Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000202.1 Kokia drynarioides strain JFW-HI SEQ_110892, 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: 20288
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:1583 original size:46 final size:46
Alignment explanation
Indices: 1508--1599 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1498 TAGAACTTAC
1508 AATAACACTATGATATTATTCCTCCAGAAAACGAAACACTGTAGCT
1 AATAACACTATGATATTATTCCTCCAGAAAACGAAACACTGTAGCT
* *
1554 AATAACACTATGATATTATTTCTCTAGAAAACGAAACACTGTAGCT
1 AATAACACTATGATATTATTCCTCCAGAAAACGAAACACTGTAGCT
1600 CGGATACCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (46 bp):
AATAACACTATGATATTATTCCTCCAGAAAACGAAACACTGTAGCT
Found at i:7846 original size:12 final size:13
Alignment explanation
Indices: 7831--7871 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
7821 AAGTAGAAAC
7831 AAAA-TAAAAAAT
1 AAAACTAAAAAAT
7843 AAAACTAAAAAA-
1 AAAACTAAAAAAT
*
7855 AAAACTAAAATAT
1 AAAACTAAAAAAT
7868 AAAA
1 AAAA
7872 AATTATCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAACTAAAAAAT
Found at i:7852 original size:18 final size:17
Alignment explanation
Indices: 7827--7864 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
7817 TCAAAAGTAG
7827 AAACAAAATAAAAAA-TA
1 AAACAAAA-AAAAAACTA
7844 AAACTAAAAAAAAAACTA
1 AAAC-AAAAAAAAAACTA
7862 AAA
1 AAA
7865 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (17 bp):
AAACAAAAAAAAAACTA
Found at i:7871 original size:18 final size:17
Alignment explanation
Indices: 7827--7873 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
7817 TCAAAAGTAG
7827 AAAC-AAAATAAAAAATA
1 AAACTAAAA-AAAAAATA
7844 AAACTAAAAAAAAAACTA
1 AAACTAAAAAAAAAA-TA
7862 AAA-TATAAAAAA
1 AAACTA-AAAAAA
7874 TTATCGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (17 bp):
AAACTAAAAAAAAAATA
Found at i:8138 original size:25 final size:26
Alignment explanation
Indices: 8108--8176 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 26
8098 ATTCATATTT
8108 AATTATTTATATTTAGTTA-TAT-ATA
1 AATTATTTATATTTA-TTATTATAATA
*
8133 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATTATTATAATA
8162 AATTATTTAATATTT
1 AATTATTT-ATATTT
8177 CGATTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
25 7 0.19
27 11 0.30
28 9 0.24
29 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
AATTATTTATATTTATTATTATAATA
Found at i:8224 original size:16 final size:15
Alignment explanation
Indices: 8183--8226 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
8173 ATTTCGATTT
8183 TATTTT-AATAATAA
1 TATTTTAAATAATAA
8197 -ATTTTAAA-AATAA
1 TATTTTAAATAATAA
8210 CTATTTTAAATAATAA
1 -TATTTTAAATAATAA
8226 T
1 T
8227 TTCACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 9 0.35
16 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTTAAATAATAA
Found at i:8276 original size:15 final size:15
Alignment explanation
Indices: 8256--8312 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
8246 ATTCAATATT
8256 AATATTTTAATAATA
1 AATATTTTAATAATA
*
8271 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
8290 AATATATTAATAATA
1 AATATTTTAATAATA
*
8305 AATGTTTT
1 AATATTTT
8313 GTAATGTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:8728 original size:14 final size:15
Alignment explanation
Indices: 8709--8746 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
8699 ATATTAACAT
8709 AAATTATTTTTC-AA
1 AAATTATTTTTCGAA
8723 AAATTATTTTTCGAA
1 AAATTATTTTTCGAA
*
8738 AAATAATTT
1 AAATTATTT
8747 CAATAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTATTTTTCGAA
Found at i:10459 original size:17 final size:17
Alignment explanation
Indices: 10424--10458 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10414 ACCTACATAT
10424 AATAAATCATAAACCAA
1 AATAAATCATAAACCAA
*
10441 AATAAAT-ATAGACCAA
1 AATAAATCATAAACCAA
10457 AA
1 AA
10459 ACCTAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (17 bp):
AATAAATCATAAACCAA
Found at i:12265 original size:28 final size:28
Alignment explanation
Indices: 12211--12263 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
12201 ATTAATAAAA
*
12211 TAAATTTAAAAATGTTAATAGTTAAACC
1 TAAATTTAAAAATGTTAAAAGTTAAACC
* *
12239 TAAATTTTAAAAT-TTAAAATTTAAA
1 TAAATTTAAAAATGTTAAAAGTTAAA
12264 ACGTAGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAATTTAAAAATGTTAAAAGTTAAACC
Found at i:15972 original size:12 final size:12
Alignment explanation
Indices: 15957--15982 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15947 ATACAATTAA
15957 AAATATTAAAAT
1 AAATATTAAAAT
15969 AAATATTAAAAT
1 AAATATTAAAAT
15981 AA
1 AA
15983 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:16020 original size:41 final size:38
Alignment explanation
Indices: 15951--16050 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 38
15941 TATCAAATAC
*
15951 AATTAAAAATATTAAAATAAATATTAAAATAACAAACA
1 AATTAAAAATATTAAAATAAATAGTAAAATAACAAACA
* *
15989 AATTAAAAACTATTTTAAAATAATTCGTAAAATAACAAACA
1 AATTAAAAA-TA--TTAAAATAAATAGTAAAATAACAAACA
* *
16030 AAGTGAAAATATAATAAAATA
1 AA-TTAAAA-ATATTAAAATA
16051 TTTCATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
38 9 0.17
39 2 0.04
40 7 0.13
41 26 0.50
42 7 0.13
43 1 0.02
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (38 bp):
AATTAAAAATATTAAAATAAATAGTAAAATAACAAACA
Found at i:16910 original size:2 final size:2
Alignment explanation
Indices: 16903--16929 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16893 TTTATAAAAT
16903 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16930 TTGAATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.