Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013059.1 Kokia drynarioides strain JFW-HI SEQ_128077, 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: 29957
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:198 original size:33 final size:30
Alignment explanation
Indices: 159--228 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
149 TTTTAATTAG
159 TAATAATATAATTACATTTTAACCCTTTAAAAA
1 TAATAAT-TAATTA-A-TTTAACCCTTTAAAAA
*
192 TAATAATTAATTAATTTAATCCTTTAAAAA
1 TAATAATTAATTAATTTAACCCTTTAAAAA
*
222 TTATAAT
1 TAATAAT
229 GATATAGACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 21 0.60
31 1 0.03
32 6 0.17
33 7 0.20
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (30 bp):
TAATAATTAATTAATTTAACCCTTTAAAAA
Found at i:1658 original size:22 final size:22
Alignment explanation
Indices: 1632--1674 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1622 CAACTATATT
1632 GTTGAAAAACTCTATTTTAATA
1 GTTGAAAAACTCTATTTTAATA
1654 GTTGAAAAACTCTATTTTAAT
1 GTTGAAAAACTCTATTTTAAT
1675 CAATGTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
GTTGAAAAACTCTATTTTAATA
Found at i:2797 original size:14 final size:14
Alignment explanation
Indices: 2778--2811 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2768 CAATCATTTA
2778 ATTATTATATTGTT
1 ATTATTATATTGTT
* *
2792 ATTATTTTGTTGTT
1 ATTATTATATTGTT
2806 ATTATT
1 ATTATT
2812 TGGGTATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (14 bp):
ATTATTATATTGTT
Found at i:3924 original size:21 final size:20
Alignment explanation
Indices: 3900--3961 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
3890 AATTTAAAAT
* *
3900 ATTATAAAAATTATTTTTTTA
1 ATTATAAAAATTA-ATATTTA
**
3921 ATTATTCAAATTAATATTTA
1 ATTATAAAAATTAATATTTA
* *
3941 AATATAAAAA-TATTATTTA
1 ATTATAAAAATTAATATTTA
3960 AT
1 AT
3962 ATATTTAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 9 0.28
20 12 0.38
21 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATAAAAATTAATATTTA
Found at i:3965 original size:28 final size:28
Alignment explanation
Indices: 3934--3989 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3924 ATTCAAATTA
*
3934 ATATTTAAA-TATAAAAATATTATTTAAT
1 ATATTTAAATTATAAAAA-ATTAATTAAT
*
3962 ATATTTAAATTTTAAAAAATTAATTAAT
1 ATATTTAAATTATAAAAAATTAATTAAT
3990 TACTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTTAAATTATAAAAAATTAATTAAT
Found at i:3971 original size:20 final size:20
Alignment explanation
Indices: 3917--3971 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3907 AAATTATTTT
*
3917 TTTAAT-TATTCAAATTAATA
1 TTTAATATATT-AAAATAATA
* *
3937 TTTAA-ATATAAAAATATTA
1 TTTAATATATTAAAATAATA
*
3956 TTTAATATATTTAAAT
1 TTTAATATATTAAAAT
3972 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAATATATTAAAATAATA
Found at i:11989 original size:5 final size:5
Alignment explanation
Indices: 11979--12007 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
11969 AGAGATGAAA
11979 TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
12008 ATTTGAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.59, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:13042 original size:35 final size:34
Alignment explanation
Indices: 13002--13077 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
12992 ATTTTTTTAT
*
13002 TTTAAAATATCACATCAATAAA-TTCAATTAAAAA
1 TTTAAAATATCA-ATCAATAAACTTAAATTAAAAA
* * * *
13036 TATTAAAGTATTAATCATTAAACTTAAATTTAAAA
1 T-TTAAAATATCAATCAATAAACTTAAATTAAAAA
13071 TTTAAAA
1 TTTAAAA
13078 AAATAAAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (34 bp):
TTTAAAATATCAATCAATAAACTTAAATTAAAAA
Found at i:14828 original size:31 final size:31
Alignment explanation
Indices: 14790--14876 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
14780 TATAAGGGTA
* **
14790 AATGACAAAACAATCACTTAACTTTGATTTC
1 AATGACAAAACAATCACTCAACTTTGACCTC
14821 AATGACAAAACAATCACTCAACTTTGACCTC
1 AATGACAAAACAATCACTCAACTTTGACCTC
*
14852 AATGACAAAACAGTCACTCAACTTT
1 AATGACAAAACAATCACTCAACTTT
14877 CAAAAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (31 bp):
AATGACAAAACAATCACTCAACTTTGACCTC
Found at i:14896 original size:30 final size:31
Alignment explanation
Indices: 14856--14914 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
14846 GACCTCAATG
14856 ACAAAACAGT-C-ACTCAACTTTCAAAAAATA
1 ACAAAACAGTCCTACT-AACTTTCAAAAAATA
* *
14886 ACAAATCAGTCCTACTAGCTTTCAAAAAA
1 ACAAAACAGTCCTACTAACTTTCAAAAAA
14915 CCAAACACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 13 0.52
32 3 0.12
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (31 bp):
ACAAAACAGTCCTACTAACTTTCAAAAAATA
Found at i:20333 original size:6 final size:6
Alignment explanation
Indices: 20322--20351 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
20312 TCTTAAACCT
20322 CATCCC CATCCC CATCCC CATCCC CATCCC
1 CATCCC CATCCC CATCCC CATCCC CATCCC
20352 AACCCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCCC
Found at i:23403 original size:13 final size:13
Alignment explanation
Indices: 23372--23405 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
23362 ATCCTAAACC
23372 CTAAAC-TCAAAT
1 CTAAACTTCAAAT
23384 CTCAAACTTCAAAT
1 CT-AAACTTCAAAT
23398 CTAAACTT
1 CTAAACTT
23406 AAACCTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 10 0.50
14 8 0.40
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (13 bp):
CTAAACTTCAAAT
Found at i:27505 original size:24 final size:24
Alignment explanation
Indices: 27476--27523 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27466 GTAGCTCTTT
27476 GTGGTAGTGTTGATTATTTATATA
1 GTGGTAGTGTTGATTATTTATATA
27500 GTGGTAGTGTTGATTATTTATATA
1 GTGGTAGTGTTGATTATTTATATA
27524 CTTATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (24 bp):
GTGGTAGTGTTGATTATTTATATA
Done.