Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006257.1 Kokia drynarioides strain JFW-HI SEQ_120828, 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: 11701
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:6193 original size:30 final size:30
Alignment explanation
Indices: 6159--6464 Score: 217
Period size: 30 Copynumber: 10.3 Consensus size: 30
6149 CTATTTGTTT
6159 AAAAATTA-CATTTTGACCCTCGAACTTCGC
1 AAAAATTACCATTTTGACCCTCGAACTTC-C
* * **
6189 AAAAATCA-CATTTTGACTCTTTAACTTTTCC
1 AAAAATTACCATTTTGACCCTCGAAC--TTCC
* * *
6220 -AAAATTACCATTTTAACCCTCAAACTTTGC
1 AAAAATTACCATTTTGACCCTCGAAC-TTCC
* *
6250 AAAAATCA-CATTTTGACCCTCAAACTTCGC
1 AAAAATTACCATTTTGACCCTCGAACTTC-C
* ** * * *
6280 AAAAAATA-TGTTTTG-GCCTCAAATTTTTCC
1 AAAAATTACCATTTTGACCCTCGAA--CTTCC
* *
6310 AAAAATTATCATTTTG-CCCCCGAA-TGTCC
1 AAAAATTACCATTTTGACCCTCGAACT-TCC
6339 AAAAATTACCATTTT-ACCCTCGAACATT-C
1 AAAAATTACCATTTTGACCCTCGAAC-TTCC
* *
6368 AAAAATTACCATTTT-ACCCTCAAACATCC
1 AAAAATTACCATTTTGACCCTCGAACTTCC
* *
6397 AAAAAATTACCATTTT-TCCCT-GAACATCC
1 -AAAAATTACCATTTTGACCCTCGAACTTCC
*
6426 AAAAATTACCATTTTG-CCCTCGAACATCC
1 AAAAATTACCATTTTGACCCTCGAACTTCC
*
6455 AAAGATTACC
1 AAAAATTACC
6465 CTTTCGCCCC
Statistics
Matches: 228, Mismatches: 32, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
28 21 0.09
29 83 0.36
30 87 0.38
31 34 0.15
32 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (30 bp):
AAAAATTACCATTTTGACCCTCGAACTTCC
Found at i:6276 original size:61 final size:60
Alignment explanation
Indices: 6160--6276 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 60
6150 TATTTGTTTA
* * * **
6160 AAAATTACATTTTGACCCTCGAACTTCGCAAAAATCACATTTTGACTCTTTAACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTCGCAAAAATCACATTTTGACCCTCAAACTTTTCC
*
6220 AAAATTACCATTTTAACCCTCAAACTTTGCAAAAATCACATTTTGACCCTCAAACTT
1 AAAATTA-CATTTTAACCCTCAAACTTCGCAAAAATCACATTTTGACCCTCAAACTT
6277 CGCAAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 7 0.14
61 43 0.86
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTCAAACTTCGCAAAAATCACATTTTGACCCTCAAACTTTTCC
Found at i:6315 original size:91 final size:91
Alignment explanation
Indices: 6159--6324 Score: 219
Period size: 91 Copynumber: 1.8 Consensus size: 91
6149 CTATTTGTTT
* * **
6159 AAAAATTACATTTTGACCCTCGAACTTCGCAAAAATCACATTTTGACTCTTTAACTTTTCCAAAA
1 AAAAATCACATTTTGACCCTCAAACTTCGCAAAAATCACATTTTGACTCTCAAACTTTTCCAAAA
6224 TTACCATTTTAACCCTCAAACTTTGC
66 TTACCATTTTAACCCTCAAACTTTGC
** * *
6250 AAAAATCACATTTTGACCCTCAAACTTCGCAAAAAAT-ATGTTTTGGC-CTCAAATTTTTCCAAA
1 AAAAATCACATTTTGACCCTCAAACTTCGC-AAAAATCACATTTTGACTCTCAAACTTTTCC-AA
*
6313 AATTATCATTTT
64 AATTACCATTTT
6325 GCCCCCGAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 10 0.16
91 48 0.75
92 6 0.09
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (91 bp):
AAAAATCACATTTTGACCCTCAAACTTCGCAAAAATCACATTTTGACTCTCAAACTTTTCCAAAA
TTACCATTTTAACCCTCAAACTTTGC
Found at i:6473 original size:29 final size:29
Alignment explanation
Indices: 6307--6464 Score: 210
Period size: 29 Copynumber: 5.4 Consensus size: 29
6297 CTCAAATTTT
* * * **
6307 TCCAAAAATTATCATTTTGCCCCCGAATG
1 TCCAAAAATTACCATTTTACCCTCGAACA
6336 TCCAAAAATTACCATTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCTCGAACA
* *
6365 TTCAAAAATTACCATTTTACCCTCAAACA
1 TCCAAAAATTACCATTTTACCCTCGAACA
*
6394 TCCAAAAAATTACCATTTTTCCCT-GAACA
1 TCC-AAAAATTACCATTTTACCCTCGAACA
*
6423 TCCAAAAATTACCATTTTGCCCTCGAACA
1 TCCAAAAATTACCATTTTACCCTCGAACA
*
6452 TCCAAAGATTACC
1 TCCAAAAATTACC
6465 CTTTCGCCCC
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.17
29 77 0.67
30 19 0.17
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAACA
Found at i:6485 original size:87 final size:90
Alignment explanation
Indices: 6296--6487 Score: 225
Period size: 87 Copynumber: 2.2 Consensus size: 90
6286 TATGTTTTGG
** * **
6296 CCTCAAATTTTTCC-AAAAATTATCATTTTGCCCCCGAATGTCCAAAAATTACCATTTTACCCTC
1 CCTCAAACATTTCCAAAAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTACCCTC
* *
6360 GAACATTCAAAAATTACCATTTTAC
66 GAACATCCAAAAATTACCATTTCAC
* * *
6385 CCTCAAACA--TCCAAAAAATTACCATTTT-TCCCTGAACATCCAAAAATTACCATTTTGCCCTC
1 CCTCAAACATTTCCAAAAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTACCCTC
* * *
6447 GAACATCCAAAGATTACCCTTTCGC
66 GAACATCCAAAAATTACCATTTCAC
6472 CC-CAAA-ATTTCCAAAA
1 CCTCAAACATTTCCAAAA
6488 TCACATTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
85 1 0.01
86 4 0.05
87 61 0.70
88 14 0.16
89 7 0.08
ACGTcount: A:0.36, C:0.30, G:0.05, T:0.30
Consensus pattern (90 bp):
CCTCAAACATTTCCAAAAAATTACCATTTTGCCCCCGAACATCCAAAAATTACCATTTTACCCTC
GAACATCCAAAAATTACCATTTCAC
Found at i:6526 original size:29 final size:30
Alignment explanation
Indices: 6473--6558 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 30
6463 CCCTTTCGCC
*
6473 CCAAAATTTCCAAAA--TCACATTTTTGACAT
1 CCAAATTTTCCAAAAGTTCA-A-TTTTGACAT
*
6503 -CAAATTTTCCAAAAGTTCGATTTT-A-AT
1 CCAAATTTTCCAAAAGTTCAATTTTGACAT
* *
6530 CCCAAGTTTTCCAAAATTTCAATTTTGAC
1 -CCAAATTTTCCAAAAGTTCAATTTTGAC
6559 CCTAAATTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
27 2 0.04
28 1 0.02
29 38 0.84
30 2 0.04
31 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (30 bp):
CCAAATTTTCCAAAAGTTCAATTTTGACAT
Found at i:9103 original size:161 final size:161
Alignment explanation
Indices: 8786--9259 Score: 666
Period size: 161 Copynumber: 2.9 Consensus size: 161
8776 GATATTAATT
* * *
8786 TATGATTTATTAAATTTTATATCTTATCTTGATTTATGATTTTAACAATTGTAGCAGCCAATCAA
1 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
* * **
8851 GACCATCCTACTATCAAGATAGACCTTTGTGAATCAATGATTGCTGAAAAAGGTGGCCATTAAGA
66 GACCATCCTAC-ATCAGGATAGACCTTTGAGAATCAATGATTGCTGAAAAAGGTGATCATTAAGA
*
8916 AACACAAGTAGTACAACACACTATTTCACCTG
130 AACACAAGTAGTACAACACACTATTTCACATG
*
8948 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGTCAATCAA
1 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
* * * * * *
9013 GACTATCTTACATCAGGATAAACCTTTGCGAATCAATAATTGCTGAAAAAAGTGATCATTAAGAA
66 GACCATCCTACATCAGGATAGACCTTTGAGAATCAATGATTGCTGAAAAAGGTGATCATTAAGAA
* *
9078 ACACAAATAATACAACACACTATTTCACATG
131 ACACAAGTAGTACAACACACTATTTCACATG
* * *
9109 TAT-AGTTTATTAAATTTTATATCATATTTTAATTTATTATTTTAACAGTTCT-GACAGCCAATC
1 TATGA-TTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAG-CAGCCAATC
* * *
9172 AAGACCATCCTACCACCAGAATAGA-CTCTTGAGAATCAATGATTACTGAAAAAGGTGATCATTA
64 AAGACCATCCTA-CATCAGGATAGACCT-TTGAGAATCAATGATTGCTGAAAAAGGTGATCATTA
*
9236 AGAAACACAAGTAGTACTACACAC
127 AGAAACACAAGTAGTACAACACAC
9260 CATGTCATCT
Statistics
Matches: 276, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
160 2 0.01
161 142 0.51
162 132 0.48
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (161 bp):
TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
GACCATCCTACATCAGGATAGACCTTTGAGAATCAATGATTGCTGAAAAAGGTGATCATTAAGAA
ACACAAGTAGTACAACACACTATTTCACATG
Done.