Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013458.1 Kokia drynarioides strain JFW-HI SEQ_128484, 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: 43081
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1874 original size:41 final size:42
Alignment explanation
Indices: 1753--1900 Score: 122
Period size: 41 Copynumber: 3.5 Consensus size: 42
1743 AGAATTTGTA
* * * * *
1753 TAAATGGAATACTCGTGACTCGAAATAAGCATGAGAA-TATGA-
1 TAAA-GGAAGACTCATGTCTCGGAATAAGAATGA-AATTATGAT
* * * *
1795 TAAAGGAAGACTCATATCTCGGGATGAGAATGAGATTAT-AT
1 TAAAGGAAGACTCATGTCTCGGAATAAGAATGAAATTATGAT
** *
1836 TAAAGGAAGACTCATGTCTCGGAATAAGCGTGAAATTATGTT
1 TAAAGGAAGACTCATGTCTCGGAATAAGAATGAAATTATGAT
* *
1878 TGAAAGGAAGACTTATGACTCGG
1 T-AAAGGAAGACTCATGTCTCGG
1901 TAGAGCATAA
Statistics
Matches: 84, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
40 2 0.02
41 57 0.68
42 6 0.07
43 19 0.23
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (42 bp):
TAAAGGAAGACTCATGTCTCGGAATAAGAATGAAATTATGAT
Found at i:2600 original size:21 final size:20
Alignment explanation
Indices: 2574--2627 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2564 GTAGTTTTTA
*
2574 GTATCGGTAGAACCATG-TCTT
1 GTATCGGTAGAA--ATGAACTT
2595 GTATCGGTAGAAATGACACTT
1 GTATCGGTAGAAATGA-ACTT
2616 GTATCGGTAGAA
1 GTATCGGTAGAA
2628 TCCTATTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 3 0.10
21 27 0.90
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATCGGTAGAAATGAACTT
Found at i:5227 original size:18 final size:18
Alignment explanation
Indices: 5204--5238 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5194 GCACTTTTTA
5204 AAGAGTCACAACCCTTTG
1 AAGAGTCACAACCCTTTG
5222 AAGAGTCACAACCCTTT
1 AAGAGTCACAACCCTTT
5239 CATGTTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (18 bp):
AAGAGTCACAACCCTTTG
Found at i:16995 original size:31 final size:31
Alignment explanation
Indices: 16957--17017 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
16947 GGAGGGGTTG
16957 GTGATGGTTCTCTTAATCCGAACAATTTGTT
1 GTGATGGTTCTCTTAATCCGAACAATTTGTT
16988 GTGATGGTTCTCTTAATCCGAACAATTTGT
1 GTGATGGTTCTCTTAATCCGAACAATTTGT
17018 CTCTTCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (31 bp):
GTGATGGTTCTCTTAATCCGAACAATTTGTT
Found at i:20222 original size:139 final size:139
Alignment explanation
Indices: 19972--20250 Score: 540
Period size: 139 Copynumber: 2.0 Consensus size: 139
19962 TTGTGCATAG
19972 ACTGAAGGATTGGAAGCAACAATCTCTGTCACTAAGAGTTAGGGAGGTGATGATCAAGCCTGTGG
1 ACTGAAGGATTGGAAGCAACAATCTCTGTCACTAAGAGTTAGGGAGGTGATGATCAAGCCTGTGG
*
20037 CTAGTGCAATTCCAACCTATACTATGGCATGCTTTAAGTTTCCTAATAAGGTTTGTTCTGAGCTT
66 CTAGTGCAATTCCAACCTATACTATGGCATGCTATAAGTTTCCTAATAAGGTTTGTTCTGAGCTT
20102 ACTTCAGCC
131 ACTTCAGCC
20111 ACTGAAGGATTGGAAGCAACAATCTCTGTCACTAAGAGTTAGGGAGGTGATGATCAAGCCTGTGG
1 ACTGAAGGATTGGAAGCAACAATCTCTGTCACTAAGAGTTAGGGAGGTGATGATCAAGCCTGTGG
*
20176 CTAGTGCGATTCCAACCTATACTATGGCATGCTATAAGTTTCCTAATAAGGTTTGTTCTGAGCTT
66 CTAGTGCAATTCCAACCTATACTATGGCATGCTATAAGTTTCCTAATAAGGTTTGTTCTGAGCTT
20241 ACTTCAGCC
131 ACTTCAGCC
20250 A
1 A
20251 TTTCTCGATT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (139 bp):
ACTGAAGGATTGGAAGCAACAATCTCTGTCACTAAGAGTTAGGGAGGTGATGATCAAGCCTGTGG
CTAGTGCAATTCCAACCTATACTATGGCATGCTATAAGTTTCCTAATAAGGTTTGTTCTGAGCTT
ACTTCAGCC
Found at i:22603 original size:6 final size:6
Alignment explanation
Indices: 22575--22622 Score: 69
Period size: 6 Copynumber: 7.5 Consensus size: 6
22565 TTTTTTTCTA
22575 TTCCCC TTCTCCGC TTCCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTC
1 TTCCCC TTC-CC-C TT-CCCC TTCCCC TTCCCC TTCCCC TTCCCC TTC
22623 TTATTTTCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 28 0.72
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.00, C:0.62, G:0.02, T:0.35
Consensus pattern (6 bp):
TTCCCC
Found at i:23501 original size:10 final size:11
Alignment explanation
Indices: 23471--23511 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
23461 TTATATTTAA
23471 AAAATAATTTT
1 AAAATAATTTT
*
23482 AAATTAATTTT
1 AAAATAATTTT
23493 AAAAT-ATTTT
1 AAAATAATTTT
*
23503 AAAAAAATT
1 AAAATAATT
23512 GATATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:23511 original size:21 final size:22
Alignment explanation
Indices: 23471--23511 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
23461 TTATATTTAA
**
23471 AAAATAATTTTAAATTAATTTT
1 AAAATAATTTTAAAAAAATTTT
23493 AAAAT-ATTTTAAAAAAATT
1 AAAATAATTTTAAAAAAATT
23512 GATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAATTTTAAAAAAATTTT
Found at i:26180 original size:2 final size:2
Alignment explanation
Indices: 26173--26207 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
26163 GAGACTAAAG
*
26173 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
26208 TTTTTCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36912 original size:25 final size:25
Alignment explanation
Indices: 36879--36929 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36869 GCTTTCCACC
*
36879 AATAATTTCCCATAAAGTTATTCAT
1 AATAATTTCCAATAAAGTTATTCAT
* * *
36904 AATAGTTTCTAATAAATTTATTCAT
1 AATAATTTCCAATAAAGTTATTCAT
36929 A
1 A
36930 TAACTCATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAATTTCCAATAAAGTTATTCAT
Found at i:38989 original size:6 final size:6
Alignment explanation
Indices: 38978--39017 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
38968 CAGAAACACA
38978 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCC
39018 AGTCTCCACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:39232 original size:19 final size:18
Alignment explanation
Indices: 39199--39235 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39189 AGTAAAATAT
39199 ATAATTTAAAATTAATTA
1 ATAATTTAAAATTAATTA
*
39217 ATAATATTAAATTTAATTA
1 ATAAT-TTAAAATTAATTA
39236 TAAGTAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATTTAAAATTAATTA
Done.