Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009323.1 Kokia drynarioides strain JFW-HI SEQ_124030, 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: 50951
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:13039 original size:12 final size:12
Alignment explanation
Indices: 13018--13049 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13008 GCTTGATTGA
*
13018 CTGCAGCAGCAG
1 CTGCAACAGCAG
13030 CTGCAACAGCAG
1 CTGCAACAGCAG
13042 CTGCAACA
1 CTGCAACA
13050 TATTCTGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.25, T:0.09
Consensus pattern (12 bp):
CTGCAACAGCAG
Found at i:20855 original size:3 final size:3
Alignment explanation
Indices: 20835--20904 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
20825 CCAAAACCAA
* *
20835 AAT AAT AAA AAC AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20882 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
20905 ACTGTTGTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28242 original size:147 final size:147
Alignment explanation
Indices: 28029--28323 Score: 477
Period size: 147 Copynumber: 2.0 Consensus size: 147
28019 GAAACTTAAT
* * *
28029 TCTCTTGAGTGCTAAGTGACCAGCAAAGAAAAAACAGAACCATAGACTTCCCTGTTTTCACATTA
1 TCTCTCGAGTGCTAAGCGACCAACAAAGAAAAAACAGAACCATAGACTTCCCTGTTTTCACATTA
* *
28094 AAAACTAGAAAAGGAGACCACCCAGATGAAGAACAGTTGAAAATTATTCACAAGAAAACAAGGAG
66 AAAACAAGAAAAGGAGACCACCCAGATGAAGAACAGCTGAAAATTATTCACAAGAAAACAAGGAG
28159 AAGAAATGCACGAGAAA
131 AAGAAATGCACGAGAAA
*
28176 TCTCTCGAGTGCTAAGCGACCAACGAAGAAAAAA-AGAAAACCATAGACTTCCCTG-TTTCACAT
1 TCTCTCGAGTGCTAAGCGACCAACAAAGAAAAAACAG--AACCATAGACTTCCCTGTTTTCACAT
* * *
28239 TAAAAACAAGAAAAGGAGACTACCCAGATGAAGAATAGCTGAAAATTATTCACAAGAAAACAGGG
64 TAAAAACAAGAAAAGGAGACCACCCAGATGAAGAACAGCTGAAAATTATTCACAAGAAAACAAGG
28304 AGAAGAAATGCACGAGAAA
129 AGAAGAAATGCACGAGAAA
28323 T
1 T
28324 ATATAAACAA
Statistics
Matches: 137, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
146 2 0.01
147 118 0.86
148 17 0.12
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (147 bp):
TCTCTCGAGTGCTAAGCGACCAACAAAGAAAAAACAGAACCATAGACTTCCCTGTTTTCACATTA
AAAACAAGAAAAGGAGACCACCCAGATGAAGAACAGCTGAAAATTATTCACAAGAAAACAAGGAG
AAGAAATGCACGAGAAA
Found at i:28950 original size:24 final size:24
Alignment explanation
Indices: 28917--28967 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
28907 AAAAATAATC
* *
28917 TTTTAGTTAAACTCTGTTTATTTG
1 TTTTAATTAAACTCTATTTATTTG
*
28941 TTTTAATTAAACTTTATTTATTTG
1 TTTTAATTAAACTCTATTTATTTG
28965 TTT
1 TTT
28968 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTTAATTAAACTCTATTTATTTG
Found at i:28976 original size:24 final size:25
Alignment explanation
Indices: 28925--28983 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
28915 TCTTTTAGTT
* * *
28925 AAACTC-TGTTTATTTGTTTTAATT
1 AAACTCTTATTTATTTGTTTGAATC
*
28949 AAACT-TTATTTATTTGTTTGAGTC
1 AAACTCTTATTTATTTGTTTGAATC
28973 AAACTCTTATT
1 AAACTCTTATT
28984 AGTCTAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
AAACTCTTATTTATTTGTTTGAATC
Found at i:34401 original size:21 final size:21
Alignment explanation
Indices: 34361--34402 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34351 TTGATCGATG
*
34361 GCTTAGCATGCAGCATGAAGA
1 GCTTACCATGCAGCATGAAGA
34382 GCTTACCA-GCAGCATGGAAGA
1 GCTTACCATGCAGCAT-GAAGA
34403 ATTAGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (21 bp):
GCTTACCATGCAGCATGAAGA
Found at i:41053 original size:20 final size:21
Alignment explanation
Indices: 41010--41053 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
41000 ACTTTCATCA
*
41010 TTAAGCCTTAATTAAACATTT
1 TTAAGCCTTAATTAAACATAT
* *
41031 TTAA-CCTTTATTAAACCTAT
1 TTAAGCCTTAATTAAACATAT
41051 TTA
1 TTA
41054 TAAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAGCCTTAATTAAACATAT
Done.