Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002007.1 Kokia drynarioides strain JFW-HI SEQ_113869, 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: 41598
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA 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 TA TA TA TA TA T
38 TAACATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12089 original size:23 final size:23
Alignment explanation
Indices: 12035--12092 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
12025 CGTCCATCCT
* *
12035 TGCTGACTAGACCTTTTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
12058 TGTTGACTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
12081 TGCTGACTGGAC
1 TGCTGACTGGAC
12093 GGCATGTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:12973 original size:14 final size:15
Alignment explanation
Indices: 12954--12986 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12944 CCCAATTTTA
*
12954 TTTTTATTTTTA-TT
1 TTTTTAGTTTTAGTT
12968 TTTTTAGTTTTAGTT
1 TTTTTAGTTTTAGTT
12983 TTTT
1 TTTT
12987 CTTGCATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTAGTTTTAGTT
Found at i:13880 original size:17 final size:16
Alignment explanation
Indices: 13840--13882 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
13830 TTCTAGAGAC
*
13840 GCCATTATTTAATACA
1 GCCATTATTTTATACA
*
13856 -CTATTATTTTATACA
1 GCCATTATTTTATACA
13871 GGCCATTATTTT
1 -GCCATTATTTT
13883 TAATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (16 bp):
GCCATTATTTTATACA
Found at i:17062 original size:16 final size:16
Alignment explanation
Indices: 17038--17069 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17028 AAACTGAAAC
*
17038 ATTAGTGTTAATTAAA
1 ATTAATGTTAATTAAA
17054 ATTAATGTTAATTAAA
1 ATTAATGTTAATTAAA
17070 CTAAAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTAATGTTAATTAAA
Found at i:21469 original size:70 final size:70
Alignment explanation
Indices: 21356--21498 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 70
21346 ATGTGTTCAA
21356 GAAGCTTTCACGAGCATTTTCGAGACAGGGAGTATTTGTAACAAGTGTTGCAACGAACTTGTTTC
1 GAAGCTTTCACGAGCATTTTCGAGACAGGGAGTATTTGTAACAAGTGTTGCAACGAACTTGTTTC
21421 GTTGG
66 GTTGG
* *
21426 GAAGCTTTCCCGAGCATTTTCGAGACAGGGAGTATTTGTAACAAGTGTTGTAACGAACTTGTTTC
1 GAAGCTTTCACGAGCATTTTCGAGACAGGGAGTATTTGTAACAAGTGTTGCAACGAACTTGTTTC
21491 GTTGG
66 GTTGG
21496 GAA
1 GAA
21499 AAGTTTGCCA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (70 bp):
GAAGCTTTCACGAGCATTTTCGAGACAGGGAGTATTTGTAACAAGTGTTGCAACGAACTTGTTTC
GTTGG
Found at i:23770 original size:17 final size:17
Alignment explanation
Indices: 23748--23788 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
23738 TACATATATA
23748 TTTTTTCTT-TTTTTCCC
1 TTTTTT-TTCTTTTTCCC
*
23765 TTTTTTTTCTTTTTCTC
1 TTTTTTTTCTTTTTCCC
23782 TTTTTTT
1 TTTTTTT
23789 ATGTGACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCCC
Found at i:30392 original size:25 final size:23
Alignment explanation
Indices: 30349--30394 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
30339 CCAAATAGGG
30349 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
30372 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
30395 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:40052 original size:13 final size:13
Alignment explanation
Indices: 40034--40058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40024 AAGATGACCA
40034 GAAGAAGAAGAAT
1 GAAGAAGAAGAAT
40047 GAAGAAGAAGAA
1 GAAGAAGAAGAA
40059 AAAGAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (13 bp):
GAAGAAGAAGAAT
Found at i:40057 original size:19 final size:18
Alignment explanation
Indices: 40033--40069 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
40023 GAAGATGACC
*
40033 AGAAGAAGAAGAATGAAGA
1 AGAAGAAAAAGAAT-AAGA
40052 AGAAGAAAAAGAATAAGA
1 AGAAGAAAAAGAATAAGA
40070 GAATGACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (18 bp):
AGAAGAAAAAGAATAAGA
Found at i:40150 original size:15 final size:15
Alignment explanation
Indices: 40130--40163 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
40120 CCCCGACAAG
40130 TATCACTCAGGATAT
1 TATCACTCAGGATAT
40145 TATCACTCAGGATAT
1 TATCACTCAGGATAT
40160 TATC
1 TATC
40164 GACAACTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (15 bp):
TATCACTCAGGATAT
Done.