Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001516.1 Kokia drynarioides strain JFW-HI SEQ_113075, 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: 11059
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2777 original size:30 final size:31
Alignment explanation
Indices: 2742--2810 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2732 TGTTAATAAT
*
2742 AAAATTATAACTT-ATCTTTTTAAAATGATA
1 AAAATTATAACTTAATCTTTTAAAAATGATA
* *
2772 AAAATT-TAATTTAATCTTTTAAAAATTATA
1 AAAATTATAACTTAATCTTTTAAAAATGATA
*
2802 TAAA-TATAA
1 AAAATTATAA
2811 ACTATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (31 bp):
AAAATTATAACTTAATCTTTTAAAAATGATA
Found at i:5821 original size:23 final size:24
Alignment explanation
Indices: 5781--5830 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
5771 CTGTTTTCAG
* *
5781 GTTGTTTGTGCTGTTATTTTTGTT
1 GTTGTTTGTGCTGCTATTTTTATT
*
5805 GTTGTTT-TGTTGCTATTTTTATT
1 GTTGTTTGTGCTGCTATTTTTATT
5828 GTT
1 GTT
5831 TTTAATGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (24 bp):
GTTGTTTGTGCTGCTATTTTTATT
Found at i:5856 original size:24 final size:24
Alignment explanation
Indices: 5829--5885 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5819 ATTTTTATTG
*
5829 TTTTTAATGTTGTTTT-GTTGTTA
1 TTTTTAATGCTGTTTTGGTTGTTA
**
5852 TTTTTGCTGCTGTTTTGGTTGTTA
1 TTTTTAATGCTGTTTTGGTTGTTA
*
5876 TTTTTTATGC
1 TTTTTAATGC
5886 ATTTTTCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.09, C:0.05, G:0.19, T:0.67
Consensus pattern (24 bp):
TTTTTAATGCTGTTTTGGTTGTTA
Found at i:6010 original size:10 final size:10
Alignment explanation
Indices: 5995--6036 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
5985 AATATAATTT
5995 TTTTAATGTA
1 TTTTAATGTA
*
6005 TTTTAAT-TT
1 TTTTAATGTA
6014 TTTTAATGT-
1 TTTTAATGTA
6023 TTTTAAGTGTA
1 TTTTAA-TGTA
6034 TTT
1 TTT
6037 GATATATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 14 0.50
10 11 0.39
11 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (10 bp):
TTTTAATGTA
Found at i:6016 original size:18 final size:18
Alignment explanation
Indices: 5989--6028 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
5979 TATCTTAATA
5989 TAATTTTTTTAATGTATTT
1 TAATTTTTTTAATGT-TTT
6008 TAATTTTTTTAATGTTTT
1 TAATTTTTTTAATGTTTT
6026 TAA
1 TAA
6029 GTGTATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TAATTTTTTTAATGTTTT
Found at i:6017 original size:9 final size:9
Alignment explanation
Indices: 5989--6028 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5979 TATCTTAATA
5989 TAATTTTTT
1 TAATTTTTT
*
5998 TAATGTATTT
1 TAAT-TTTTT
6008 TAATTTTTT
1 TAATTTTTT
*
6017 TAATGTTTT
1 TAATTTTTT
6026 TAA
1 TAA
6029 GTGTATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TAATTTTTT
Found at i:6596 original size:5 final size:5
Alignment explanation
Indices: 6586--6625 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
6576 AAACTAGAAA
*
6586 ACAAT ACAAT ATAAT ACAAT ACAAT ACAAT ACAAT ACAAT
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT
6626 CATATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (5 bp):
ACAAT
Done.