Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001711.1 Kokia drynarioides strain JFW-HI SEQ_113405, 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: 13696
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:1825 original size:25 final size:23
Alignment explanation
Indices: 1797--1842 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1787 GTTTGATCCA
1797 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
1822 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
1843 CCTTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:6082 original size:23 final size:23
Alignment explanation
Indices: 6026--6070 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6016 TGACATAGCG
*
6026 TCCAGTCAGCAGCTTCTAGAAGA
1 TCCAGTCAACAGCTTCTAGAAGA
6049 TCCAGTCAACAGCTTCTAGAAG
1 TCCAGTCAACAGCTTCTAGAAG
6071 GTTTAGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
TCCAGTCAACAGCTTCTAGAAGA
Found at i:9638 original size:31 final size:30
Alignment explanation
Indices: 9576--9699 Score: 167
Period size: 30 Copynumber: 4.1 Consensus size: 30
9566 CTCAAGAAAT
* *
9576 CCCTAAATTTTTCCAAAATCATATTTTGAC
1 CCCTAAACTTTTCCAAAATCACATTTTGAC
* *
9606 CCCTAAACTTTTCCAAAAATTACATTTCGAC
1 CCCTAAACTTTTCC-AAAATCACATTTTGAC
* *
9637 CCCTCAAACTTTTCCAAAATCATATTTTAAC
1 CCCT-AAACTTTTCCAAAATCACATTTTGAC
*
9668 CCTTAAACTTTTCCAAAATCACATTTTGAC
1 CCCTAAACTTTTCCAAAATCACATTTTGAC
9698 CC
1 CC
9700 TTGAACTTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
30 39 0.48
31 32 0.40
32 10 0.12
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.35
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATCACATTTTGAC
Found at i:9660 original size:62 final size:60
Alignment explanation
Indices: 9576--9699 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 60
9566 CTCAAGAAAT
* * *
9576 CCCTAAATTTTTCCAAAATCATATTTTGACCCCTAAACTTTTCCAAAAATTACATTTCGAC
1 CCCTAAACTTTTCCAAAATCATATTTTAACCCCTAAACTTTTCC-AAAATCACATTTCGAC
* *
9637 CCCTCAAACTTTTCCAAAATCATATTTTAACCCTTAAACTTTTCCAAAATCACATTTTGAC
1 CCCT-AAACTTTTCCAAAATCATATTTTAACCCCTAAACTTTTCCAAAATCACATTTCGAC
9698 CC
1 CC
9700 TTGAACTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 20 0.35
62 37 0.65
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.35
Consensus pattern (60 bp):
CCCTAAACTTTTCCAAAATCATATTTTAACCCCTAAACTTTTCCAAAATCACATTTCGAC
Found at i:10842 original size:30 final size:29
Alignment explanation
Indices: 10784--10987 Score: 214
Period size: 30 Copynumber: 6.8 Consensus size: 29
10774 GTCCCTAAAT
* *
10784 TTTTCTAAAATTACATTTTG-CCCCAAAC
1 TTTTCCAAAATCACATTTTGACCCCAAAC
*
10812 TTTTCCAAAAAT-ATATTTTGACCTCCAAAC
1 TTTTCC-AAAATCACATTTTGACC-CCAAAC
* * *
10842 TTTTACAAAATCACAATTTAACCCCTAAAC
1 TTTTCCAAAATCACATTTTGACCCC-AAAC
*
10872 TTTTCCAAAATCATATTTTGACCCCTAAAC
1 TTTTCCAAAATCACATTTTGACCCC-AAAC
* *
10902 TTTTCCAAAAATTACATTTCGACCCCTCAAAC
1 TTTTCC-AAAATCACATTTTGA-CCC-CAAAC
* * *
10934 TTTTCCAAAATCATATTTTAACCCTTAAAC
1 TTTTCCAAAATCACATTTTGACCC-CAAAC
10964 TTTTCCAAAATCACATTTTGACCC
1 TTTTCCAAAATCACATTTTGACCC
10988 TTGAACTTCT
Statistics
Matches: 148, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
28 12 0.08
29 14 0.09
30 85 0.57
31 23 0.16
32 13 0.09
33 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTTCCAAAATCACATTTTGACCCCAAAC
Found at i:10955 original size:92 final size:89
Alignment explanation
Indices: 10776--10987 Score: 291
Period size: 92 Copynumber: 2.4 Consensus size: 89
10766 CTCAAGAGGT
* * * * * *
10776 CCCTAAATTTTTCTAAAATTACATTTTG-CCCCAAACTTTTCCAAAAATATATTTTGACCTCCAA
1 CCCTAAACTTTTCCAAAATCACATTTTGACCCCAAACTTTTCCAAAAATACATTTCGACCCCCAA
10840 ACTTTTACAAAATCACAATTTAAC
66 ACTTTTACAAAATCACAATTTAAC
*
10864 CCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAACTTTTCCAAAAATTACATTTCGACCCCT
1 CCCTAAACTTTTCCAAAATCACATTTTGACCCC-AAACTTTTCCAAAAA-TACATTTCGACCCC-
* * *
10929 CAAACTTTTCCAAAATCATATTTTAAC
63 CAAACTTTTACAAAATCACAATTTAAC
*
10956 CCTTAAACTTTTCCAAAATCACATTTTGACCC
1 CCCTAAACTTTTCCAAAATCACATTTTGACCC
10988 TTGAACTTCT
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
88 24 0.22
89 4 0.04
90 15 0.14
91 11 0.10
92 54 0.50
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (89 bp):
CCCTAAACTTTTCCAAAATCACATTTTGACCCCAAACTTTTCCAAAAATACATTTCGACCCCCAA
ACTTTTACAAAATCACAATTTAAC
Found at i:10963 original size:62 final size:61
Alignment explanation
Indices: 10779--10987 Score: 250
Period size: 62 Copynumber: 3.5 Consensus size: 61
10769 AAGAGGTCCC
* * *
10779 TAAATTTTTCTAAAATTACATTTTG--CCC-CAAACTTTTCCAAAAAT-ATATTTTGA-CCT
1 TAAACTTTTCCAAAATCACATTTTGACCCCTCAAACTTTTCC-AAAATCATATTTTGACCCT
* * * * *
10836 CCAAACTTTTACAAAATCACAATTTAACCCCT-AAACTTTTCCAAAATCATATTTTGACCCC
1 -TAAACTTTTCCAAAATCACATTTTGACCCCTCAAACTTTTCCAAAATCATATTTTGACCCT
* * *
10897 TAAACTTTTCCAAAAATTACATTTCGACCCCTCAAACTTTTCCAAAATCATATTTTAACCCT
1 TAAACTTTTCC-AAAATCACATTTTGACCCCTCAAACTTTTCCAAAATCATATTTTGACCCT
10959 TAAACTTTTCCAAAATCACATTTTGACCC
1 TAAACTTTTCCAAAATCACATTTTGACCC
10988 TTGAACTTCT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
58 18 0.14
59 5 0.04
60 31 0.25
61 34 0.27
62 38 0.30
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (61 bp):
TAAACTTTTCCAAAATCACATTTTGACCCCTCAAACTTTTCCAAAATCATATTTTGACCCT
Found at i:12105 original size:88 final size:88
Alignment explanation
Indices: 11911--12097 Score: 356
Period size: 88 Copynumber: 2.1 Consensus size: 88
11901 CAATAACTTT
*
11911 AAAAATAATTTGGGTGGTGTCAATATTTTTGACGTCTCACGTATAATATTCGTACCCAATATTTG
1 AAAAATAATTTGGGTGGTGTCAATATTTTTAACGTCTCACGTATAATATTCGTACCCAATATTTG
11976 TATTACCCATATTTTGTAACAAG
66 TATTACCCATATTTTGTAACAAG
11999 AAAAATAATTTGGGTGGTGTCAATATTTTTAACGTCTCACGTATAATATTCGTACCCAATATTTG
1 AAAAATAATTTGGGTGGTGTCAATATTTTTAACGTCTCACGTATAATATTCGTACCCAATATTTG
*
12064 TATTACCCATATTTTGTAACAGG
66 TATTACCCATATTTTGTAACAAG
12087 AAAAATAATTT
1 AAAAATAATTT
12098 AAGTGGTGCC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (88 bp):
AAAAATAATTTGGGTGGTGTCAATATTTTTAACGTCTCACGTATAATATTCGTACCCAATATTTG
TATTACCCATATTTTGTAACAAG
Done.