Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010097.1 Kokia drynarioides strain JFW-HI SEQ_124878, 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: 18692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5873 original size:6 final size:6
Alignment explanation
Indices: 5864--5902 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5854 ATACATTAAC
*
5864 ATATGT ATATGT ATATGT ATATGT ATATGT ATATAT ATA
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA
5903 CATGTGGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:6717 original size:6 final size:6
Alignment explanation
Indices: 6706--6738 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
6696 CGCCTTTGCC
6706 CCCTTT CCCTTT CCCTTT CCCTTT CCCTCTT CC
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCT-TT CC
6739 TCTCTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
CCCTTT
Found at i:6753 original size:9 final size:7
Alignment explanation
Indices: 6732--6775 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
6722 TTCCCTTTCC
6732 CTCTTC-
1 CTCTTCT
6738 CTC-TCT
1 CTCTTCT
*
6744 CTTTTCT
1 CTCTTCT
6751 CTCTTCT
1 CTCTTCT
6758 CTCTTCT
1 CTCTTCT
6765 CTCTTCT
1 CTCTTCT
6772 CTCT
1 CTCT
6776 CACATTTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 2 0.06
6 5 0.15
7 27 0.79
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
CTCTTCT
Found at i:12597 original size:15 final size:15
Alignment explanation
Indices: 12573--12602 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12563 AAATTCACAG
12573 AGAATAAAAAAATAA
1 AGAATAAAAAAATAA
*
12588 AGAATTAAAAAATAA
1 AGAATAAAAAAATAA
12603 TTGAGGATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AGAATAAAAAAATAA
Found at i:12625 original size:21 final size:21
Alignment explanation
Indices: 12601--12688 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
12591 ATTAAAAAAT
* **
12601 AATTGAGGATTGAAAATTCCA
1 AATTGAGAATTGAAAATTGAA
*
12622 AATTGA-AATTTGAAATTTGAA
1 AATTGAGAA-TTGAAAATTGAA
* *
12643 AATTGATAATAGAAAATTGAA
1 AATTGAGAATTGAAAATTGAA
* * *
12664 AATTGAGGATTGAGAATTGAG
1 AATTGAGAATTGAAAATTGAA
12685 AATT
1 AATT
12689 TAAGAAGGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.94
22 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (21 bp):
AATTGAGAATTGAAAATTGAA
Found at i:12664 original size:7 final size:7
Alignment explanation
Indices: 12609--12688 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
12599 ATAATTGAGG
12609 ATTGAAA
1 ATTGAAA
**
12616 ATTCCAA
1 ATTGAAA
12623 ATTGAAA
1 ATTGAAA
*
12630 TTTGAAA
1 ATTGAAA
*
12637 TTTGAAA
1 ATTGAAA
*
12644 ATTGATA
1 ATTGAAA
*
12651 ATAGAAA
1 ATTGAAA
12658 ATTGAAA
1 ATTGAAA
**
12665 ATTGAGG
1 ATTGAAA
*
12672 ATTGAGA
1 ATTGAAA
*
12679 ATTGAGA
1 ATTGAAA
12686 ATT
1 ATT
12689 TAAGAAGGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (7 bp):
ATTGAAA
Done.