Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002673.1 Kokia drynarioides strain JFW-HI SEQ_114929, 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: 16606
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:124 original size:11 final size:11
Alignment explanation
Indices: 107--174 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
97 TATTGGACTT
*
107 TTTAATTTAAA
1 TTTAAATTAAA
*
118 -TTAAATTCAA
1 TTTAAATTAAA
* *
128 TTTAAATTTAG
1 TTTAAATTAAA
139 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
151 TTTAAATCAAA
1 TTTAAATTAAA
*
162 TTTAAAATAAA
1 TTTAAATTAAA
173 TT
1 TT
175 AAAAAAAGTC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 8 0.17
11 29 0.63
12 9 0.20
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:135 original size:6 final size:6
Alignment explanation
Indices: 110--167 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
100 TGGACTTTTT
* *
110 AATTTA AA-TTA AA-TTC AATTTA AATTT- AGTTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
155 AA-TCA AATTTA AA
1 AATTTA AATTTA AA
168 ATAAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 17 0.40
6 26 0.60
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:162 original size:17 final size:17
Alignment explanation
Indices: 110--167 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
100 TGGACTTTTT
110 AATTTAAA-TTAAATTC-
1 AATTTAAATTTAAA-TCA
** *
126 AATTTAAATTTAGTTTA
1 AATTTAAATTTAAATCA
143 AATTTAAATTTAAATCA
1 AATTTAAATTTAAATCA
160 AATTTAAA
1 AATTTAAA
168 ATAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.26
17 25 0.74
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAATCA
Found at i:7744 original size:22 final size:23
Alignment explanation
Indices: 7701--7745 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
7691 GATATTTTTG
*
7701 TTAAAAATTTCATTCATTTATGC
1 TTAAAAATTTCATTCATATATGC
7724 TTAAAAATTT-ATCTC-TATATGC
1 TTAAAAATTTCAT-TCATATATGC
7746 CAATATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
TTAAAAATTTCATTCATATATGC
Found at i:9690 original size:27 final size:27
Alignment explanation
Indices: 9637--9694 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
9627 AAGTTTTAAG
* * *
9637 ATATTTTTTTAATTCTAAATTTGAAAT
1 ATATTTTTTTAAATCTAAAATTAAAAT
9664 ATATATTTTTTAAAT-TAAAATTAAAAT
1 ATAT-TTTTTTAAATCTAAAATTAAAAT
9691 -TATT
1 ATATT
9695 AAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 14 0.52
28 9 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATATTTTTTTAAATCTAAAATTAAAAT
Found at i:9840 original size:27 final size:27
Alignment explanation
Indices: 9810--9866 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
9800 TTATTTTTTT
* *
9810 AATA-TAATTTTTTAATTTTAAATTCAA
1 AATACTAATTTTTTAAATTGAAATT-AA
**
9837 AATACTTTTTTTTTAAATTGAAATTAA
1 AATACTAATTTTTTAAATTGAAATTAA
9864 AAT
1 AAT
9867 TAAATATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
AATACTAATTTTTTAAATTGAAATTAA
Found at i:10040 original size:115 final size:111
Alignment explanation
Indices: 9817--10042 Score: 267
Period size: 115 Copynumber: 2.0 Consensus size: 111
9807 TTTAATATAA
* * * * *
9817 TTTTTTAATTTTAAATTCAAAATACTTTTTTTTTAAATTGAAATTAAAATTAAATATATTAAAAG
1 TTTTTTAATTTTAAATTCAAAATACTTTTTTTTAAAACTAAAACTAAAAATAAATATATTAAAAG
* * *
9882 TATTTAAACGATAAGTAAAGAGTTGATGTTTTAAAATGTAAATTTAT
66 TATTTAAACGATAAATAAAGAGTTGA-GTTTTAAAAAGAAAATTTAT
*
9929 TTTTTTAATTTTAAA-TCAAAAATACATATTTTTTTAAAAACTAAAACTAAAAATAAATATATTG
1 TTTTTTAATTTTAAATTC-AAAATAC-T-TTTTTTT-AAAACTAAAACTAAAAATAAATATATTA
* * *
9993 GAAGTATTTAAAGGTTAAATAAAGAGTT-AGATTTTAAAACAGAAAATTTA
62 AAAGTATTTAAACGATAAATAAAGAGTTGAG-TTTTAAAA-AGAAAATTTA
10043 CTGTATAATT
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
111 2 0.02
112 22 0.23
113 2 0.02
114 16 0.17
115 54 0.56
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (111 bp):
TTTTTTAATTTTAAATTCAAAATACTTTTTTTTAAAACTAAAACTAAAAATAAATATATTAAAAG
TATTTAAACGATAAATAAAGAGTTGAGTTTTAAAAAGAAAATTTAT
Found at i:10616 original size:26 final size:29
Alignment explanation
Indices: 10587--10640 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10577 ATTAAAATAA
10587 ATTTAAA-TTT-CA-AATAATTAGAAAAT
1 ATTTAAATTTTACATAATAATTAGAAAAT
*
10613 ATTTAAATTTTAGATAATAATTAGAAAA
1 ATTTAAATTTTACATAATAATTAGAAAA
10641 CTCGCAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 3 0.12
28 1 0.04
29 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (29 bp):
ATTTAAATTTTACATAATAATTAGAAAAT
Done.