Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010999.1 Kokia drynarioides strain JFW-HI SEQ_125969, 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: 35054
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:86 original size:4 final size:4
Alignment explanation
Indices: 67--131 Score: 60
Period size: 4 Copynumber: 16.0 Consensus size: 4
57 ACACATTACA
* * * * *
67 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
115 TTTCC TTTC TTTC TTTC
1 TTT-C TTTC TTTC TTTC
132 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:114 original size:29 final size:27
Alignment explanation
Indices: 72--129 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
62 TTACATTTCT
72 TTCCTTCTTCTTTCTTTCCTCTCCTTC
1 TTCCTTCTTCTTTCTTTCCTCTCCTTC
* *
99 TTCCTTCCTTTCTTTCTTTCCTTTCTTTC
1 TTCCTT-C-TTCTTTCTTTCCTCTCCTTC
128 TT
1 TT
130 TCCCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 1 0.04
29 20 0.74
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (27 bp):
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Found at i:119 original size:13 final size:14
Alignment explanation
Indices: 67--132 Score: 73
Period size: 13 Copynumber: 4.6 Consensus size: 14
57 ACACATTACA
67 TTTCTTTCCTTCTTC
1 TTTCTTTCC-TCTTC
*
82 TTTCTTTCCTCTCC
1 TTTCTTTCCTCTTC
*
96 TTCTTCCTTCCT-TTC
1 -T-TTCTTTCCTCTTC
111 TTTCTTTCCT-TTC
1 TTTCTTTCCTCTTC
124 TTTCTTTCC
1 TTTCTTTCC
133 CGTTTATTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
13 20 0.44
14 5 0.11
15 12 0.27
16 8 0.18
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTTCCTCTTC
Found at i:7525 original size:16 final size:16
Alignment explanation
Indices: 7504--7535 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7494 TCCGGTTATA
7504 GTTTTACTAAATGTGG
1 GTTTTACTAAATGTGG
7520 GTTTTACTAAATGTGG
1 GTTTTACTAAATGTGG
7536 TAATTGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
GTTTTACTAAATGTGG
Found at i:8798 original size:2 final size:2
Alignment explanation
Indices: 8791--8815 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8781 AATGAAAAGA
8791 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
8816 TATACAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15887 original size:2 final size:2
Alignment explanation
Indices: 15880--15905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15870 TGTAGATGAC
15880 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15906 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15910 original size:2 final size:2
Alignment explanation
Indices: 15905--15931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15895 ATATATATAT
15905 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
15932 ACTTAGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21790 original size:51 final size:50
Alignment explanation
Indices: 21700--21817 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 50
21690 GGTTTCAAAG
* * ** * *
21700 TTTACACATTATGTCAATTGGTCTTGATTTAGTAAATTTAGTCTACAATA
1 TTTACACATTATGTCAATTGGTCATAATTTAACAAATTTAGCCTACAACA
*
21750 TTTACACATTCTGTCAATTTGGTCATAATTTAACAAATTTAGCCTACAACA
1 TTTACACATTATGTCAA-TTGGTCATAATTTAACAAATTTAGCCTACAACA
21801 TTTACACATTATGTCAA
1 TTTACACATTATGTCAA
21818 CATTTACACA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 16 0.27
51 43 0.73
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (50 bp):
TTTACACATTATGTCAATTGGTCATAATTTAACAAATTTAGCCTACAACA
Found at i:21840 original size:21 final size:19
Alignment explanation
Indices: 21797--21841 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21787 TTTAGCCTAC
* *
21797 AACATTTACACATTATGTC
1 AACATTTACACATTATATA
21816 AACATTTACACAGATTATATA
1 AACATTTACAC--ATTATATA
21837 AACAT
1 AACAT
21842 CAAAGACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (19 bp):
AACATTTACACATTATATA
Found at i:26749 original size:23 final size:23
Alignment explanation
Indices: 26719--26867 Score: 237
Period size: 23 Copynumber: 6.4 Consensus size: 23
26709 AACACTAGCA
* *
26719 TGCTCTCTGTTTAGCAC-GTCTCG
1 TGCTCTCTGATTAGCACTGTGT-G
26742 TGCTCTCTGTTATTAGCACTGTGTG
1 TGCTCTCTG--ATTAGCACTGTGTG
26767 TGCTCTCTGATTAGCACTGTGTG
1 TGCTCTCTGATTAGCACTGTGTG
26790 TGCTCTCTGATTAGCACTGTGTG
1 TGCTCTCTGATTAGCACTGTGTG
26813 TGCTCTCTGATTAGCACTGTGTG
1 TGCTCTCTGATTAGCACTGTGTG
*
26836 TGCTCTCTGATTAGCACTTTGTG
1 TGCTCTCTGATTAGCACTGTGTG
26859 TGCTCTCTG
1 TGCTCTCTG
26868 TTGCCCAGCA
Statistics
Matches: 120, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
23 100 0.83
25 17 0.14
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.41
Consensus pattern (23 bp):
TGCTCTCTGATTAGCACTGTGTG
Found at i:26911 original size:69 final size:69
Alignment explanation
Indices: 26719--26913 Score: 220
Period size: 69 Copynumber: 2.8 Consensus size: 69
26709 AACACTAGCA
* * *
26719 TGCTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCA
1 TGCTCTCTGATTAGCACTGTAT-GTGCTCTCTG--ATTAGCACTGTGTGTACTCTCTGATTAGCA
26783 CTGTGTG
63 CTGTGTG
* * *
26790 TGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTT
1 TGCTCTCTGATTAGCACTGTATGTGCTCTCTGATTAGCACTGTGTGTACTCTCTGATTAGCACTG
26855 TGTG
66 TGTG
* *
26859 TGCTCTCTG-TTGCCCAGCACT-TATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCTG
1 TGCTCTCTGATT----AGCACTGTATGTGCTCTCTGATTAGCACTGTGTGTACTCTCTG
26914 TTTGTTTCAT
Statistics
Matches: 112, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
68 2 0.02
69 54 0.48
70 9 0.08
71 38 0.34
72 9 0.08
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (69 bp):
TGCTCTCTGATTAGCACTGTATGTGCTCTCTGATTAGCACTGTGTGTACTCTCTGATTAGCACTG
TGTG
Found at i:28518 original size:24 final size:25
Alignment explanation
Indices: 28483--28530 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
28473 CCCGATTATT
*
28483 CTTTTTTATATTTTT-GTATTATAC
1 CTTTTTTATATTTTTCATATTATAC
28507 CTTTATTT-TATTTTTCATATTATA
1 CTTT-TTTATATTTTTCATATTATA
28531 TCATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (25 bp):
CTTTTTTATATTTTTCATATTATAC
Done.