Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002813.1 Kokia drynarioides strain JFW-HI SEQ_115167, 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: 14079
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1646 original size:25 final size:26
Alignment explanation
Indices: 1600--1651 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
1590 ATATAGTGAG
*
1600 AAAAATTATAAAACTATGATAATTAT
1 AAAAATTATAAAACTATGATAAATAT
* * *
1626 AAAATTTATTAAA-TATTATAAATAT
1 AAAAATTATAAAACTATGATAAATAT
1651 A
1 A
1652 CTATGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAAATTATAAAACTATGATAAATAT
Found at i:1696 original size:30 final size:30
Alignment explanation
Indices: 1626--1698 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
1616 TGATAATTAT
*
1626 AAAATTTATTAAATATTATAAATATACTATG
1 AAAA-TTATTAAAAATTATAAATATACTATG
* *
1657 AAAAATATTAAAAATTATAAA-ATCATTA-G
1 AAAATTATTAAAAATTATAAATAT-ACTATG
1686 AAGAATTATTAAA
1 AA-AATTATTAAA
1699 TTTGTTTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.14
30 27 0.75
31 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTATTAAAAATTATAAATATACTATG
Found at i:1785 original size:6 final size:6
Alignment explanation
Indices: 1774--1805 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1764 GGTTCAGTGA
1774 ATGGAT ATGGAT ATGGAT ATGGAT ATGGAT AT
1 ATGGAT ATGGAT ATGGAT ATGGAT ATGGAT AT
1806 TTCAACCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
ATGGAT
Found at i:4502 original size:70 final size:67
Alignment explanation
Indices: 4376--4508 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
4366 ATAAACAATA
* * *
4376 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
4441 CT
66 CT
* * *
4443 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTACTTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
4508 T
63 T
4509 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.04
70 36 0.63
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:6993 original size:24 final size:23
Alignment explanation
Indices: 6949--6993 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
6939 TATATCTTTA
** *
6949 TAAATTTTTAAAGGAATATTGGC
1 TAAATTTTTAAAAAAAAATTGGC
6972 TAAATTTTATAAAAAAAAATTG
1 TAAATTTT-TAAAAAAAAATTG
6994 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (23 bp):
TAAATTTTTAAAAAAAAATTGGC
Found at i:7000 original size:19 final size:19
Alignment explanation
Indices: 6976--7023 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
6966 ATTGGCTAAA
6976 TTTTATAAAAAAAAA-TTGT
1 TTTTATAAAAAAAAAGTT-T
6995 TTTTATAATAAAAAAAGTTT
1 TTTTATAA-AAAAAAAGTTT
*
7015 TTTTTTAAA
1 TTTTATAAA
7024 GATATTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTTATAAAAAAAAAGTTT
Found at i:13910 original size:4 final size:4
Alignment explanation
Indices: 13901--13964 Score: 58
Period size: 4 Copynumber: 16.0 Consensus size: 4
13891 AAATAAACAG
* * ** *
13901 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGC GAAA AAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
13950 G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
13965 TGTAATGTGT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
3 3 0.06
4 40 0.85
5 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13917 original size:13 final size:13
Alignment explanation
Indices: 13899--13964 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
13889 GCAAATAAAC
13899 AGGAAAGAAAGAA
1 AGGAAAGAAAGAA
13912 AGGAAAGAAAGAA
1 AGGAAAGAAAGAA
*
13925 A-GAAAGGAAGAA
1 AGGAAAGAAAGAA
*
13937 GGAGCGAAAAAAAGAAGA
1 --AG-GAAAGAAAG-A-A
13955 AGGAAAGAAA
1 AGGAAAGAAA
13965 TGTAATGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 10 0.23
13 14 0.33
14 1 0.02
15 7 0.16
16 9 0.21
17 1 0.02
18 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (13 bp):
AGGAAAGAAAGAA
Found at i:13923 original size:17 final size:17
Alignment explanation
Indices: 13901--13933 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13891 AAATAAACAG
13901 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
13918 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
13934 GAAGGAGCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.