Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007515.1 Kokia drynarioides strain JFW-HI SEQ_122139, 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: 46693
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:24590 original size:52 final size:52
Alignment explanation
Indices: 24492--24729 Score: 266
Period size: 52 Copynumber: 4.6 Consensus size: 52
24482 GCATGTATGT
* * * * *
24492 TACTCACAATGACACAGAGTCATCGGACC-CTTAATCCGCAATAGGATTC-TAA
1 TACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAA-AGGATTCAT-A
* *
24544 TACTCACGATAACACATAGTCATCGAACCTAATAATCCGTAAAGGATTCATA
1 TACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATA
* * * *
24596 CACTCACGATGACACATAATCAT-TAGACCTCATAATCCGTAAATGATTCATA
1 TACTCACGATGACACATAGTCATCGA-ACCTCATAATCCGTAAAGGATTCATA
* * * *
24648 TACTCATGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGGTTCATA
1 TACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATA
* * *
24700 TACTCACGACGGCACATAGTCATCGGACCT
1 TACTCACGATGACACATAGTCATCGAACCT
24730 TTTCATTTAC
Statistics
Matches: 158, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.01
52 147 0.93
53 10 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (52 bp):
TACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATA
Found at i:25983 original size:17 final size:17
Alignment explanation
Indices: 25952--26014 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
25942 TACTAGTAAG
** *
25952 CATTGTCATCGCATTCC
1 CATTGTCATTACATTTC
*
25969 CATTGTCATTACATTTT
1 CATTGTCATTACATTTC
* *
25986 AATTGTCATTGCATTTC
1 CATTGTCATTACATTTC
26003 CATTTGTCATTA
1 CA-TTGTCATTA
26015 TAATTGAGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (17 bp):
CATTGTCATTACATTTC
Found at i:27939 original size:16 final size:15
Alignment explanation
Indices: 27901--27941 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
27891 CATTTCATCC
27901 TTACTATT--CACAT
1 TTACTATTCACACAT
27914 TTACTATTCACACAT
1 TTACTATTCACACAT
27929 TTACTTATTCACA
1 TTAC-TATTCACA
27942 TTAAGAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (15 bp):
TTACTATTCACACAT
Found at i:36283 original size:39 final size:39
Alignment explanation
Indices: 36229--36309 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
36219 GCACACAAGG
*
36229 GTAGATTGATACAATATAAACCTCTAGTAAAATGCCCCT
1 GTAGATTGATACAATATAAACCTCTAGTAAAACGCCCCT
36268 GTAGATTGATACAATATAAACCTCTAGTAAAACGCCCCT
1 GTAGATTGATACAATATAAACCTCTAGTAAAACGCCCCT
36307 GTA
1 GTA
36310 ACCCAACGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (39 bp):
GTAGATTGATACAATATAAACCTCTAGTAAAACGCCCCT
Found at i:36843 original size:22 final size:23
Alignment explanation
Indices: 36818--36862 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
36808 GTGAGTAATA
*
36818 GAATTATT-TTTTCGCTGTTCAT
1 GAATTATTATTTACGCTGTTCAT
*
36840 GAATTATTATTTAGGCTGTTCAT
1 GAATTATTATTTACGCTGTTCAT
36863 ACCATCCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (23 bp):
GAATTATTATTTACGCTGTTCAT
Found at i:41599 original size:17 final size:17
Alignment explanation
Indices: 41577--41633 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
41567 TAATTTTCCC
*
41577 TGCATTATTAATGTCAT
1 TGCATTATTATTGTCAT
*
41594 TGCATTTTTATTGTCAT
1 TGCATTATTATTGTCAT
*
41611 TGCATCTA-CATTGTCAT
1 TGCAT-TATTATTGTCAT
41628 TGCATT
1 TGCATT
41634 TCCATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (17 bp):
TGCATTATTATTGTCAT
Found at i:43486 original size:14 final size:14
Alignment explanation
Indices: 43454--43487 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43444 GATTACTTTG
43454 ATTCTTATTTGATT
1 ATTCTTATTTGATT
* *
43468 CTTCTTATTTGTTT
1 ATTCTTATTTGATT
43482 ATTCTT
1 ATTCTT
43488 GGACTTAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTCTTATTTGATT
Done.