Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007038.1 Kokia drynarioides strain JFW-HI SEQ_121646, 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: 12910
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:5509 original size:47 final size:47
Alignment explanation
Indices: 5437--5544 Score: 135
Period size: 47 Copynumber: 2.3 Consensus size: 47
5427 AAGGTGGAAG
* * * **
5437 TTATTGGGAGTTTATTTGCGGTTTTGTTGGCTTGCCCACAATATTGA
1 TTATTGGTAGTTTATATGCGATTTTGGCGGCTTGCCCACAATATTGA
* ** *
5484 TTATTGGTAGTTTATATGCGATTTTGGCGGCTTGTCCATGATTTTGA
1 TTATTGGTAGTTTATATGCGATTTTGGCGGCTTGCCCACAATATTGA
5531 TTATTGGTAGTTTA
1 TTATTGGTAGTTTA
5545 CCTGTGATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (47 bp):
TTATTGGTAGTTTATATGCGATTTTGGCGGCTTGCCCACAATATTGA
Found at i:9322 original size:20 final size:20
Alignment explanation
Indices: 9298--9357 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
9288 AAAAATACAA
9298 AAAAAATTCAAAAATACTTT-T
1 AAAAAATTC-AAAATA-TTTAT
9319 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
9339 -AAAAATTCCAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
9357 A
1 A
9358 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 6 0.17
19 14 0.39
20 7 0.19
21 9 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:9322 original size:21 final size:18
Alignment explanation
Indices: 9298--9352 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 18
9288 AAAAATACAA
9298 AAAAAATTCAAAAATACTTTT
1 AAAAAATTC-AAAATA--TTT
9319 AAAAAATTCAAAATATTT
1 AAAAAATTCAAAATATTT
9337 ATAAAAATTCCAAAAT
1 A-AAAAATT-CAAAAT
9353 TTATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.12
19 7 0.22
20 12 0.38
21 9 0.28
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATTCAAAATATTT
Found at i:10314 original size:27 final size:26
Alignment explanation
Indices: 10271--10360 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
10261 TTTTTAAAGT
*
10271 TTAAAGATTT-TAT-TTTTATTTTTATA
1 TTAAA-ATTTATATATTTTATTATTA-A
*
10297 TTAAAATTTATATATTTTATTAATAAA
1 TTAAAATTTATATATTTTATT-ATTAA
* *
10324 TT-TAATTTAAATATTTTTATTAATTAA
1 TTAAAATTTATATA-TTTTATT-ATTAA
10351 TTAAAATTTA
1 TTAAAATTTA
10361 AGTTGAGCTG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.08
26 17 0.32
27 24 0.45
28 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTAAAATTTATATATTTTATTATTAA
Found at i:10337 original size:26 final size:28
Alignment explanation
Indices: 10281--10361 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 28
10271 TTAAAGATTT
** * *
10281 TATTTTTATTTTTATATTAAAATTTATA
1 TATTTTTATTAATAAATTAAAATTTAAA
*
10309 TA-TTTTATTAATAAATT-TAATTTAAA
1 TATTTTTATTAATAAATTAAAATTTAAA
*
10335 TATTTTTATTAATTAATTAAAATTTAA
1 TATTTTTATTAATAAATTAAAATTTAA
10362 GTTGAGCTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 9 0.20
27 26 0.59
28 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTTATTAATAAATTAAAATTTAAA
Found at i:11118 original size:13 final size:13
Alignment explanation
Indices: 11100--11124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11090 TTCAAGTATT
11100 TTTTTAATTAATG
1 TTTTTAATTAATG
11113 TTTTTAATTAAT
1 TTTTTAATTAAT
11125 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Done.