Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005997.1 Kokia drynarioides strain JFW-HI SEQ_120422, 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: 11477
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:607 original size:12 final size:12
Alignment explanation
Indices: 583--638 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
573 AAATATTATC
*
583 AAAT-TAAATTT
1 AAATATAAAATT
594 AAATATAAAATT
1 AAATATAAAATT
606 AAAAATATAAAATT
1 --AAATATAAAATT
* *
620 AGATAAAAAATTT
1 AAATATAAAA-TT
633 AAATAT
1 AAATAT
639 TAGATTAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 4 0.11
12 14 0.39
13 6 0.17
14 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:613 original size:14 final size:14
Alignment explanation
Indices: 594--620 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
584 AATTAAATTT
594 AAATATAAAATTAA
1 AAATATAAAATTAA
608 AAATATAAAATTA
1 AAATATAAAATTA
621 GATAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATAAAATTAA
Found at i:616 original size:26 final size:25
Alignment explanation
Indices: 583--640 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
573 AAATATTATC
* *
583 AAATTAAATTTAAATATAAAATTAA
1 AAATTAAAATTAAATAAAAAATTAA
*
608 AAATATAAAATTAGATAAAAAATTTAA
1 AAAT-TAAAATTAAATAAAAAA-TTAA
*
635 ATATTA
1 AAATTA
641 GATTAGAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 16 0.59
27 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATTAAAATTAAATAAAAAATTAA
Found at i:640 original size:20 final size:20
Alignment explanation
Indices: 588--643 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
578 TTATCAAATT
* * *
588 AAATTTAAATATAAAATTAA
1 AAATTTAAATATTAGATAAA
*
608 AAATATAAA-ATTAGATAAA
1 AAATTTAAATATTAGATAAA
627 AAATTTAAATATTAGAT
1 AAATTTAAATATTAGAT
644 TAGAGAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAATTTAAATATTAGATAAA
Found at i:2756 original size:20 final size:23
Alignment explanation
Indices: 2731--2775 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
2721 ATGATGTTAA
2731 ATATGTGATA-A-A-ATGATGAT
1 ATATGTGATATATACATGATGAT
2751 ATATGTGATATATACATGATGAT
1 ATATGTGATATATACATGATGAT
2774 AT
1 AT
2776 GTTTGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 1 0.05
22 1 0.05
23 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATGTGATATATACATGATGAT
Found at i:2968 original size:23 final size:23
Alignment explanation
Indices: 2920--3067 Score: 106
Period size: 23 Copynumber: 6.3 Consensus size: 23
2910 TTAGCATTGC
*
2920 GTGTGCTCT-TCGATTAGCACTGT
1 GTGTGCTCTCT-GATTAGCACTTT
*
2943 GTGTGCTCTCTGATTAGTACTTT
1 GTGTGCTCTCTGATTAGCACTTT
* * * *
2966 GTGTACT-TTTCGTTTAGCATTTT
1 GTGTGCTCTCT-GATTAGCACTTT
** *
2989 GTGTGCTCTCTTTTTAACA-TGTT
1 GTGTGCTCTCTGATTAGCACT-TT
* *
3012 -TCGTGCTCTCCGTTATTAGCACTTC
1 GT-GTGCTCT-C-TGATTAGCACTTT
*
3037 GTGTGCTCTCTAATTAGCACTTT
1 GTGTGCTCTCTGATTAGCACTTT
3060 GTGTGCTC
1 GTGTGCTC
3068 AGTACTTTGT
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
22 4 0.04
23 74 0.74
24 5 0.05
25 15 0.15
26 2 0.02
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (23 bp):
GTGTGCTCTCTGATTAGCACTTT
Found at i:2968 original size:25 final size:23
Alignment explanation
Indices: 2901--2997 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
2891 GAATACTAGC
* * * *
2901 GCTCTCCGGTTAGCATTGCGTGT
1 GCTCTTCGATTAGCACTGTGTGT
2924 GCTCTTCGATTAGCACTGTGTGT
1 GCTCTTCGATTAGCACTGTGTGT
* *
2947 GCTC-TCTGATTAGTACTTTGTGT
1 GCTCTTC-GATTAGCACTGTGTGT
* * * * *
2970 ACTTTTCGTTTAGCATTTTGTGT
1 GCTCTTCGATTAGCACTGTGTGT
2993 GCTCT
1 GCTCT
2998 CTTTTTAACA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.03
23 55 0.93
24 2 0.03
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (23 bp):
GCTCTTCGATTAGCACTGTGTGT
Done.