Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006522.1 Kokia drynarioides strain JFW-HI SEQ_121106, 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: 35005
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:9989 original size:21 final size:21
Alignment explanation
Indices: 9949--10008 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
9939 AACTGTGTAG
* ** *
9949 ACTTCTACTGATACCTGTGAC
1 ACTTCTACCGATACAAGTGAA
*
9970 AGTTCTACCGATACAAGTGAA
1 ACTTCTACCGATACAAGTGAA
* *
9991 ACTTCTACCAAAACAAGT
1 ACTTCTACCGATACAAGT
10009 CATGCTTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAA
Found at i:19384 original size:19 final size:19
Alignment explanation
Indices: 19362--19402 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19352 TAAAATTTCT
19362 AAAATAT-TCAAAGTATAAA
1 AAAATATAT-AAAGTATAAA
*
19381 AAAATATATAAATTATAAA
1 AAAATATATAAAGTATAAA
19400 AAA
1 AAA
19403 GAGTTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATATATAAAGTATAAA
Found at i:23800 original size:40 final size:40
Alignment explanation
Indices: 23756--23936 Score: 168
Period size: 40 Copynumber: 4.5 Consensus size: 40
23746 TTGCTTATTG
* * **
23756 GCAGTGACACTGTAAACACTACAATATTATTACTGAACTA
1 GCAGTGACACTGTAAACACTGCAATATGACAACTGAACTA
* * *
23796 GCAGTGACATTATAAACACTGCAATATGACAACTGAACTG
1 GCAGTGACACTGTAAACACTGCAATATGACAACTGAACTA
* * * * *
23836 GTAATGACACTGTAAACACTTCAATATGACAACT-AATTG
1 GCAGTGACACTGTAAACACTGCAATATGACAACTGAACTA
* * * * *
23875 GCAGTGACACTATAAACACTGCACTATTACCA-TCGAACCA
1 GCAGTGACACTGTAAACACTGCAATATGACAACT-GAACTA
* *
23915 GCAGTGACACTGCAAATACTGC
1 GCAGTGACACTGTAAACACTGC
23937 TAGGTTATCA
Statistics
Matches: 113, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
38 1 0.01
39 29 0.26
40 83 0.73
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (40 bp):
GCAGTGACACTGTAAACACTGCAATATGACAACTGAACTA
Found at i:23923 original size:79 final size:80
Alignment explanation
Indices: 23756--23926 Score: 193
Period size: 79 Copynumber: 2.1 Consensus size: 80
23746 TTGCTTATTG
* ** *
23756 GCAGTGACACTGTAAACACTACAATATTATTACTGAACTAGCAGTGACATTATAAACACTGCAAT
1 GCAGTGACACTGTAAACACTACAATATGACAACTGAACTAGCAGTGACACTATAAACACTGCAAT
**
23821 ATGACAACTGAACTG
66 ATGACAACTGAACCA
* * * * * *
23836 GTAATGACACTGTAAACACTTCAATATGACAACT-AATTGGCAGTGACACTATAAACACTGCACT
1 GCAGTGACACTGTAAACACTACAATATGACAACTGAACTAGCAGTGACACTATAAACACTGCAAT
* *
23900 ATTACCA-TCGAACCA
66 ATGACAACT-GAACCA
23915 GCAGTGACACTG
1 GCAGTGACACTG
23927 CAAATACTGC
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
78 1 0.01
79 45 0.61
80 28 0.38
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (80 bp):
GCAGTGACACTGTAAACACTACAATATGACAACTGAACTAGCAGTGACACTATAAACACTGCAAT
ATGACAACTGAACCA
Found at i:29158 original size:15 final size:16
Alignment explanation
Indices: 29118--29172 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
29108 TAATGTTAAA
* *
29118 TTTAATTTTTAATATT
1 TTTAGTTTTTATTATT
* *
29134 TATATTTTTTATTCA-T
1 TTTAGTTTTTATT-ATT
29150 TTTAGTTTTTATTATT
1 TTTAGTTTTTATTATT
29166 TTTAGTT
1 TTTAGTT
29173 AAATTTTAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTAGTTTTTATTATT
Found at i:29329 original size:21 final size:20
Alignment explanation
Indices: 29295--29349 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
29285 TTCGTGCTAA
29295 TTTTATGAATTTTATGAACTCTT
1 TTTTAT-AATTTTAT-AA-TCTT
*
29318 TTTTATAA-TTTATAATTTT
1 TTTTATAATTTTATAATCTT
*
29337 TTTTATACTTTTA
1 TTTTATAATTTTA
29350 ATACTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 10 0.34
20 6 0.21
21 5 0.17
22 2 0.07
23 6 0.21
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTATAATCTT
Found at i:32023 original size:19 final size:19
Alignment explanation
Indices: 31999--32041 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31989 AAACATAAAT
31999 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
32018 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
32037 TAAAT
1 TAAAT
32042 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:32656 original size:109 final size:109
Alignment explanation
Indices: 32452--32670 Score: 267
Period size: 109 Copynumber: 2.0 Consensus size: 109
32442 ACTTTTTCTT
* ** * * * *
32452 TAGGTACATGGATGACCCGAATTTAAGCTATTTTTATAGAAAATAAACACTTGATCAGTGGACCG
1 TAGGTACATCGATGACCAAAATTTAAGCTATTTTTATAGAAAATAAACACTCGATCAATAGACCA
*
32517 CAACTTGAAATTTGATTCACTATTTAGATTTTAATCATTTGTTA
66 CAACTTGAAATTTGATTCACTATTTAGATTTTAACCATTTGTTA
* * * * *
32561 TAGGTGCATCGATGACCAAAATTTAGGTTATTTTTATAGAAAATAAATACTCGATCAATAGATCA
1 TAGGTACATCGATGACCAAAATTTAAGCTATTTTTATAGAAAATAAACACTCGATCAATAGACCA
** * * * *
32626 CAACTTGAGGTTTGGTTCATTGTTTTGATTTTAACCATTTGTTA
66 CAACTTGAAATTTGATTCACTATTTAGATTTTAACCATTTGTTA
32670 T
1 T
32671 GCAACTTAAA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (109 bp):
TAGGTACATCGATGACCAAAATTTAAGCTATTTTTATAGAAAATAAACACTCGATCAATAGACCA
CAACTTGAAATTTGATTCACTATTTAGATTTTAACCATTTGTTA
Found at i:33398 original size:5 final size:5
Alignment explanation
Indices: 33388--33421 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
33378 AGGTGCTCAT
33388 GGGGC GGGGC GGGGC GGGGC GGGGC GGGGC GGGG
1 GGGGC GGGGC GGGGC GGGGC GGGGC GGGGC GGGG
33422 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.82, T:0.00
Consensus pattern (5 bp):
GGGGC
Done.