Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002223.1 Kokia drynarioides strain JFW-HI SEQ_114218, 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: 10911
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:2133 original size:30 final size:28
Alignment explanation
Indices: 2085--2147 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
2075 TTTTCTATAG
*
2085 TTTACCCAAAAATATATTTACTTTTTTT
1 TTTACCCAAAAATATATTTACTTTTTCT
*
2113 TTTACCCAAAAAAATGTATTTACTTTTTCT
1 TTTACCC--AAAAATATATTTACTTTTTCT
2143 TTTAC
1 TTTAC
2148 GAGAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 7 0.23
30 24 0.77
ACGTcount: A:0.32, C:0.16, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTACCCAAAAATATATTTACTTTTTCT
Found at i:2591 original size:29 final size:27
Alignment explanation
Indices: 2559--2625 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 27
2549 AAAAACTAGA
2559 AAAATATATTAAAAAATAATAAAAATTAT
1 AAAA-ATATTAAAAAATAATAAAAA-TAT
* ***
2588 AAAAATTACTAAATTTTAATAAAAATAT
1 AAAAA-TATTAAAAAATAATAAAAATAT
2616 AAAAAATATT
1 -AAAAATATT
2626 TAAATTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAAATATTAAAAAATAATAAAAATAT
Found at i:2600 original size:19 final size:21
Alignment explanation
Indices: 2545--2592 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2535 CTCCTACTTT
* *
2545 TATTAAAAACT-AGAAAAATA
1 TATTAAAAAATAATAAAAATA
2565 TATTAAAAAATAATAAAAAT-
1 TATTAAAAAATAATAAAAATA
2585 TA-TAAAAA
1 TATTAAAAA
2593 TTACTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TATTAAAAAATAATAAAAATA
Found at i:2620 original size:28 final size:29
Alignment explanation
Indices: 2575--2650 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
2565 TATTAAAAAA
2575 TAATAAAAATTATAAAAATTA-CTAAATTT
1 TAATAAAAA-TATAAAAATTATCTAAATTT
* *
2604 TAATAAAAATATAAAAAATATTTAAATTT
1 TAATAAAAATATAAAAATTATCTAAATTT
* *
2633 TATTAAAAAT-TAGAAATT
1 TAATAAAAATATAAAAATT
2651 TTTTTTATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 16 0.39
29 25 0.61
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
TAATAAAAATATAAAAATTATCTAAATTT
Found at i:2979 original size:27 final size:26
Alignment explanation
Indices: 2949--3011 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
2939 ATATATTTTA
* *
2949 TAATTTTTTATGATCTTTATAAA-ATTT
1 TAATTTTTTATAAT-TTT-TAAATATAT
2976 TAATTTTTTATAATTTTTAAATATAT
1 TAATTTTTTATAATTTTTAAATATAT
3002 TATATTTTTT
1 TA-ATTTTTT
3012 TATTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 20 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TAATTTTTTATAATTTTTAAATATAT
Found at i:4927 original size:15 final size:15
Alignment explanation
Indices: 4903--4932 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4893 GTTCATGTTG
4903 GAGGAGAGAGAAAAT
1 GAGGAGAGAGAAAAT
*
4918 GAGGATAGAGAAAAT
1 GAGGAGAGAGAAAAT
4933 AAAACTAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (15 bp):
GAGGAGAGAGAAAAT
Found at i:6064 original size:21 final size:21
Alignment explanation
Indices: 6040--6093 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
6030 CTTGTGATAG
6040 TTCTACCGATACAAG-TATAAC
1 TTCTACCGATACAAGTTAT-AC
*
6061 TTCTACCGAAACAAGTTATAC
1 TTCTACCGATACAAGTTATAC
*
6082 TTCCACCGATAC
1 TTCTACCGATAC
6094 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTTATAC
Found at i:10887 original size:17 final size:18
Alignment explanation
Indices: 10864--10911 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
10854 CCATACTCCC
10864 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
*
10882 -TTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAA
10898 TTTAAATTTATTTT
1 TTTAAATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 7 0.27
17 16 0.62
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Done.