Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001822.1 Kokia drynarioides strain JFW-HI SEQ_113566, 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: 45569
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:7067 original size:61 final size:61
Alignment explanation
Indices: 6970--7091 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
6960 AAGTCCGACC
* *
6970 CAATCCGTCTCTTTTTGTAAGCATTGTAATAATTTTACCATGTTATTTTCATATATTATTA
1 CAATCCGTATCTTTTCGTAAGCATTGTAATAATTTTACCATGTTATTTTCATATATTATTA
* *
7031 CAATCCGTATGTTTTCGTAAGCATTGTAATATTTTTACCATGTTATTTTCATATATTATTA
1 CAATCCGTATCTTTTCGTAAGCATTGTAATAATTTTACCATGTTATTTTCATATATTATTA
7092 TAATGTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (61 bp):
CAATCCGTATCTTTTCGTAAGCATTGTAATAATTTTACCATGTTATTTTCATATATTATTA
Found at i:7409 original size:17 final size:18
Alignment explanation
Indices: 7378--7411 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7368 TTAATTTTTT
*
7378 TAAATTAAAAGTTAAATC
1 TAAATTAAAAATTAAATC
7396 TAAA-TAAAAATTAAAT
1 TAAATTAAAAATTAAAT
7412 TAACAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAATTAAAAATTAAATC
Found at i:19362 original size:20 final size:20
Alignment explanation
Indices: 19333--19401 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
19323 AAAATTCAAA
*
19333 AAAATCATAAAATTATTTTT
1 AAAATTATAAAATTATTTTT
19353 AAAATTATAAAATTA--TTT
1 AAAATTATAAAATTATTTTT
*
19371 AAAA-TATAAAAAATATTTTT
1 AAAATTAT-AAAATTATTTTT
19391 AAAATTA-AAAA
1 AAAATTATAAAA
19402 AAAATTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
17 3 0.07
18 13 0.30
19 4 0.09
20 21 0.49
21 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTATAAAATTATTTTT
Found at i:19365 original size:38 final size:38
Alignment explanation
Indices: 19322--19402 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
19312 TTTAATTTTC
*
19322 AAAAATTCA-AAAAAATCAT-AAAATTATTTTTAAAATTA
1 AAAAATT-ATAAAAAAT-ATAAAAAATATTTTTAAAATTA
* **
19360 TAAAATTATTTAAAATATAAAAAATATTTTTAAAATTA
1 AAAAATTATAAAAAATATAAAAAATATTTTTAAAATTA
19398 AAAAA
1 AAAAA
19403 AAATTAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
37 3 0.08
38 33 0.92
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (38 bp):
AAAAATTATAAAAAATATAAAAAATATTTTTAAAATTA
Found at i:19399 original size:19 final size:19
Alignment explanation
Indices: 19341--19402 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
19331 AAAAAATCAT
*
19341 AAAATTATTTTTAAAATTA
1 AAAAATATTTTTAAAATTA
* *
19360 TAAAAT-TATTTAAAATATA
1 AAAAATATTTTTAAAAT-TA
19379 AAAAATATTTTTAAAATTA
1 AAAAATATTTTTAAAATTA
19398 AAAAA
1 AAAAA
19403 AAATTAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 9 0.25
19 18 0.50
20 9 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATATTTTTAAAATTA
Found at i:22727 original size:18 final size:18
Alignment explanation
Indices: 22704--22738 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22694 CCATAGCCAC
22704 CTTCAC-CAATCACATTCT
1 CTTCACACAATC-CATTCT
22722 CTTCACACAATCCATTC
1 CTTCACACAATCCATTC
22739 GTAGCTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (18 bp):
CTTCACACAATCCATTCT
Done.