Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001463.1 Kokia drynarioides strain JFW-HI SEQ_112985, 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: 4562
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Found at i:707 original size:108 final size:107
Alignment explanation
Indices: 595--795 Score: 244
Period size: 108 Copynumber: 1.9 Consensus size: 107
585 ATACTTTGGA
* * * * * * *
595 CCTTTTGACGTAAAATGAAATGACACCCAAGCATTTCATCCCTGTTACTCAACCGAACATACTCT
1 CCTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAACCGAACACA-TCT
660 C-AATTTTTTTCTTCTCTTTTTTTTT-TTTGTAAAATGTGTTAGC
65 CGAATTTTTTT-TT-TCTTTTTTTTTATTTGTAAAATGTGTTAGC
* * ** * *
703 CCTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCAGTTACTCAGTCTAACACATTTC
1 CCTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAACCGAACACATCTC
768 GAATTTTTTTTTTCTTTTTTTTTATTTG
66 GAATTTTTTTTTTCTTTTTTTTTATTTG
796 GGTCAGCGGA
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
106 11 0.14
107 9 0.12
108 58 0.74
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (107 bp):
CCTTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCAGTTACTCAACCGAACACATCTC
GAATTTTTTTTTTCTTTTTTTTTATTTGTAAAATGTGTTAGC
Found at i:1546 original size:4 final size:4
Alignment explanation
Indices: 1537--1587 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
1527 TCCTAGACAA
1537 AAAT AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAA- AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
1585 AAA
1 AAA
1588 AATAATTGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 8 0.19
4 25 0.60
5 8 0.19
6 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:1588 original size:8 final size:8
Alignment explanation
Indices: 1535--1592 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
1525 TTTCCTAGAC
1535 AAAAATAA
1 AAAAATAA
*
1543 ATAAATAA
1 AAAAATAA
*
1551 ATAAATAA
1 AAAAATAA
*
1559 AATAAGATAG
1 AA-AA-ATAA
1569 AAAAATAA
1 AAAAATAA
1577 AAAAA-AA
1 AAAAATAA
1584 TAAAAATAA
1 -AAAAATAA
1593 TTGGGTTGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 2 0.05
8 29 0.69
9 6 0.14
10 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:2856 original size:22 final size:22
Alignment explanation
Indices: 2799--2845 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2789 CGATCTAAGG
2799 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAAAGAAAACAAAATT
*
2820 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAAAATT
2842 AAAA
1 AAAA
2846 GAAATAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAAAATT
Found at i:3641 original size:50 final size:50
Alignment explanation
Indices: 3566--3669 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
3556 TCCAATCTAA
3566 ATTCTAGAAGATAATTAGAATTATATCTAACATTTAATTTTCCTAATTGG
1 ATTCTAGAAGATAATTAGAATTATATCTAACATTTAATTTTCCTAATTGG
3616 ATTCTAGAAGATAATTAGAATTATATCTAACATTTAATTTTCCTAATTGG
1 ATTCTAGAAGATAATTAGAATTATATCTAACATTTAATTTTCCTAATTGG
3666 ATTC
1 ATTC
3670 AATTTAAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (50 bp):
ATTCTAGAAGATAATTAGAATTATATCTAACATTTAATTTTCCTAATTGG
Found at i:3736 original size:19 final size:19
Alignment explanation
Indices: 3712--3754 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3702 AAACATAAAT
3712 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
3731 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
3750 TAAAT
1 TAAAT
3755 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:4001 original size:24 final size:23
Alignment explanation
Indices: 3958--4002 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3948 AGGATCATAC
3958 TCTAAAAATATATATATTTAATA
1 TCTAAAAATATATATATTTAATA
* *
3981 TCTAAAAGTATGTCATATTTAA
1 TCTAAAAATATAT-ATATTTAA
4003 GCATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
TCTAAAAATATATATATTTAATA
Done.