Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004663.1 Kokia drynarioides strain JFW-HI SEQ_118207, 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: 20530
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:347 original size:5 final size:5
Alignment explanation
Indices: 339--363 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
329 GGGCACATGC
339 CTCAA CTCAA CTCAA CTCAA CTCAA
1 CTCAA CTCAA CTCAA CTCAA CTCAA
364 ACCCTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCAA
Found at i:6653 original size:23 final size:24
Alignment explanation
Indices: 6610--6655 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
6600 AGTTGGATTC
6610 AAATTAAATTCTAAAAGATAATTA
1 AAATTAAATTCTAAAAGATAATTA
6634 AAATTAAA-TCTAAACA-ATAATT
1 AAATTAAATTCTAAA-AGATAATT
6656 CCCTAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATTAAATTCTAAAAGATAATTA
Found at i:9252 original size:30 final size:31
Alignment explanation
Indices: 9216--9287 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
9206 CAAATAATTT
9216 TAAAATTATTAAAATGATTTTTAAAAAAT-A
1 TAAAATTATTAAAATGATTTTTAAAAAATAA
* ***
9246 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATGATTTTTAAAAAATAA
9277 TAAAATTATTA
1 TAAAATTATTA
9288 GATAATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAAATTATTAAAATGATTTTTAAAAAATAA
Found at i:10057 original size:3 final size:3
Alignment explanation
Indices: 10051--10075 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10041 GATGAAAAAG
10051 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
10076 ATTGGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10128 original size:31 final size:29
Alignment explanation
Indices: 10093--10198 Score: 133
Period size: 30 Copynumber: 3.6 Consensus size: 29
10083 ATTAAAATTA
10093 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
*
10124 TTTAATAATTTTATATTTTAAAAAATAA-
1 TTTAATAATTTTATATTTAAAAAAATAAT
* *
10152 TTTACAAAATTTTATATTTAGAAATAATAAT
1 TTTA-ATAATTTTATATTTA-AAAAAATAAT
*
10183 TTTTATAATTTTATAT
1 TTTAATAATTTTATAT
10199 AAAATAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
28 4 0.06
29 22 0.33
30 24 0.36
31 16 0.24
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:10181 original size:59 final size:59
Alignment explanation
Indices: 10086--10198 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
10076 ATTGGAAATT
* *
10086 AAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATTTAAAAATTTTATTATTTCAAAAAAATAATTTTAATAATTTTATATTTTAA
* *
10145 AAAATAATTTACAAAATTTTA-TATTT-AGAAATAATAATTTTTATAATTTTATAT
1 AAAATAATTTA-AAAATTTTATTATTTCA-AAAAAATAATTTTAATAATTTTATAT
10199 AAAATAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.02
59 39 0.81
60 8 0.17
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (59 bp):
AAAATAATTTAAAAATTTTATTATTTCAAAAAAATAATTTTAATAATTTTATATTTTAA
Found at i:11742 original size:29 final size:30
Alignment explanation
Indices: 11708--11769 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
11698 GTTTAACGTG
11708 TATAATT-ACATCAAATTAAAATTCATGTA
1 TATAATTAACATCAAATTAAAATTCATGTA
* *
11737 TATAATTACACATTAAATTAAAATTTATGTA
1 TATAATTA-ACATCAAATTAAAATTCATGTA
11768 TA
1 TA
11770 ATTTTTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
31 22 0.76
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (30 bp):
TATAATTAACATCAAATTAAAATTCATGTA
Found at i:12789 original size:40 final size:35
Alignment explanation
Indices: 12745--12817 Score: 83
Period size: 35 Copynumber: 1.9 Consensus size: 35
12735 TTATTTTAAT
12745 TAAATAAATAATTTTGAAATATTATTTATATAAAATAAAA
1 TAAATAAAT-ATTTT---ATATTATTT-TATAAAATAAAA
* *
12785 TAAATATATATTTTATATTATTTTATTAAATAA
1 TAAATAAATATTTTATATTATTTTATAAAATAA
12818 TCCTAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 9 0.29
36 9 0.29
39 5 0.16
40 8 0.26
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
TAAATAAATATTTTATATTATTTTATAAAATAAAA
Found at i:18921 original size:58 final size:58
Alignment explanation
Indices: 18831--18949 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 58
18821 CTTTGACCTA
* *
18831 GTATCATTAGAACTTGGAAGGAATTGGTTATACTGCTGTTGTATGTTATTTGCTCGAG
1 GTATCATTAGAACTTGGAAGCAATTGGTTATACTGCTGTTGTATGTTATTTACTCGAG
* *
18889 GTATCATTAGAACTTGGAAGCCATTGGTTATACTGCTGTTGTATGTTATTTACTTGAG
1 GTATCATTAGAACTTGGAAGCAATTGGTTATACTGCTGTTGTATGTTATTTACTCGAG
18947 GTA
1 GTA
18950 GATACAGTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (58 bp):
GTATCATTAGAACTTGGAAGCAATTGGTTATACTGCTGTTGTATGTTATTTACTCGAG
Found at i:20296 original size:19 final size:19
Alignment explanation
Indices: 20272--20335 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
20262 CTCATGTCTC
*
20272 AATTTTCATTGGATACTAA
1 AATTTTTATTGGATACTAA
* * *
20291 AATTTTTAATGCAATACAAA
1 AATTTTTATTG-GATACTAA
*
20311 ATATTTTTATTGGATATTAA
1 A-ATTTTTATTGGATACTAA
20331 AATTT
1 AATTT
20336 ATAATCCATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 13 0.37
20 13 0.37
21 9 0.26
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (19 bp):
AATTTTTATTGGATACTAA
Found at i:20323 original size:40 final size:38
Alignment explanation
Indices: 20273--20357 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 38
20263 TCATGTCTCA
* *
20273 ATTTTCATTGGATACTAAAATTTTTAATGCAATACAAAAT
1 ATTTTTATTGGATACTAAAATTTATAAT-CAATAC-AAAT
* * *
20313 ATTTTTATTGGATATTAAAATTTATAATCCATACCAAT
1 ATTTTTATTGGATACTAAAATTTATAATCAATACAAAT
20351 ATTTTTA
1 ATTTTTA
20358 ATACAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 10 0.25
39 5 0.12
40 25 0.62
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (38 bp):
ATTTTTATTGGATACTAAAATTTATAATCAATACAAAT
Done.