Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000321.1 Kokia drynarioides strain JFW-HI SEQ_111085, 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: 11000
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:1530 original size:29 final size:28
Alignment explanation
Indices: 1474--1886 Score: 278
Period size: 30 Copynumber: 14.1 Consensus size: 28
1464 CCCTGGAGGT
1474 CCCTAAACTATCCAAAAATTACCATTTTAC
1 CCCTAAACT-TCCAAAAA-TACCATTTTAC
* *
1504 CCCTAAACTTCTAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATACCA-TTTT-AC
* * * *
1534 CTCGTACA-TTCTAAAAACTACCACTTTAC
1 C-CCTAAACTTCCAAAAA-TACCATTTTAC
* *
1563 CCCCAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATACCA-TTTT-AC
* * * *
1593 CCATAACCTTCTAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATACCATTTTAC
* *
1621 CCCTGAACTTCCAAAAATCCCATTTTGAC
1 CCCTAAACTTCCAAAAATACCATTTT-AC
* *
1650 CCCTAAATTATCTAAAAATTACCATTTTAC
1 CCCTAAACT-TCCAAAAA-TACCATTTTAC
* *
1680 CCC-GAACTTCTAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAA-TACCATTTTAC
*
1708 CCCTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATACCA-TTTT-AC
* * *
1738 CCCGAACCTTCTAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAA-TACCATTTTAC
** * *
1767 CCCCGAACTTCCAAAAATTCAATTTTTGAC
1 CCCTAAACTTCCAAAAATACCA-TTTT-AC
* * *
1797 CCCGAACCTTCCAAAATTTACCATTTTA-
1 CCCTAAACTTCCAAAA-ATACCATTTTAC
*
1825 CCCTCGAACTTCCAAAAAT-CTCATTTTTGA-
1 CCCT-AAACTTCCAAAAATAC-CA-TTTT-AC
* * * *
1855 CTCTGAACCTTCCAAAACTACCATTTTGC
1 CCCT-AAACTTCCAAAAATACCATTTTAC
1884 CCC
1 CCC
1887 CGTGCATCTA
Statistics
Matches: 300, Mismatches: 60, Indels: 47
0.74 0.15 0.12
Matches are distributed among these distances:
27 1 0.00
28 69 0.23
29 96 0.32
30 110 0.37
31 24 0.08
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATACCATTTTAC
Found at i:1697 original size:87 final size:87
Alignment explanation
Indices: 1474--1843 Score: 330
Period size: 87 Copynumber: 4.2 Consensus size: 87
1464 CCCTGGAGGT
* * *
1474 CCCTAAACTATCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAA-TCCCATTTTTGACCTCG
1 CCCTAAACT-TCCAAAAATTACCATTTTACCCC-GAACTTCTAAAAATTACCATTTTTGACCCCG
* * * *
1538 TACATTCTAAAAACTACCACTTT-AC
64 AAC-TTCCAAAAA-TCCCATTTTGAC
* * **
1563 CCCCAAACTTCCAAAAA-TCCCATTTTTGACCCATAACCTTCT-AAAATTACCA-TTTT-ACCCC
1 CCCTAAACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCTAAAAATTACCATTTTTGACCCC
1624 TGAACTTCCAAAAATCCCATTTTGAC
63 -GAACTTCCAAAAATCCCATTTTGAC
* * *
1650 CCCTAAATTATCTAAAAATTACCATTTTACCCCGAACTTCTAAAAATTACCA-TTTT-ACCCCTA
1 CCCTAAACT-TCCAAAAATTACCATTTTACCCCGAACTTCTAAAAATTACCATTTTTGACCCC-G
1713 AACTTCCAAAAATCCCATTTTTGAC
64 AACTTCCAAAAATCCCA-TTTTGAC
* * * * *
1738 CCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT-CAATTTTTGACCCCGA
1 CCCTAAACTTCCAAAAATTACCATTTTA-CCCCGAACTTCTAAAAATTACCATTTTTGACCCCGA
* *
1802 ACCTTCCAAAATTTACCATTTT-A-
65 A-CTTCCAAAA-ATCCCATTTTGAC
*
1825 CCCTCGAACTTCCAAAAAT
1 CCCT-AAACTTCCAAAAAT
1844 CTCATTTTTG
Statistics
Matches: 236, Mismatches: 29, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
86 12 0.05
87 92 0.39
88 85 0.36
89 43 0.18
90 4 0.02
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (87 bp):
CCCTAAACTTCCAAAAATTACCATTTTACCCCGAACTTCTAAAAATTACCATTTTTGACCCCGAA
CTTCCAAAAATCCCATTTTGAC
Found at i:1710 original size:58 final size:57
Alignment explanation
Indices: 1474--1887 Score: 308
Period size: 59 Copynumber: 7.1 Consensus size: 57
1464 CCCTGGAGGT
* * *
1474 CCCTAAACTATCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATCCCATTTTTGAC
1 CCCTAAACT-TCCAAAAATTACCATTTTACCCC-GAACTTCCAAAAATACCA-TTTTGAC
* * * * * * *
1534 CTCGTACA-TTCTAAAAACTACCACTTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC
1 C-CCTAAACTTCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATACCA-TTTTGAC
* * * *
1593 CCATAACCTT-CTAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTGAC
1 CCCTAAACTTCCAAAAATTACCATTTTACCCC-GAACTTCCAAAAATACCATTTTGAC
* * *
1650 CCCTAAATTATCTAAAAATTACCATTTTACCCCGAACTTCTAAAAATTACCATTTT-AC
1 CCCTAAACT-TCCAAAAATTACCATTTTACCCCGAACTTCCAAAAA-TACCATTTTGAC
* *
1708 CCCTAAACTTCCAAAAA-TCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTT-AC
1 CCCTAAACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAAA-TACCATTTTGAC
** * *
1767 CCCCGAACTTCCAAAAATT-CAATTTTTGACCCCGAACCTTCCAAAATTTACCATTTT-A-
1 CCCTAAACTTCCAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAA-ATACCATTTTGAC
* * * * *
1825 CCCTCGAACTTCCAAAAA-T-CTCATTTTTGACTCTGAACCTTCCAAAACTACCATTTTGCC
1 CCCT-AAACTTCCAAAAATTAC-CA-TTTT-ACCCCGAA-CTTCCAAAAATACCATTTTGAC
1885 CCC
1 CCC
1888 GTGCATCTAA
Statistics
Matches: 303, Mismatches: 35, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.01
57 28 0.09
58 78 0.26
59 179 0.59
60 10 0.03
61 4 0.01
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.31
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATACCATTTTGAC
Found at i:7526 original size:23 final size:22
Alignment explanation
Indices: 7482--7527 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
7472 TTTTAATATA
* * *
7482 GGTTTATTTGCTTTTTTGGCAC
1 GGTTTATTTGCTTCTATAGCAC
7504 GGTTATATTTGCTTCTATAGCAC
1 GGTT-TATTTGCTTCTATAGCAC
7527 G
1 G
7528 ATAGTTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (22 bp):
GGTTTATTTGCTTCTATAGCAC
Found at i:10527 original size:17 final size:17
Alignment explanation
Indices: 10484--10536 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
10474 TAATTTCGAA
*
10484 TAATACATTTTATTATT
1 TAATACATATTATTATT
* *
10501 TATTATATATTATT-TT
1 TAATACATATTATTATT
10517 TAAATACATATTTATTATT
1 T-AATACATA-TTATTATT
10536 T
1 T
10537 CTAATATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 5 0.18
19 3 0.11
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATACATATTATTATT
Found at i:10552 original size:35 final size:34
Alignment explanation
Indices: 10485--10553 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
10475 AATTTCGAAT
*
10485 AATACATTTTATTATTTATTATATATTATTTTTA
1 AATACATTTTATTATTTATAATATATTATTTTTA
* *
10519 AATACATATTTATTATTTCTAATATGATTTTTTTT
1 AATACAT-TTTATTATTTATAATAT-ATTATTTTT
10554 TTTGTATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 7 0.23
35 15 0.50
36 8 0.27
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (34 bp):
AATACATTTTATTATTTATAATATATTATTTTTA
Done.