Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006043.1 Kokia drynarioides strain JFW-HI SEQ_120509, 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: 19406
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1435 original size:27 final size:25
Alignment explanation
Indices: 1391--1455 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
1381 TTTAAAAATA
**
1391 TTAATTTTTAGTAATTTTA-ATGATTT
1 TTAATTTTTAAAAATTTTATAT--TTT
1417 TTAATTTTTAAAAAGTTTTATATTTT
1 TTAATTTTTAAAAA-TTTTATATTTT
1443 TTGAATTTTTAAA
1 TT-AATTTTTAAA
1456 TTTTTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 17 0.50
27 15 0.44
28 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (25 bp):
TTAATTTTTAAAAATTTTATATTTT
Found at i:6085 original size:20 final size:20
Alignment explanation
Indices: 6047--6085 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6037 GTCTAAGTTC
* * *
6047 ATTTAAATATTTTTTAAAAA
1 ATTTAAAAATTATTAAAAAA
6067 ATTTAAAAATTATTAAAAA
1 ATTTAAAAATTATTAAAAA
6086 GTAATATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAAAATTATTAAAAAA
Found at i:6615 original size:12 final size:11
Alignment explanation
Indices: 6591--6665 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
6581 ATATTTAGAA
6591 TTTTTAATAA-
1 TTTTTAATAAT
6601 TTTTT-ATAAT
1 TTTTTAATAAT
*
6611 TATTTTAAAAAT
1 T-TTTTAATAAT
* *
6623 ATTTT-ATGA-
1 TTTTTAATAAT
6632 TTTTTAGATAAT
1 TTTTTA-ATAAT
* *
6644 ATTTTAATGAT
1 TTTTTAATAAT
6655 TTTTTAATAAT
1 TTTTTAATAAT
6666 CACATCCGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
9 8 0.16
10 8 0.16
11 24 0.49
12 9 0.18
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:6615 original size:22 final size:21
Alignment explanation
Indices: 6590--6665 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
6580 TATATTTAGA
*
6590 ATTTTTAATAATTTTTATAATT
1 ATTTTTAATAATATTT-TAATT
* *
6612 A-TTTTAAAAATATTTT-ATG
1 ATTTTTAATAATATTTTAATT
*
6631 ATTTTTAGATAATATTTTAATG
1 ATTTTTA-ATAATATTTTAATT
6653 ATTTTTTAATAAT
1 A-TTTTTAATAAT
6666 CACATCCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.07
20 6 0.13
21 21 0.46
22 10 0.22
23 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTTTAATAATATTTTAATT
Found at i:12100 original size:40 final size:40
Alignment explanation
Indices: 12041--12134 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
12031 TTTGGAAAGA
* *
12041 AAACGCCGCAAAAGGTAAAGCAATAGCCGTGCTTTTCAAT
1 AAACGCCGCTAAAGATAAAGCAATAGCCGTGCTTTTCAAT
* *
12081 AAACGCCGCTCAAGATAAAGCAATAGCGGTGCTTTTCAAT
1 AAACGCCGCTAAAGATAAAGCAATAGCCGTGCTTTTCAAT
12121 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
12135 GTCATAGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (40 bp):
AAACGCCGCTAAAGATAAAGCAATAGCCGTGCTTTTCAAT
Found at i:12164 original size:51 final size:51
Alignment explanation
Indices: 12104--12207 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
12094 GATAAAGCAA
12104 TAGCGGTGCTTTTCAATAAACGCCGCTAAAGGTCATAGCATTAGCGACGCT
1 TAGCGGTGCTTTTCAATAAACGCCGCTAAAGGTCATAGCATTAGCGACGCT
12155 TAGCGGTGCTTTTCAATAAACGCCGCTAAAGGTCATAGCATTAGCGACGCT
1 TAGCGGTGCTTTTCAATAAACGCCGCTAAAGGTCATAGCATTAGCGACGCT
12206 TA
1 TA
12208 TGAGGAAGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (51 bp):
TAGCGGTGCTTTTCAATAAACGCCGCTAAAGGTCATAGCATTAGCGACGCT
Done.