Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011046.1 Kokia drynarioides strain JFW-HI SEQ_126017, 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: 2735
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.29
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:48 original size:12 final size:12
Alignment explanation
Indices: 33--58 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23 ATACACTTAA
33 AAATATTAAAAC
1 AAATATTAAAAC
45 AAATATTAAAAC
1 AAATATTAAAAC
57 AA
1 AA
59 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:96 original size:41 final size:40
Alignment explanation
Indices: 31--114 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 40
21 AAATACACTT
* *
31 AAAAATATTAAAACAAATATTAAAACAACAAACAAATTAA
1 AAAAATATTAAAACAAATAGTAAAACAAAAAACAAATTAA
* * *
71 AAAAGATATTAAAATAAATCGTAAAACAAAAAACAAATTGA
1 AAAA-ATATTAAAACAAATAGTAAAACAAAAAACAAATTAA
112 AAA
1 AAA
115 TACAATAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (40 bp):
AAAAATATTAAAACAAATAGTAAAACAAAAAACAAATTAA
Found at i:809 original size:24 final size:23
Alignment explanation
Indices: 770--815 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
760 TATTACAAGC
770 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
793 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
816 CCGGGTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:2024 original size:12 final size:12
Alignment explanation
Indices: 2007--2067 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
1997 CAACATTAAA
2007 AACAACAAAAAT
1 AACAACAAAAAT
* *
2019 AGCAACAAAAAC
1 AACAACAAAAAT
2031 AACAACAAAAAT
1 AACAACAAAAAT
* * *
2043 AATAGC-AAAAC
1 AACAACAAAAAT
2054 AACAACAAAAAT
1 AACAACAAAAAT
2066 AA
1 AA
2068 TAGCAAAACA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:2064 original size:56 final size:56
Alignment explanation
Indices: 1950--2168 Score: 162
Period size: 56 Copynumber: 3.9 Consensus size: 56
1940 AATAACATCC
* * * * * **
1950 AAACAACAAAAATAATAACCAAAGCAGCAGCAAAAATAATAGCAAAACAACATTAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAATAGCAAAACAACAACAA
*
2006 AAACAACAAAAATAGCAACAAAAACAACAACAAAAATAATAGCAAAACAACAACAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAATAGCAAAACAACAACAA
* * ** * * * * *
2062 AAATAATAGCAA-AACAACATGAAAATAGCAACCAAAACAGTA--AAAA-AAC-ACAA
1 AAACAACAAAAATAACAACA--AAAACAACAACAAAAATAATAGCAAAACAACAACAA
* * * * *
2115 AAACAACAAAAAAAACAACTAAAACAGTA-AAAAAAAATAGTACCAAAACAACAA
1 AAACAACAAAAATAACAACAAAAACA--ACAACAAAAATAATAGCAAAACAACAA
2169 TATAAATTTT
Statistics
Matches: 126, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
52 5 0.04
53 22 0.17
54 9 0.07
55 14 0.11
56 59 0.47
57 17 0.13
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.08
Consensus pattern (56 bp):
AAACAACAAAAATAACAACAAAAACAACAACAAAAATAATAGCAAAACAACAACAA
Found at i:2086 original size:23 final size:23
Alignment explanation
Indices: 2007--2080 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
1997 CAACATTAAA
** *
2007 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAATAGC-AAAAC
2031 AACAACAAAAATAATAGCAAAAC
1 AACAACAAAAATAATAGCAAAAC
2054 AACAACAAAAATAATAGCAAAAC
1 AACAACAAAAATAATAGCAAAAC
2077 AACA
1 AACA
2081 TGAAAATAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 32 0.68
24 15 0.32
ACGTcount: A:0.70, C:0.19, G:0.04, T:0.07
Consensus pattern (23 bp):
AACAACAAAAATAATAGCAAAAC
Found at i:2143 original size:40 final size:41
Alignment explanation
Indices: 2072--2149 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
2062 AAATAATAGC
* *
2072 AAAACAACATGAAAATAGCAACCAAAACAGTAAAAAAACACA
1 AAAACAACA-GAAAAAAACAACCAAAACAGTAAAAAAACACA
*
2114 AAAACAACA-AAAAAAACAACTAAAACAGTAAAAAAA
1 AAAACAACAGAAAAAAACAACCAAAACAGTAAAAAAA
2150 AATAGTACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 24 0.73
42 9 0.27
ACGTcount: A:0.72, C:0.17, G:0.05, T:0.06
Consensus pattern (41 bp):
AAAACAACAGAAAAAAACAACCAAAACAGTAAAAAAACACA
Found at i:2146 original size:20 final size:20
Alignment explanation
Indices: 2090--2149 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2080 ATGAAAATAG
*
2090 CAACCAAAACAGTAAAAAAA
1 CAACAAAAACAGTAAAAAAA
**
2110 C-ACAAAAACAACAAAAAAAA
1 CAACAAAAAC-AGTAAAAAAA
*
2130 CAACTAAAACAGTAAAAAAA
1 CAACAAAAACAGTAAAAAAA
2150 AATAGTACCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.22
20 18 0.56
21 7 0.22
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.05
Consensus pattern (20 bp):
CAACAAAAACAGTAAAAAAA
Found at i:2146 original size:21 final size:21
Alignment explanation
Indices: 2090--2150 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
2080 ATGAAAATAG
*
2090 CAACCAAAACAGT-AAAAAAA
1 CAACAAAAACAGTAAAAAAAA
**
2110 C-ACAAAAACAACAAAAAAAA
1 CAACAAAAACAGTAAAAAAAA
*
2130 CAACTAAAACAGTAAAAAAAA
1 CAACAAAAACAGTAAAAAAAA
2151 ATAGTACCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.24
20 9 0.27
21 16 0.48
ACGTcount: A:0.74, C:0.18, G:0.03, T:0.05
Consensus pattern (21 bp):
CAACAAAAACAGTAAAAAAAA
Done.