Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008566.1 Kokia drynarioides strain JFW-HI SEQ_123244, 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: 19011
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:8110 original size:58 final size:58
Alignment explanation
Indices: 8025--8137 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 58
8015 GGTTTTTGAT
* * *
8025 CTTGACAATGGTTCTCACATTAAGTTTT-GA-GTTGTTTGATTCTAAGTTAATCTTTAAA
1 CTTGACAATGATTCTCACAATAAGTTTTAAACGTTGTTTG-TTC-AAGTTAATCTTTAAA
* ** *
8083 CTTGACAATTATTCTCACAATGGGTTTTAAACTTTGTTTGTTCAAGTTAATCTTT
1 CTTGACAATGATTCTCACAATAAGTTTTAAACGTTGTTTGTTCAAGTTAATCTTT
8138 GATAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 35 0.76
59 4 0.09
60 7 0.15
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (58 bp):
CTTGACAATGATTCTCACAATAAGTTTTAAACGTTGTTTGTTCAAGTTAATCTTTAAA
Found at i:10326 original size:227 final size:218
Alignment explanation
Indices: 9932--10366 Score: 577
Period size: 227 Copynumber: 2.0 Consensus size: 218
9922 GCTAACATAC
*
9932 ATCAAACATTGTAAAATAACTTTTTAAAAAATAATATCTTCAATAATCACATTCCATTAAAATCA
1 ATCAAACATTGTAAAATAACTTTTTAAAAAATAATATCTTCAACAATCACATTCCATTAAAATCA
* * *
9997 TAATATAAAAAGCAACTGCCTAAATTCATTTATAGATTTTCATATGCATGTATATATATTGTTCA
66 TAACATAAAAAGCAACTACCTAAATTCATTCATAGATTTTCATATGCATGTATATATATTGTTCA
* *
10062 TTAAAGCATTTTCATATGCATACATGCATATGATAATTATCTGTAAAGAAAGAGAG-GGAGGGGT
131 TTAAAGCATTTTCATATGCATACATGCATACGATAATTATCTGCAAAGAAAGAGAGAGG-GGGGT
10126 CTCAAATAATTGAAATCAATGTAT
195 CTCAAATAATTGAAATCAATGTAT
* * ** * * **
10150 ATCAAATATTGTAAAGTAA-TTTTTCTGAAAATTATATTTTCAACAATCACATTTTATTAAAATC
1 ATCAAACATTGTAAAATAACTTTTT-AAAAAATAATATCTTCAACAATCACATTCCATTAAAATC
* ** *
10214 ATAACATAAGAAATCATTTACTTAAATTCATTCATTCATGTATTTTCATATGCATGTATATATAT
65 ATAACATAA-AAAGCAACTACCTAAATTCATTCA-T-A-G-ATTTTCATATGCATG----TATAT
* *
10279 ATATTGTTCATTAAAGCATTTTCATATGCATATATGTATACGATAATTATCTGCAAAGAAAGAGA
121 ATATTGTTCATTAAAGCATTTTCATATGCATACATGCATACGATAATTATCTGCAAAGAAAGAGA
10344 GAGGGGGGTCTCAAATAATTGAA
186 GAGGGGGGTCTCAAATAATTGAA
10367 CCCAAAAAGA
Statistics
Matches: 186, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
217 5 0.03
218 57 0.31
219 18 0.10
220 1 0.01
221 1 0.01
222 1 0.01
223 15 0.08
227 86 0.46
228 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (218 bp):
ATCAAACATTGTAAAATAACTTTTTAAAAAATAATATCTTCAACAATCACATTCCATTAAAATCA
TAACATAAAAAGCAACTACCTAAATTCATTCATAGATTTTCATATGCATGTATATATATTGTTCA
TTAAAGCATTTTCATATGCATACATGCATACGATAATTATCTGCAAAGAAAGAGAGAGGGGGGTC
TCAAATAATTGAAATCAATGTAT
Found at i:12034 original size:31 final size:32
Alignment explanation
Indices: 11968--12035 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
11958 ATTTTTTAAA
11968 ATGTATACAGTTGAATCGAAATCAAAAGTTTT
1 ATGTATACAGTTGAATCGAAATCAAAAGTTTT
12000 ATGTATACA-TTCGAATC-ACAATCAAAA-TTTT
1 ATGTATACAGTT-GAATCGA-AATCAAAAGTTTT
12031 ATGTA
1 ATGTA
12036 CATAATTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (32 bp):
ATGTATACAGTTGAATCGAAATCAAAAGTTTT
Found at i:14547 original size:26 final size:27
Alignment explanation
Indices: 14497--14547 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
14487 TTTCATGTAT
* *
14497 ATTATATACACATGTAAGTATATTTCA
1 ATTATATACACATATAAATATATTTCA
*
14524 ATTATATTC-CATATAAATATATTT
1 ATTATATACACATATAAATATATTT
14548 ATACGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTATATACACATATAAATATATTTCA
Found at i:18488 original size:30 final size:29
Alignment explanation
Indices: 18443--18506 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
18433 AATTAATTTG
** *
18443 TAAAAAATAATTATAATTAACGATAACAA
1 TAAAAAATAATTATAAAAAACAATAACAA
*
18472 TAAAAATATTATTATAAAAAACAATAACAA
1 TAAAAA-ATAATTATAAAAAACAATAACAA
18502 TAAAA
1 TAAAA
18507 TTTATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.27
Consensus pattern (29 bp):
TAAAAAATAATTATAAAAAACAATAACAA
Found at i:18946 original size:31 final size:29
Alignment explanation
Indices: 18879--18946 Score: 68
Period size: 31 Copynumber: 2.2 Consensus size: 29
18869 TGATCCTAAT
18879 TTTAAA-ATTTCAAAGAAATATATAAAAA
1 TTTAAATATTTCAAAGAAATATATAAAAA
*
18907 TACATAAATACTTTCAAA-AAATATAATAATAAA
1 T--TTAAATA-TTTCAAAGAAATAT-ATAA-AAA
18940 TTTAAAT
1 TTTAAAT
18947 TTAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
28 1 0.03
30 4 0.12
31 12 0.38
32 11 0.34
33 4 0.12
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (29 bp):
TTTAAATATTTCAAAGAAATATATAAAAA
Found at i:18954 original size:24 final size:23
Alignment explanation
Indices: 18925--19003 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 23
18915 TACTTTCAAA
18925 AAATATAATAATAAAT-TTAAATTT
1 AAATATAATAATAAATATTAAA--T
*
18949 AAATATAAT-ATTAATATTAAAT
1 AAATATAATAATAAATATTAAAT
18971 AAATATAATTAATATTAATATTAAAT
1 AAATATAA-TAATA--AATATTAAAT
18997 AAA-ATAA
1 AAATATAA
19004 AATCCCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
22 9 0.19
23 6 0.12
24 16 0.33
25 4 0.08
26 13 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATAATAATAAATATTAAAT
Found at i:18962 original size:12 final size:12
Alignment explanation
Indices: 18925--19002 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
18915 TACTTTCAAA
*
18925 AAATATAATAAT
1 AAATATAATATT
*
18937 AAATTTAA-ATTT
1 AAATATAATA-TT
18949 AAATATAATATT
1 AAATATAATATT
18961 -AATATTAA-A-T
1 AAATA-TAATATT
18971 AAATAT-A-ATT
1 AAATATAATATT
18981 -AATATTAATATT
1 AAATA-TAATATT
*
18993 AAATAAAATA
1 AAATATAATA
19003 AAATCCCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
9 6 0.11
10 4 0.08
11 11 0.21
12 27 0.51
13 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATAATATT
Found at i:18985 original size:26 final size:25
Alignment explanation
Indices: 18954--19003 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
18944 AATTTAAATA
18954 TAATATTAATATTAAATAAATATAAT
1 TAATATTAATATTAAATAAA-ATAAT
18980 TAATATTAATATTAAATAAAATAA
1 TAATATTAATATTAAATAAAATAA
19004 AATCCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATATTAATATTAAATAAAATAAT
Done.