Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001853.1 Kokia drynarioides strain JFW-HI SEQ_113609, 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: 63593
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4257 original size:22 final size:23
Alignment explanation
Indices: 4217--4259 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4207 GTGATAGATT
4217 AATTGAAGATAATTCATTATTAG
1 AATTGAAGATAATTCATTATTAG
* *
4240 AATTTAAGA-AATTGATTATT
1 AATTGAAGATAATTCATTATT
4260 GGTTTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
AATTGAAGATAATTCATTATTAG
Found at i:5320 original size:12 final size:12
Alignment explanation
Indices: 5303--5329 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5293 TAAAATATCA
5303 AAATTATTTTTT
1 AAATTATTTTTT
5315 AAATTATTTTTT
1 AAATTATTTTTT
5327 AAA
1 AAA
5330 ATATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AAATTATTTTTT
Found at i:5362 original size:30 final size:30
Alignment explanation
Indices: 5315--5376 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
5305 ATTATTTTTT
5315 AAATTATTTTTTAAAAT-ATAAAATTATTA
1 AAATTATTTTTTAAAATAATAAAATTATTA
*
5344 AAATTATTTTTTTGAAATAATAAAATTATTA
1 AAATTA-TTTTTTAAAATAATAAAATTATTA
5375 AA
1 AA
5377 TAATTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.20
30 10 0.33
31 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
AAATTATTTTTTAAAATAATAAAATTATTA
Found at i:5383 original size:30 final size:29
Alignment explanation
Indices: 5290--5383 Score: 100
Period size: 30 Copynumber: 3.0 Consensus size: 29
5280 CAGAAAATGA
5290 TTTTAAAATATCAAAATTATTTTTTAAATTA-TT
1 TTTTAAAATAT-AAAATTA----TTAAATTATTT
5323 TTTTAAAATATAAAATTATTAAAATTATTT
1 TTTTAAAATATAAAATTATT-AAATTATTT
* *
5353 TTTTGAAATAATAAAATTATTAAATAATTT
1 TTTTAAAAT-ATAAAATTATTAAATTATTT
5383 T
1 T
5384 AATATTCAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.04
29 6 0.11
30 19 0.34
31 11 0.20
32 7 0.12
33 11 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTTAAAATATAAAATTATTAAATTATTT
Found at i:5464 original size:15 final size:17
Alignment explanation
Indices: 5440--5476 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5430 TACAACACAT
*
5440 TTTTTGGAAATTTG-AA
1 TTTTTGGAAATCTGAAA
5456 TTTTT-GAAATCTGAAA
1 TTTTTGGAAATCTGAAA
5472 TTTTT
1 TTTTT
5477 TTTGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.54
Consensus pattern (17 bp):
TTTTTGGAAATCTGAAA
Found at i:6360 original size:32 final size:30
Alignment explanation
Indices: 6324--6410 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 30
6314 GAAAATCCCC
*
6324 AAACCTAAATCTAGAAAATCCCCAAAATTTTG
1 AAACCTAAA-CT-GAAAATCCCCAAAATTTTA
* *
6356 AAACCTAAAACCCGAAAATCTCCAAAATTTTA
1 AAACCT-AAA-CTGAAAATCCCCAAAATTTTA
6388 AAACCTAAACT-AAAATCCCCAAA
1 AAACCTAAACTGAAAATCCCCAAA
6411 CTCAATAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 11 0.23
30 1 0.02
31 3 0.06
32 29 0.60
33 4 0.08
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (30 bp):
AAACCTAAACTGAAAATCCCCAAAATTTTA
Found at i:14194 original size:6 final size:6
Alignment explanation
Indices: 14183--14212 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
14173 ATTTTATTAG
14183 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
14213 ACAACTAACC
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:20045 original size:2 final size:2
Alignment explanation
Indices: 20038--20079 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20028 AAAACAAATA
20038 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20080 GATAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29693 original size:25 final size:24
Alignment explanation
Indices: 29665--29716 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
29655 CTACAATATG
* * *
29665 AATATTAATATATTTTTATATCATA
1 AATATCAATATA-TGTTATATAATA
*
29690 AATATCCATATATGTTATATAATA
1 AATATCAATATATGTTATATAATA
29714 AAT
1 AAT
29717 TTATTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
AATATCAATATATGTTATATAATA
Found at i:37426 original size:15 final size:16
Alignment explanation
Indices: 37397--37429 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37387 AAAGTCACTA
*
37397 TTCATACATTTAAATT
1 TTCATACATTCAAATT
37413 TTCA-ACATTCAAATT
1 TTCATACATTCAAATT
37428 TT
1 TT
37430 ATTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (16 bp):
TTCATACATTCAAATT
Found at i:43061 original size:25 final size:24
Alignment explanation
Indices: 43024--43089 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
43014 TATCAATTTT
43024 TTTATATTGAATAAATAT-AATTA
1 TTTATATTGAATAAATATAAATTA
*
43047 TTTATATATGCAATATATATAAATTA
1 TTTATAT-TG-AATAAATATAAATTA
*
43073 -TTATATT-AATAATTATA
1 TTTATATTGAATAAATATA
43090 TTGATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 3 0.08
25 14 0.38
26 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (24 bp):
TTTATATTGAATAAATATAAATTA
Found at i:57109 original size:18 final size:16
Alignment explanation
Indices: 57082--57122 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
57072 TTAGGATTTA
*
57082 AAAAATTTAATTAATT
1 AAAAATTTATTTAATT
57098 --AAATTTATTTAATT
1 AAAAATTTATTTAATT
57112 AAAAATTTATT
1 AAAAATTTATT
57123 CTCATTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATTTATTTAATT
Done.