Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008780.1 Kokia drynarioides strain JFW-HI SEQ_123463, 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: 8710
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:2941 original size:11 final size:10
Alignment explanation
Indices: 2925--2999 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
2915 AAAATTATAT
2925 ATTTTTTTAGA
1 ATTTTTTTA-A
2936 A-TTTTTTAA
1 ATTTTTTTAA
2945 ATTTTTTATAA
1 ATTTTTT-TAA
*
2956 A-TTTTTGAA
1 ATTTTTTTAA
*
2965 ATTTTTATAA
1 ATTTTTTTAA
* *
2975 A-TATTTTGA
1 ATTTTTTTAA
2984 ATTTTTTGT-A
1 ATTTTTT-TAA
2994 ATTTTT
1 ATTTTT
3000 GTTGAGAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
9 11 0.21
10 35 0.67
11 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:2947 original size:9 final size:9
Alignment explanation
Indices: 2927--2990 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 9
2917 AATTATATAT
2927 TTTTTTAGAA
1 TTTTTTA-AA
2937 TTTTTTAAA
1 TTTTTTAAA
2946 TTTTTTATAAA
1 -TTTTT-TAAA
*
2957 TTTTTGAAA
1 TTTTTTAAA
2966 TTTTTATAAA
1 TTTTT-TAAA
* *
2976 TATTTTGAA
1 TTTTTTAAA
2985 TTTTTT
1 TTTTTT
2991 GTAATTTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 18 0.39
10 24 0.52
11 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:2950 original size:20 final size:19
Alignment explanation
Indices: 2925--2999 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
2915 AAAATTATAT
2925 ATTTTTTTAGAATTTTTTAA
1 ATTTTTTTA-AATTTTTTAA
*
2945 ATTTTTTATAAATTTTTGAA
1 ATTTTTT-TAAATTTTTTAA
* * *
2965 ATTTTTATAAATATTTTGA
1 ATTTTTTTAAATTTTTTAA
2984 ATTTTTTGT-AATTTTT
1 ATTTTTT-TAAATTTTT
3000 GTTGAGAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 21 0.46
20 23 0.50
21 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAAATTTTTTAA
Found at i:2951 original size:19 final size:19
Alignment explanation
Indices: 2927--2999 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
2917 AATTATATAT
2927 TTTTTTAGAATTTTTTAAA
1 TTTTTTAGAATTTTTTAAA
* *
2946 TTTTTTATAAATTTTTGAAA
1 TTTTTTA-GAATTTTTTAAA
* *
2966 TTTTTATA-AATATTTTGAA
1 TTTTT-TAGAATTTTTTAAA
2985 TTTTTT-GTAATTTTT
1 TTTTTTAG-AATTTTT
3000 GTTGAGAGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 26 0.59
20 15 0.34
21 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTTAGAATTTTTTAAA
Found at i:6889 original size:18 final size:17
Alignment explanation
Indices: 6846--6889 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
6836 GTTTTATTCC
6846 TTTTTA-TTTTTGCTTA
1 TTTTTATTTTTTGCTTA
* *
6862 TTTATCTTTTTATGCTTA
1 TTTTTATTTTT-TGCTTA
6880 TTTTTATTTT
1 TTTTTATTTT
6890 ATTTTCTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTGCTTA
Found at i:7106 original size:21 final size:21
Alignment explanation
Indices: 7082--7132 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
7072 TGTCATAATG
7082 TATTTTATTT-TTTTATGTGAT
1 TATTTTATTTATTTT-TGTGAT
* *
7103 TATTTCATTTATTTTTGTTAT
1 TATTTTATTTATTTTTGTGAT
*
7124 TATTATATT
1 TATTTTATT
7133 GTATGTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.71
Consensus pattern (21 bp):
TATTTTATTTATTTTTGTGAT
Done.