Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002426.1 Kokia drynarioides strain JFW-HI SEQ_114529, 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: 42679
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:218 original size:15 final size:15
Alignment explanation
Indices: 198--254 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
188 GTTCAATATT
198 AATATTTTAATAATA
1 AATATTTTAATAATA
*
213 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
232 AGTATATTAATAATA
1 AATATTTTAATAATA
247 AATATTTT
1 AATATTTT
255 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 9 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:732 original size:14 final size:14
Alignment explanation
Indices: 713--751 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
703 TTAGAAAAGT
713 AAATCATTTTCCAG
1 AAATCATTTTCCAG
**
727 AAATCATTTTTGAG
1 AAATCATTTTCCAG
*
741 AAACCATTTTC
1 AAATCATTTTC
752 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:16222 original size:29 final size:30
Alignment explanation
Indices: 16189--16247 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
16179 AGATGAATGG
16189 AATTTGTTTCGTGAG-AAAGATTAAGTGTA
1 AATTTGTTTCGTGAGAAAAGATTAAGTGTA
*
16218 AATTTGTTTCGTGCGAAAAGATTAAGTGTA
1 AATTTGTTTCGTGAGAAAAGATTAAGTGTA
16248 GACCGAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (30 bp):
AATTTGTTTCGTGAGAAAAGATTAAGTGTA
Found at i:16722 original size:36 final size:36
Alignment explanation
Indices: 16682--16752 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
16672 GGTGAAAGTG
*
16682 AATATGAGAGTATGTTATTCATGTCATGTGGCAATA
1 AATATGAGAGTATGTTATTCATGTCATGTGACAATA
* * *
16718 AATATGTGGGTATGTTTTTCATGTCATGTGACAAT
1 AATATGAGAGTATGTTATTCATGTCATGTGACAAT
16753 GATTATATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (36 bp):
AATATGAGAGTATGTTATTCATGTCATGTGACAATA
Found at i:17966 original size:21 final size:21
Alignment explanation
Indices: 17942--17992 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17932 AGAGTTTTTG
**
17942 GTATCGGTAGATGT-ATGACTT
1 GTATCGGTAGAAATCAT-ACTT
*
17963 GTATCAGTAGAAATCATACTT
1 GTATCGGTAGAAATCATACTT
17984 GTATCGGTA
1 GTATCGGTA
17993 AATCTAGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAATCATACTT
Found at i:28215 original size:2 final size:2
Alignment explanation
Indices: 28208--28233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28198 GTCAATTATT
28208 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28234 AATGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30487 original size:12 final size:12
Alignment explanation
Indices: 30470--30494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30460 TTTTAGCTCA
30470 TTTCCTTACAGT
1 TTTCCTTACAGT
30482 TTTCCTTACAGT
1 TTTCCTTACAGT
30494 T
1 T
30495 ACCTGAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTCCTTACAGT
Found at i:42467 original size:43 final size:43
Alignment explanation
Indices: 42361--42599 Score: 289
Period size: 43 Copynumber: 5.5 Consensus size: 43
42351 CTGTATTAAC
* * * * * *
42361 CTTATGCTCCAACCGAGTCCTAAGTTCTTCCATTTACAAATAAC
1 CTTATGCTCCAACCGAGACATAAG-TCTTCCTTTTATAAACAAT
** * *
42405 CTTATGCTCCTGCCCAGACATAAGTCTTCCTTCTATAAACAAT
1 CTTATGCTCCAACCGAGACATAAGTCTTCCTTTTATAAACAAT
* * * *
42448 CATATACTCCAACCGAGACATAAGTCTTCCTTTTATGAATAAT
1 CTTATGCTCCAACCGAGACATAAGTCTTCCTTTTATAAACAAT
* *
42491 CTTATGCTCTAACCAAGACATAAGTCTTCCTTTTATAAACAAT
1 CTTATGCTCCAACCGAGACATAAGTCTTCCTTTTATAAACAAT
** *
42534 CTTATGCTCCAACCGAGACATAAGTCTTCAATTTATAAATAAT
1 CTTATGCTCCAACCGAGACATAAGTCTTCCTTTTATAAACAAT
*
42577 CTTATGCTCTAACCGAGACATAA
1 CTTATGCTCCAACCGAGACATAA
42600 TGTAACATCC
Statistics
Matches: 165, Mismatches: 30, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
43 146 0.88
44 19 0.12
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (43 bp):
CTTATGCTCCAACCGAGACATAAGTCTTCCTTTTATAAACAAT
Found at i:42513 original size:86 final size:86
Alignment explanation
Indices: 42367--42599 Score: 324
Period size: 86 Copynumber: 2.7 Consensus size: 86
42357 TAACCTTATG
* * * * * *
42367 CTCCAACCGAGTCCTAAGTTCTTCCATTTACAAATAACCTTATGCTCCT-GCCCAGACATAAGTC
1 CTCCAACCGAGACATAAG-TCTTCCATTTATAAATAATCTTATGCT-CTAACCAAGACATAAGTC
42431 TTCCTTCTATAAACAATCATATA
64 TTCCTTCTATAAACAATCATATA
* *
42454 CTCCAACCGAGACATAAGTCTTCCTTTTATGAATAATCTTATGCTCTAACCAAGACATAAGTCTT
1 CTCCAACCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCTCTAACCAAGACATAAGTCTT
* * *
42519 CCTTTTATAAACAATCTTATG
66 CCTTCTATAAACAATCATATA
* *
42540 CTCCAACCGAGACATAAGTCTTCAATTTATAAATAATCTTATGCTCTAACCGAGACATAA
1 CTCCAACCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCTCTAACCAAGACATAA
42600 TGTAACATCC
Statistics
Matches: 130, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 2 0.02
86 112 0.86
87 16 0.12
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (86 bp):
CTCCAACCGAGACATAAGTCTTCCATTTATAAATAATCTTATGCTCTAACCAAGACATAAGTCTT
CCTTCTATAAACAATCATATA
Done.