Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007245.1 Kokia drynarioides strain JFW-HI SEQ_121860, 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: 2195
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:637 original size:7 final size:7
Alignment explanation
Indices: 625--750 Score: 82
Period size: 7 Copynumber: 17.7 Consensus size: 7
615 TGTTAGGTAA
625 TAAACAC
1 TAAACAC
*
632 TAAACAT
1 TAAACAC
639 TAAAC-C
1 TAAACAC
*
645 ATAAACTC
1 -TAAACAC
653 TAAACTAC
1 TAAAC-AC
661 TAAAC-C
1 TAAACAC
*
667 TTAAACCC
1 -TAAACAC
* *
675 TAAATAT
1 TAAACAC
682 TAAACAC
1 TAAACAC
*
689 TAAACCC
1 TAAACAC
696 TAAACCAC
1 TAAA-CAC
*
704 TAAACTC
1 TAAACAC
711 TAAAC-C
1 TAAACAC
717 TAAAACAC
1 T-AAACAC
725 TAAAC-C
1 TAAACAC
*
731 TTAAATTA-
1 -TAAA-CAC
739 TAAACAC
1 TAAACAC
746 TAAAC
1 TAAAC
751 CTTAAACCTT
Statistics
Matches: 94, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
6 5 0.05
7 73 0.78
8 16 0.17
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACAC
Found at i:650 original size:21 final size:21
Alignment explanation
Indices: 624--757 Score: 96
Period size: 21 Copynumber: 6.3 Consensus size: 21
614 TTGTTAGGTA
*
624 ATAAACACTAAACATTAAACC
1 ATAAACACTAAACACTAAACC
*
645 ATAAACTCTAAACTACTAAACC
1 ATAAACACTAAAC-ACTAAACC
* * * *
667 TTAAACCCTAAATATTAAA-C
1 ATAAACACTAAACACTAAACC
*
687 ACTAAACCCTAAACCACTAAACTC
1 A-TAAACACTAAA-CACTAAAC-C
711 -TAAAC-CTAAAACACTAAACC
1 ATAAACACT-AAACACTAAACC
* *
731 TTAAATTA-TAAACACTAAACC
1 ATAAA-CACTAAACACTAAACC
*
752 TTAAAC
1 ATAAAC
758 CTTAACCTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.02
21 59 0.63
22 31 0.33
24 1 0.01
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAACACTAAACACTAAACC
Found at i:708 original size:36 final size:35
Alignment explanation
Indices: 646--735 Score: 90
Period size: 36 Copynumber: 2.5 Consensus size: 35
636 CATTAAACCA
* * * *
646 TAAACTCTAAACTACTAAACCTTAAACCCTAAATAT
1 TAAACACTAAAC-CCTAAACCCTAAACCCTAAACAT
* *
682 TAAACACTAAACCCTAAACCACTAAACTCTAAACCT
1 TAAACACTAAACCCTAAACC-CTAAACCCTAAACAT
* *
718 AAAACACTAAACCTTAAA
1 TAAACACTAAACCCTAAA
736 TTATAAACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
35 7 0.16
36 38 0.84
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (35 bp):
TAAACACTAAACCCTAAACCCTAAACCCTAAACAT
Found at i:756 original size:7 final size:7
Alignment explanation
Indices: 661--784 Score: 55
Period size: 7 Copynumber: 17.6 Consensus size: 7
651 TCTAAACTAC
661 TAAACCT
1 TAAACCT
*
668 TAAACCC
1 TAAACCT
**
675 TAAATAT
1 TAAACCT
682 TAAACAC-
1 TAAAC-CT
*
689 TAAACCC
1 TAAACCT
*
696 TAAACCAC
1 TAAACC-T
704 TAAA-CT
1 TAAACCT
710 CTAAACCT
1 -TAAACCT
*
718 AAAACAC-
1 TAAAC-CT
725 TAAACCT
1 TAAACCT
*
732 TAAA-TT
1 TAAACCT
738 ATAAACAC-
1 -TAAAC-CT
746 TAAACCT
1 TAAACCT
753 TAAACCT
1 TAAACCT
760 T-AACC-
1 TAAACCT
*
765 TATAGCCT
1 TA-AACCT
773 CTAAACCT
1 -TAAACCT
781 TAAA
1 TAAA
785 TCCTAAACAT
Statistics
Matches: 89, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
5 1 0.01
6 8 0.09
7 66 0.74
8 12 0.13
9 2 0.02
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:756 original size:14 final size:14
Alignment explanation
Indices: 625--784 Score: 84
Period size: 14 Copynumber: 11.3 Consensus size: 14
615 TGTTAGGTAA
*
625 TAAACACTAAACAT
1 TAAACACTAAACCT
639 TAAAC-CATAAA-CT
1 TAAACAC-TAAACCT
652 CTAAACTACTAAACCT
1 -TAAAC-ACTAAACCT
* **
668 TAAACCCTAAATAT
1 TAAACACTAAACCT
*
682 TAAACACTAAACCC
1 TAAACACTAAACCT
696 TAAACCACTAAA-CT
1 TAAA-CACTAAACCT
710 CTAAAC-CTAAAACAC-
1 -TAAACACT-AAAC-CT
*
725 TAAAC-CTTAAA-TT
1 TAAACAC-TAAACCT
738 ATAAACACTAAACCT
1 -TAAACACTAAACCT
*
753 TAAAC-CTTAACCT
1 TAAACACTAAACCT
** *
766 ATAGCCTCTAAACCT
1 -TAAACACTAAACCT
781 TAAA
1 TAAA
785 TCCTAAACAT
Statistics
Matches: 112, Mismatches: 17, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
13 11 0.10
14 67 0.60
15 30 0.27
16 4 0.04
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.24
Consensus pattern (14 bp):
TAAACACTAAACCT
Found at i:817 original size:26 final size:26
Alignment explanation
Indices: 788--870 Score: 148
Period size: 26 Copynumber: 3.2 Consensus size: 26
778 CCTTAAATCC
*
788 TAAACATAATTAATTAAATACAAACA
1 TAAACATAATTAATGAAATACAAACA
*
814 TAAACATGATTAATGAAATACAAACA
1 TAAACATAATTAATGAAATACAAACA
840 TAAACATAATTAATGAAATACAAACA
1 TAAACATAATTAATGAAATACAAACA
866 TAAAC
1 TAAAC
871 TGAGTTTGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.60, C:0.12, G:0.04, T:0.24
Consensus pattern (26 bp):
TAAACATAATTAATGAAATACAAACA
Done.