Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012914.1 Kokia drynarioides strain JFW-HI SEQ_127930, 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: 15844
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:2198 original size:245 final size:245
Alignment explanation
Indices: 1768--2280 Score: 1008
Period size: 245 Copynumber: 2.1 Consensus size: 245
1758 TGAATACGTT
1768 ATCACAAATAAAATCAATTCAATAATAAATAGCAAATAAATCCAATAAAGATGAGTATAGCAAGG
1 ATCACAAATAAAATCAATTCAATAATAAATAGCAAATAAATCCAATAAAGATGAGTATAGCAAGG
1833 AAGGAAATGTTGGATTTTTGCTCAATTGGAATCTGTAAACTTATTTTTTGTCCTTGAATCATATG
66 AAGGAAATGTTGGATTTTTGCTCAATTGGAATCTGTAAACTTATTTTTTGTCCTTGAATCATATG
1898 TGTGGTCTCTCATTGGTTTGAGTGCATTCGATACAATCTGCACATAGGTAAGCAACAAGAGTGAA
131 TGTGGTCTCTCATTGGTTTGAGTGCATTCGATACAATCTGCACATAGGTAAGCAACAAGAGTGAA
1963 AGCTCGTCCAAGATTAATTAAGTTAAAGATTTTAATTTTTAGATTATAAA
196 AGCTCGTCCAAGATTAATTAAGTTAAAGATTTTAATTTTTAGATTATAAA
2013 ATCACAAATAAAATCAATTCAATAATAAATAGCAAATAAATCCAATAAAGATGAGTATAGCAAGG
1 ATCACAAATAAAATCAATTCAATAATAAATAGCAAATAAATCCAATAAAGATGAGTATAGCAAGG
2078 AAGGAAATGTTGGATTTTTGCTCAATTGGAATCTGTAAACTTATTTTTTGTCCTTGAATCATATG
66 AAGGAAATGTTGGATTTTTGCTCAATTGGAATCTGTAAACTTATTTTTTGTCCTTGAATCATATG
2143 TGTGGTCTCTCATTGGTTTGAGTGCATTCGATACAATCTGCACATAGGTAAGCAACAAGAGTGAA
131 TGTGGTCTCTCATTGGTTTGAGTGCATTCGATACAATCTGCACATAGGTAAGCAACAAGAGTGAA
*
2208 AGCTCGTCCAAGATTAATTAAGTTAAAGATTTTAATTTTTAGATTGTAAA
196 AGCTCGTCCAAGATTAATTAAGTTAAAGATTTTAATTTTTAGATTATAAA
*
2258 ATCACAAATAAAATCAACTCAAT
1 ATCACAAATAAAATCAATTCAAT
2281 TCCTTTCTCG
Statistics
Matches: 266, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 266 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (245 bp):
ATCACAAATAAAATCAATTCAATAATAAATAGCAAATAAATCCAATAAAGATGAGTATAGCAAGG
AAGGAAATGTTGGATTTTTGCTCAATTGGAATCTGTAAACTTATTTTTTGTCCTTGAATCATATG
TGTGGTCTCTCATTGGTTTGAGTGCATTCGATACAATCTGCACATAGGTAAGCAACAAGAGTGAA
AGCTCGTCCAAGATTAATTAAGTTAAAGATTTTAATTTTTAGATTATAAA
Found at i:3231 original size:50 final size:50
Alignment explanation
Indices: 3156--3255 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
3146 AATCTTTTCC
3156 ATTTCAACTTTATTACGTGAGATGTGATGGACAAAAAAATACTTCATACA
1 ATTTCAACTTTATTACGTGAGATGTGATGGACAAAAAAATACTTCATACA
*
3206 ATTTCAACTTTATTACGTGAGATGTGATGGACAAAAAAATACTTTATACA
1 ATTTCAACTTTATTACGTGAGATGTGATGGACAAAAAAATACTTCATACA
3256 TACTTTTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (50 bp):
ATTTCAACTTTATTACGTGAGATGTGATGGACAAAAAAATACTTCATACA
Found at i:12966 original size:24 final size:24
Alignment explanation
Indices: 12937--12999 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
12927 ATAAATAATC
12937 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
12961 TTTCAATTAAATTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
12985 TTTGAGTTAAACTCT
1 TTTCAATTAAACTCT
13000 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:14926 original size:24 final size:24
Alignment explanation
Indices: 14898--14984 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
14888 GAAAAAAATC
* *
14898 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
14922 TTTCAAATAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
14946 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
14970 TTTGAGTTAAACTCT
1 TTTCAATTAAACTCT
14985 TATTAGTCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:15125 original size:15 final size:16
Alignment explanation
Indices: 15100--15129 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15090 TAATGTTTAC
15100 GTTTTGAGGGTTTTTT
1 GTTTTGAGGGTTTTTT
15116 GTTTTG-GGGTTTTT
1 GTTTTGAGGGTTTTT
15130 AGGGTTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (16 bp):
GTTTTGAGGGTTTTTT
Found at i:15811 original size:2 final size:2
Alignment explanation
Indices: 15806--15837 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15796 ATACTTCTTA
15806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15838 TTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.