Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003120.1 Kokia drynarioides strain JFW-HI SEQ_115693, 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: 18073
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:730 original size:14 final size:14
Alignment explanation
Indices: 711--754 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
701 CCAAAAATTA
*
711 TAAAAAATTAAAAT
1 TAAAAAATAAAAAT
725 TAAAAAATAAAAAT
1 TAAAAAATAAAAAT
*
739 AAAAATAATAAAAAT
1 TAAAA-AATAAAAAT
754 T
1 T
755 TCAAATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAAATAAAAAT
Found at i:735 original size:13 final size:14
Alignment explanation
Indices: 710--753 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
700 TCCAAAAATT
710 ATAAAAAATTAAAA
1 ATAAAAAATTAAAA
*
724 TTAAAAAA-TAAAA
1 ATAAAAAATTAAAA
*
737 ATAAAAATAATAAAA
1 ATAAAAA-ATTAAAA
752 AT
1 AT
754 TTCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 8 0.31
15 7 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAAAATTAAAA
Found at i:3298 original size:2 final size:2
Alignment explanation
Indices: 3293--3335 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3283 TAATTTTAGA
3293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3335 A
1 A
3336 ATTTTTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3433 original size:18 final size:18
Alignment explanation
Indices: 3410--3451 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3400 TTTTCTAAAA
3410 TTTTAATTATTTTAATAT
1 TTTTAATTATTTTAATAT
*
3428 TTTTAATTATTTTTATAT
1 TTTTAATTATTTTAATAT
3446 TTTTAA
1 TTTTAA
3452 ACATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTAATTATTTTAATAT
Found at i:3440 original size:10 final size:9
Alignment explanation
Indices: 3410--3461 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
3400 TTTTCTAAAA
3410 TTTTAAT-T
1 TTTTAATAT
3418 ATTTTAATAT
1 -TTTTAATAT
3428 TTTTAATTAT
1 TTTTAA-TAT
3438 TTTT-ATAT
1 TTTTAATAT
*
3446 TTTTAAACAT
1 TTTT-AATAT
3456 TTTTAA
1 TTTTAA
3462 AAATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 7 0.18
9 16 0.42
10 15 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTAATAT
Found at i:3516 original size:27 final size:27
Alignment explanation
Indices: 3468--3532 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
3458 TTAAAAATAT
* * *
3468 ATATTTTATTAAATTTTAAAATGTTTTA
1 ATATTTT-TTAAATTATAAAATATTTAA
*
3496 ATATTTTTTAAATTATCAAATATTTAA
1 ATATTTTTTAAATTATAAAATATTTAA
*
3523 ATAATTTTTA
1 ATATTTTTTA
3533 TTTTTATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATTTTTTAAATTATAAAATATTTAA
Found at i:3599 original size:19 final size:17
Alignment explanation
Indices: 3559--3593 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3549 TAAAATTTGG
3559 ATTTTTACAATTTTTAA
1 ATTTTTACAATTTTTAA
3576 ATTTTATACATATTTTTA
1 ATTTT-TACA-ATTTTTA
3594 GGTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACAATTTTTAA
Done.