Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009890.1 Kokia drynarioides strain JFW-HI SEQ_124626, 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: 220235
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:198210 original size:40 final size:40
Alignment explanation
Indices: 198155--198499 Score: 369
Period size: 40 Copynumber: 8.7 Consensus size: 40
198145 AAATGGACAA
* * *
198155 ATTGAAGACCATCCGATCTCTTACCCCGACTAAAGGGCAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGCAG
*
198195 ATTGAAAACCATCCGATCTTTTACCCCGACCATGA-GGCAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCA-GAGGGCAG
*
198235 ATTGAAGACCATCCAATCTTTTACCCCGACCAGAGGGCAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGCAG
* * *
198275 ATTGAAGATCATCCGATCTTTTACCCCGATCATG-GGGCAA
1 ATTGAAGACCATCCGATCTTTTACCCCGACCA-GAGGGCAG
* ** *
198315 ATTGAAGATCATCCGATCTTTTACCCTAACCAGAGGGTAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGCAG
* * * *
198355 ATTTAAGACCATCCGATCTCTTACCCTGACCATAGGGCAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGCAG
* * **
198395 ATTAAAGTA--ATCCAATCTTTTACCCTAACCAGAGGGCAG
1 ATTGAAG-ACCATCCGATCTTTTACCCCGACCAGAGGGCAG
* ** *
198434 ATTGAAGACCATTCGATCTCCTACCCCAACCATG-GGGCAG
1 ATTGAAGACCATCCGATCTTTTACCCCGACCA-GAGGGCAG
* **
198474 ATTGAA-ACAATCTAATCTTTTACCCC
1 ATTGAAGACCATCCGATCTTTTACCCC
198500 TAAAATTATA
Statistics
Matches: 259, Mismatches: 38, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.00
39 49 0.19
40 205 0.79
41 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (40 bp):
ATTGAAGACCATCCGATCTTTTACCCCGACCAGAGGGCAG
Found at i:199120 original size:63 final size:64
Alignment explanation
Indices: 199043--199166 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 64
199033 TTATGAATAT
*
199043 AAATAAATATTAATTTTGTTTTATTATTTATTTATTATTGTATTAATATAAATAAATAAATGTA
1 AAATAAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAATGTA
* *
199107 AAAT-AATATTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAGATAAATAAAT
1 AAATAAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAAT
199167 AAATAAATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 53 0.93
64 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (64 bp):
AAATAAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAATGTA
Found at i:206252 original size:20 final size:20
Alignment explanation
Indices: 206175--206264 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
206165 TTTGGTTTGT
* **
206175 TTTAAAAATATTTTGAAGTG
1 TTTAAAATTATTTTGACTTG
* *
206195 -TTAAAATGATTTTGACTGG
1 TTTAAAATTATTTTGACTTG
* *
206214 GTTCAAATTATTTTGACTTG
1 TTTAAAATTATTTTGACTTG
*
206234 TTTAAAATTATTTTAACTTG
1 TTTAAAATTATTTTGACTTG
206254 ATCTTAAAATT
1 -T-TTAAAATT
206265 GTTTCAAACT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.25
20 33 0.59
21 1 0.02
22 8 0.14
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (20 bp):
TTTAAAATTATTTTGACTTG
Found at i:208109 original size:86 final size:86
Alignment explanation
Indices: 208012--208183 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
208002 GGGATTGTTC
208012 TGTAGCGAGAAGTATTTGGGATCAGTTAATTCTAATAGAACGACAAGCTTGGTTTTATTCTAGTA
1 TGTAGCGAGAAGTATTTGGGATCAGTTAATTCTAATAGAACGACAAGCTTGGTTTTATTCTAGTA
208077 ATTTGTAGGAATGGCTTGTAT
66 ATTTGTAGGAATGGCTTGTAT
208098 TGTAGCGAGAAGTATTTGGGATCAGTTAATTCTAATAGAACGACAAGCTTGGTTTTATTCTAGTA
1 TGTAGCGAGAAGTATTTGGGATCAGTTAATTCTAATAGAACGACAAGCTTGGTTTTATTCTAGTA
*
208163 ATTTGTAGGAATGGTTTGTAT
66 ATTTGTAGGAATGGCTTGTAT
208184 CAAACTTGCA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (86 bp):
TGTAGCGAGAAGTATTTGGGATCAGTTAATTCTAATAGAACGACAAGCTTGGTTTTATTCTAGTA
ATTTGTAGGAATGGCTTGTAT
Found at i:210432 original size:24 final size:25
Alignment explanation
Indices: 210403--210454 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
210393 TTATTATTAA
210403 ATATAATTTAATAAAAATA-ATAAT
1 ATATAATTTAATAAAAATATATAAT
* *
210427 ATATAATTTAATAACAATATTTAAT
1 ATATAATTTAATAAAAATATATAAT
210452 ATA
1 ATA
210455 ATTATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAATTTAATAAAAATATATAAT
Found at i:210445 original size:18 final size:18
Alignment explanation
Indices: 210418--210456 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
210408 ATTTAATAAA
* *
210418 AATAATAATATATAATTT
1 AATAACAATATATAATAT
*
210436 AATAACAATATTTAATAT
1 AATAACAATATATAATAT
210454 AAT
1 AAT
210457 TATTTTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAACAATATATAATAT
Found at i:210956 original size:23 final size:24
Alignment explanation
Indices: 210930--210982 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
210920 TAATTTATAT
210930 TTAATAATTAAATATATT-TAAAA
1 TTAATAATTAAATATATTATAAAA
** *
210953 TTAAT-ATTTCATATATTATAATA
1 TTAATAATTAAATATATTATAAAA
210976 TTAATAA
1 TTAATAA
210983 ATTTTGATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.40
23 14 0.56
24 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATAATTAAATATATTATAAAA
Found at i:210959 original size:15 final size:17
Alignment explanation
Indices: 210925--210956 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
210915 ATAAGTAATT
210925 TATATTTAATAATTAAA
1 TATATTTAATAATTAAA
210942 TATATTTAA-AATTAA
1 TATATTTAATAATTAA
210957 TATTTCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTTAATAATTAAA
Found at i:212406 original size:130 final size:130
Alignment explanation
Indices: 212173--212434 Score: 497
Period size: 130 Copynumber: 2.0 Consensus size: 130
212163 GCCTGCTTCC
* * *
212173 ATCAGTGAATCACTAGAAATTCTTGTTCTTGATGAGGTAAGAGTTTGAGTAGAATGTAGAGCGAC
1 ATCAGTGAATCACTAGAAATTCTAGTCCTTGATGAGGTAAGAATTTGAGTAGAATGTAGAGCGAC
212238 TTTCTAAAGTTAGTTGGGTTCATGCAGCTATTTTTATCATAAGTGAAGTTATGATTTGAGCAAGT
66 TTTCTAAAGTTAGTTGGGTTCATGCAGCTATTTTTATCATAAGTGAAGTTATGATTTGAGCAAGT
212303 ATCAGTGAATCACTAGAAATTCTAGTCCTTGATGAGGTAAGAATTTGAGTAGAATGTAGAGCGAC
1 ATCAGTGAATCACTAGAAATTCTAGTCCTTGATGAGGTAAGAATTTGAGTAGAATGTAGAGCGAC
212368 TTTCTAAAGTTAGTTGGGTTCATGCAGCTATTTTTATCATAAGTGAAGTTATGATTTGAGCAAGT
66 TTTCTAAAGTTAGTTGGGTTCATGCAGCTATTTTTATCATAAGTGAAGTTATGATTTGAGCAAGT
212433 AT
1 AT
212435 GTACTCATAT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (130 bp):
ATCAGTGAATCACTAGAAATTCTAGTCCTTGATGAGGTAAGAATTTGAGTAGAATGTAGAGCGAC
TTTCTAAAGTTAGTTGGGTTCATGCAGCTATTTTTATCATAAGTGAAGTTATGATTTGAGCAAGT
Done.