Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014900.1 Kokia drynarioides strain JFW-HI SEQ_129943, 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: 26832
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1630 original size:4 final size:4
Alignment explanation
Indices: 1621--1677 Score: 71
Period size: 4 Copynumber: 14.2 Consensus size: 4
1611 GGTATCAGAG
* * *
1621 AAGA AAGA AAGA AAGA AATA AAGA AAGA AAGA AAG- AAGA AGGA GAGGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAGA
1669 AAGA AAGA A
1 AAGA AAGA A
1678 TGAGAGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 3 0.06
4 40 0.85
5 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:2020 original size:5 final size:5
Alignment explanation
Indices: 2010--2035 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2000 ATTTTTAATG
2010 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
2036 TATTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:2979 original size:4 final size:4
Alignment explanation
Indices: 2972--2996 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2962 TTAATTTATA
2972 TTAC TTAC TTAC TTAC TTAC TTAC T
1 TTAC TTAC TTAC TTAC TTAC TTAC T
2997 ACTACTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAC
Found at i:3040 original size:5 final size:5
Alignment explanation
Indices: 3030--3061 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
3020 TACTAACAAT
3030 ATAAA ATAAA ATAAA ATAAA ATAAA ATTAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A-TAAA A
3062 ATAACCAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:3193 original size:31 final size:30
Alignment explanation
Indices: 3133--3200 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
3123 AACAAATCAA
3133 TTAAAA-AATAAATTAAACAAAATAAATAAC
1 TTAAAATAATAAATTAAACAAAAT-AATAAC
3163 TTAAAATAATAAATACTAAACAAAAT-ATAAC
1 TTAAAATAATAAAT--TAAACAAAATAATAAC
*
3194 TTTAAAT
1 TTAAAAT
3201 TACCAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.18
31 18 0.53
33 10 0.29
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (30 bp):
TTAAAATAATAAATTAAACAAAATAATAAC
Found at i:3954 original size:39 final size:36
Alignment explanation
Indices: 3896--3968 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 36
3886 TAATGTAAAT
*
3896 ATTAAAAAAATTAAGATAATTAAATATGAAATTTTA
1 ATTAAAAAAATTAAAATAATTAAATATGAAATTTTA
* *
3932 ATTAATAAAAATTATATAATAATTTAATATTAAATTT
1 ATTAA-AAAAATTA-A-AATAATTAAATATGAAATTT
3969 AAAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 8 0.26
38 1 0.03
39 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (36 bp):
ATTAAAAAAATTAAAATAATTAAATATGAAATTTTA
Found at i:3992 original size:23 final size:23
Alignment explanation
Indices: 3949--4004 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
3939 AAAATTATAT
*
3949 AATAATTTAATATTAAATTTAAA
1 AATAATATAATATTAAATTTAAA
* *
3972 AATAATATAATA-TATATTTTAA
1 AATAATATAATATTAAATTTAAA
3994 AA-AA-ATAATAT
1 AATAATATAATAT
4005 CAACGAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 10 0.34
23 11 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAATATAATATTAAATTTAAA
Found at i:9440 original size:14 final size:14
Alignment explanation
Indices: 9421--9449 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9411 TATAGTACTA
9421 TAAATTAGAGGTGC
1 TAAATTAGAGGTGC
9435 TAAATTAGAGGTGC
1 TAAATTAGAGGTGC
9449 T
1 T
9450 TACATAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (14 bp):
TAAATTAGAGGTGC
Found at i:12537 original size:18 final size:19
Alignment explanation
Indices: 12506--12541 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12496 CCAAGAAATC
12506 TTTATCATTATCCAACCCT
1 TTTATCATTATCCAACCCT
*
12525 TTTATC-TTGTCCAACCC
1 TTTATCATTATCCAACCC
12542 AATATGATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.22, C:0.33, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTATCATTATCCAACCCT
Found at i:14306 original size:18 final size:20
Alignment explanation
Indices: 14263--14306 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
14253 ATACAATCAT
14263 AATAGTATTTTAATTTTAAGA
1 AATA-TATTTTAATTTTAAGA
14284 AATATATTTT-ATTTTAA-A
1 AATATATTTTAATTTTAAGA
14302 AATAT
1 AATAT
14307 TTATATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 7 0.30
20 6 0.26
21 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AATATATTTTAATTTTAAGA
Found at i:25257 original size:51 final size:51
Alignment explanation
Indices: 25181--25280 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
25171 ATCTGAAAAG
* *
25181 CTCCGATAAGAACTAGGAGAGAGAGACTGGATAAGTAAGAGATAAGGCAAT
1 CTCCGATAACAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
*
25232 CTCCGATAACAACTAAGG-GAGAGAGATTGGAGAAGTAAGAGATAAGGCA
1 CTCCGATAACAACT-AGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCA
25281 GTGGCTAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.93
52 3 0.07
ACGTcount: A:0.43, C:0.12, G:0.30, T:0.15
Consensus pattern (51 bp):
CTCCGATAACAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
Done.