Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013194.1 Kokia drynarioides strain JFW-HI SEQ_128213, 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: 31311
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:24719 original size:31 final size:30
Alignment explanation
Indices: 24679--24753 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 30
24669 GGTTAAGTAG
*
24679 ATTTTTTAAAATTATAAT-AAAA-AATACATAA
1 ATTTATTAAAATTA-AATGAAAATAAT--ATAA
24710 ATTTATTAAATATTAAATGAAAATAATATAA
1 ATTTATTAAA-ATTAAATGAAAATAATATAA
* *
24741 TTTTAATAAAATT
1 ATTTATTAAAATT
24754 TAAAAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 3 0.08
31 24 0.63
32 8 0.21
33 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
ATTTATTAAAATTAAATGAAAATAATATAA
Found at i:27191 original size:114 final size:117
Alignment explanation
Indices: 26941--27328 Score: 353
Period size: 122 Copynumber: 3.3 Consensus size: 117
26931 TAAAAAATAC
* * * * ** * * **
26941 AATTTTTTTGTGTTGGCCATGCAATGGCCGACATCCCATTTT-GAGAAAAAAAAATTGCATTTTT
1 AATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCCCTTTTCTCGGATAAAAAATTGCAAATTT
* * * * * * *
27005 GGGTGTTGACCATTCGATGGCCGACACCTC-CTTTTTCAGA-AAAAAAAATTCAA
66 --GTGTTGGCCATACAATGGTCGACACC-CAATTTTTCACATAAAAAAATTTCAA
* * *
27058 AATTTTCTGAG-GTTAGCCATGCAATGGCTGACACCCTCTTTTCTCGGATAAAAATATTGCAAA-
1 AATTTTTTG-GTGTTAGCCATGCAATGGCCGACACCCCCTTTTCTCGGATAAAAA-ATTGCAAAT
*
27121 TT-T-TT-GCCATACAATGGTCGACACCCAATTTTTCACATAAAAAATTTTCAA
64 TTGTGTTGGCCATACAATGGTCGACACCCAATTTTTCACATAAAAAAATTTCAA
* * *
27172 AATTTTTTGGTGTTTGCCATGCAATGGCCGATACCCCCTTTTCTCGGATAAAAAATTGTAAATTT
1 AATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCCCTTTTCTCGGATAAAAAATTGCAAA---
* **
27237 TTTTTGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTCACATAAAAAAAATTT-AA
63 --TTTGTGTTGGCCATACAATGGTCGACACCCAATTTTTCACAT-AAAAAAATTTCAA
* *
27294 AATTTTTTGGTGTTGGTCATGCAATGGCCGACACC
1 AATTTTTTGGTGTTAGCCATGCAATGGCCGACACC
27329 AACTTCCCTT
Statistics
Matches: 221, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
112 1 0.00
113 32 0.14
114 60 0.27
115 1 0.00
117 33 0.15
118 10 0.05
119 8 0.04
120 1 0.00
121 2 0.01
122 64 0.29
123 9 0.04
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (117 bp):
AATTTTTTGGTGTTAGCCATGCAATGGCCGACACCCCCTTTTCTCGGATAAAAAATTGCAAATTT
GTGTTGGCCATACAATGGTCGACACCCAATTTTTCACATAAAAAAATTTCAA
Found at i:27225 original size:61 final size:60
Alignment explanation
Indices: 27126--27328 Score: 253
Period size: 61 Copynumber: 3.3 Consensus size: 60
27116 GCAAATTTTT
* * ** *
27126 GCCATACAATGGTCGACACCCAATTTTTCACATAAAAAATTTTCAAAATTTTTTGGTGTTT
1 GCCATGCAATGGCCGACACCCCCTTTTTCACATAAAAAATTTT-AAAATTTTTTGGTGTTG
* ** * * *
27187 GCCATGCAATGGCCGATACCCCCTTTTCTCGGATAAAAAATTGTAAATTTTTTTTGTGTTG
1 GCCATGCAATGGCCGACACCCCCTTTT-TCACATAAAAAATTTTAAAATTTTTTGGTGTTG
* *
27248 GCCATGCAATGGTCGACACCCCCTTTTTCACATAAAAAAAATTTAAAATTTTTTGGTGTTG
1 GCCATGCAATGGCCGACACCCCCTTTTTCACAT-AAAAAATTTTAAAATTTTTTGGTGTTG
*
27309 GTCATGCAATGGCCGACACC
1 GCCATGCAATGGCCGACACC
27329 AACTTCCCTT
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
60 4 0.03
61 102 0.86
62 13 0.11
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (60 bp):
GCCATGCAATGGCCGACACCCCCTTTTTCACATAAAAAATTTTAAAATTTTTTGGTGTTG
Done.