Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001512.1 Kokia drynarioides strain JFW-HI SEQ_113063, 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: 34195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3850 original size:24 final size:24
Alignment explanation
Indices: 3790--3860 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
3780 CAAGATGCGT
* *
3790 CGTTGTGGTCAAACCACTAAATAG
1 CGTTGTGGTCAAGCCACTAAATAA
* * * * *
3814 TGTTATGGGCAAGTCACTCAATAA
1 CGTTGTGGTCAAGCCACTAAATAA
3838 CGTTGTGGTCAAGCCACTAAATA
1 CGTTGTGGTCAAGCCACTAAATA
3861 TTGCAGTAAA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTAAATAA
Found at i:3995 original size:42 final size:42
Alignment explanation
Indices: 3948--4050 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
3938 TTCAGTGGAC
**
3948 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGGG
1 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
* ** *
3990 ATGCTTAAGATGTGAATCGGATTTATAATCAACATAGTTGAA
1 ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
* *
4032 ATGCTAAACATGCGAATCA
1 ATGCTTAACATGTGAATCA
4051 TATCTCAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCTTAACATGTGAATCAAATTTATAATCAACATAGTCGAA
Found at i:4922 original size:16 final size:16
Alignment explanation
Indices: 4901--4933 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4891 ATGTTTTTTC
*
4901 TTTTTATTTAGTTACA
1 TTTTTATTTAATTACA
4917 TTTTTATTTAATTACA
1 TTTTTATTTAATTACA
4933 T
1 T
4934 GTTGATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTTATTTAATTACA
Found at i:10650 original size:19 final size:20
Alignment explanation
Indices: 10619--10657 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10609 AAATCTAATT
10619 CCAATATCAAAAA-AAGAAA
1 CCAATATCAAAAATAAGAAA
10638 CCAA-ATCAGAAAATAAGAAA
1 CCAATATCA-AAAATAAGAAA
10658 ATATCTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.67, C:0.15, G:0.08, T:0.10
Consensus pattern (20 bp):
CCAATATCAAAAATAAGAAA
Found at i:16886 original size:29 final size:30
Alignment explanation
Indices: 16853--16968 Score: 155
Period size: 29 Copynumber: 3.9 Consensus size: 30
16843 ATTAAAACCG
*
16853 GGTCAAATTTGAATTTTTGG-AAGTTCGGA
1 GGTCAAATTTGAATTTTTGGAAAGTTTGGA
* *
16882 GGTCAAATTTGAATTTCTGGAAAGTTTGGG
1 GGTCAAATTTGAATTTTTGGAAAGTTTGGA
* *
16912 GGTCAAATTGGATTTTTTGGAAAGTTTGGA
1 GGTCAAATTTGAATTTTTGGAAAGTTTGGA
**
16942 -GTCAAATTTGAATTTTTAAAAAGTTTG
1 GGTCAAATTTGAATTTTTGGAAAGTTTG
16969 AGGGTAAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 42 0.56
30 33 0.44
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTGGAAAGTTTGGA
Found at i:16965 original size:59 final size:59
Alignment explanation
Indices: 16852--16973 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
16842 CATTAAAACC
* ** *
16852 GGGTCAAATTTGAATTTTTGGAAGTTCGGAGGTCAAATTTGAATTTCTGGAAAGTTTGG
1 GGGTCAAATTGGAATTTTTGGAAGTTCGGAGGTCAAATTTGAATTTCTAAAAAGTTTGA
* * *
16911 GGGTCAAATTGGATTTTTTGGAAAGTTTGGA-GTCAAATTTGAATTTTTAAAAAGTTTGA
1 GGGTCAAATTGGAATTTTTGG-AAGTTCGGAGGTCAAATTTGAATTTCTAAAAAGTTTGA
16970 GGGT
1 GGGT
16974 AAAAACATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 47 0.85
60 8 0.15
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.39
Consensus pattern (59 bp):
GGGTCAAATTGGAATTTTTGGAAGTTCGGAGGTCAAATTTGAATTTCTAAAAAGTTTGA
Found at i:18024 original size:4 final size:4
Alignment explanation
Indices: 18003--18037 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
17993 TGTAATTATT
*
18003 TAAA T-AA TAAA TAGA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
18038 GTTAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:18655 original size:40 final size:40
Alignment explanation
Indices: 18603--18897 Score: 355
Period size: 40 Copynumber: 7.4 Consensus size: 40
18593 ATAACTTTAG
18603 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
* * *
18643 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
* * *
18682 GGGTAAAAGATTGTATGGTCTTCAATATGCCCTCTAGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
* **
18722 GGGTAAAAGATTGGATGATCTTCAATCTGCCCTCTTATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
* * * **
18762 GGGTAAAAGATTGGATGATCTTCAATTTGTCCTCTAATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
* * *
18802 GGGTAAAAGATTGGAT-GACATTTAATCTACCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTC-TTCAATCTGCCCTCTGGTTA
* * **
18842 GGGTAAAAGATTGAATTG-CTTCAATCTGCCC-CATGGTCG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGGTTA
18881 GGGTAAAAGATTGGATG
1 GGGTAAAAGATTGGATG
18898 TGGTGACTTC
Statistics
Matches: 219, Mismatches: 32, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
38 1 0.00
39 65 0.30
40 152 0.69
41 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
Found at i:18866 original size:119 final size:119
Alignment explanation
Indices: 18603--18896 Score: 337
Period size: 119 Copynumber: 2.5 Consensus size: 119
18593 ATAACTTTAG
* *
18603 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAAT
1 GGGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTGCTTCAAT
** * * * *
18668 CTGCCCTATGGTTGGGGTAAAAGATTGTATGGTCTTCAATATGCCCTCTAGTTA
66 CTGCCCTATAATTAGGGTAAAAGATTGGATGGACTTCAATATACCCTCTAGTTA
*
18722 GGGTAAAAGATTGGA-TGATCTTCAATCTGCCCTCTTATTAGGGTAAAAGATTGGA-TGATCTTC
1 GGGTAAAAGATTGGATTG-TCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTG--CTTC
* * * * * *
18785 AATTTGTCCTCTAATTAGGGTAAAAGATTGGAT-GACATTTAATCTACCCTCTGGTTA
63 AATCTGCCCTATAATTAGGGTAAAAGATTGGATGGAC-TTCAATATACCCTCTAGTTA
* * **
18842 GGGTAAAAGATTGAATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAAAGATTGGAT
1 GGGTAAAAGATTGGATTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGAT
18897 GTGGTGACTT
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.03
119 82 0.55
120 60 0.41
121 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (119 bp):
GGGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATTGCTTCAAT
CTGCCCTATAATTAGGGTAAAAGATTGGATGGACTTCAATATACCCTCTAGTTA
Found at i:19158 original size:49 final size:50
Alignment explanation
Indices: 19097--19203 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 50
19087 GCTCTTGTTG
*
19097 CTTCAATCTGCCC-TCTATAGCTTTAAGTAAATGAG-TTTCGTCATTACGA
1 CTTCAATCTGCCCTTCTATAGCTTTAAGTAAATGAGATTT-GCCATTACGA
* * * ** *
19146 CTTCAATTTGCCCTTCTATAGTTTTAGGTGTATGAGATTTGCCATTGCGA
1 CTTCAATCTGCCCTTCTATAGCTTTAAGTAAATGAGATTTGCCATTACGA
19196 CTTCAATC
1 CTTCAATC
19204 CATTCCTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 12 0.25
50 33 0.69
51 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (50 bp):
CTTCAATCTGCCCTTCTATAGCTTTAAGTAAATGAGATTTGCCATTACGA
Found at i:26127 original size:12 final size:12
Alignment explanation
Indices: 26102--26144 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
26092 TCAGTCATTT
26102 AAAAAGAAATGAG
1 AAAAAGAAA-GAG
26115 AAAAAGAAAGAG
1 AAAAAGAAAGAG
26127 -AAAAGAAAAGAAG
1 AAAAAG-AAAG-AG
26140 AAAAA
1 AAAAA
26145 TATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.19
12 7 0.26
13 11 0.41
14 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAGAG
Found at i:28039 original size:26 final size:26
Alignment explanation
Indices: 28002--28058 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
27992 TTTTGGGCAT
28002 AATTCTATACATGTTCATGCAGCAAC
1 AATTCTATACATGTTCATGCAGCAAC
*
28028 AATTCTGA-ACATGTTCATGCAGCGAC
1 AATTCT-ATACATGTTCATGCAGCAAC
28054 -ATTCT
1 AATTCT
28059 TGAGTGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
26 23 0.79
27 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (26 bp):
AATTCTATACATGTTCATGCAGCAAC
Found at i:28085 original size:37 final size:38
Alignment explanation
Indices: 28044--28154 Score: 111
Period size: 38 Copynumber: 3.0 Consensus size: 38
28034 GAACATGTTC
*
28044 ATGCAGCGACATTCTTGAGTGCAA-TTGAAGAATATTT
1 ATGCAACGACATTCTTGAGTGCAATTTGAAGAATATTT
* *
28081 ATGCAACGATAGTTCTAGA-TGCAATTTGAAGAATATTT
1 ATGCAACGACA-TTCTTGAGTGCAATTTGAAGAATATTT
* * * * * *
28119 GTACAACGACAATCTTGGGTGCATTTTGGA-AATATT
1 ATGCAACGACATTCTTGAGTGCAATTTGAAGAATATT
28155 CCTATGGTGA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 24 0.40
38 36 0.60
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (38 bp):
ATGCAACGACATTCTTGAGTGCAATTTGAAGAATATTT
Found at i:31075 original size:12 final size:12
Alignment explanation
Indices: 31058--31082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31048 TCTCTCACAC
31058 CACCAATCATAG
1 CACCAATCATAG
31070 CACCAATCATAG
1 CACCAATCATAG
31082 C
1 C
31083 CGAATTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CACCAATCATAG
Done.