAATGAGATTATA
*
5945 TTAAAGGAAGACCCATGTCTCA
1 TTAAAGGAAGACTCATGTCTCA
5967 AAATGAGCAT
Statistics
Matches: 215, Mismatches: 11, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.00
41 133 0.62
42 78 0.36
43 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTATA
Found at i:7118 original size:158 final size:158
Alignment explanation
Indices: 6830--7150 Score: 597
Period size: 158 Copynumber: 2.0 Consensus size: 158
6820 GAAAAGATAA
*
6830 TTTTACCCTTTTTGAGTTATGTTAACTTTCAATTAATGATTCTTGTCGAGTTTATTACAATATTC
1 TTTTACCCTTTTTGAGTTATGTTAACTTTCAATTAATGATTCTTGTCAAGTTTATTACAATATTC
6895 TATAAAAATATGGTTAAATGAAACTATAATGTAAGATAAACTGCGATAGATGATCGAAAGGACAC
66 TATAAAAATATGGTTAAATGAAACTATAATGTAAGATAAACTGCGATAGATGATCGAAAGGACAC
6960 TAGGACCCTAACTAACGATGGTATTGAG
131 TAGGACCCTAACTAACGATGGTATTGAG
* *
6988 TTTTACCCTTTTTGAGTTATGTTGACTTTCAATTATTGATTCTTGTCAAGTTTATTACAATATTC
1 TTTTACCCTTTTTGAGTTATGTTAACTTTCAATTAATGATTCTTGTCAAGTTTATTACAATATTC
* *
7053 TATAAAAATATGGTTAAATGGAACTATAATGTAAGATAAACTGCGGTAGATGATCGAAAGGACAC
66 TATAAAAATATGGTTAAATGAAACTATAATGTAAGATAAACTGCGATAGATGATCGAAAGGACAC
7118 TAGGACCCTAACTAACGATGGTATTGAG
131 TAGGACCCTAACTAACGATGGTATTGAG
7146 TTTTA
1 TTTTA
7151 AGTGTTACAT
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (158 bp):
TTTTACCCTTTTTGAGTTATGTTAACTTTCAATTAATGATTCTTGTCAAGTTTATTACAATATTC
TATAAAAATATGGTTAAATGAAACTATAATGTAAGATAAACTGCGATAGATGATCGAAAGGACAC
TAGGACCCTAACTAACGATGGTATTGAG
Done.