Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003989.1 Kokia drynarioides strain JFW-HI SEQ_117095, 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: 44029
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:3449 original size:53 final size:53
Alignment explanation
Indices: 3357--3656 Score: 447
Period size: 53 Copynumber: 5.6 Consensus size: 53
3347 GTAAATGCAA
*
3357 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCTTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* ** * * *
3410 AAATGTCAAATTACTCTGTGCCATCGTGAGTTATATGAATCCAATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
*
3463 AAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * *
3516 AAAGGTCCGATGACTCTATGTCGTCGTGAGTTATATAAATCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * *
3569 AAAGGTCCGATGACTTTGTGTCATCATGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* *
3622 AAAAGGTCTGATAACTCTGTGTCATCGTGAGTTAT
1 -AAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
3657 CAAATGTGAA
Statistics
Matches: 218, Mismatches: 28, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
53 188 0.86
54 30 0.14
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:11526 original size:2 final size:2
Alignment explanation
Indices: 11519--11555 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11509 AGCGTTGTTA
11519 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11556 ATAATAGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:21298 original size:18 final size:18
Alignment explanation
Indices: 21277--21315 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21267 TCATCATCTC
* *
21277 CATCACCATCTTTATCAG
1 CATCACCACCTGTATCAG
*
21295 CATCACCGCCTGTATCAG
1 CATCACCACCTGTATCAG
21313 CAT
1 CAT
21316 TCTCCTCACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.28
Consensus pattern (18 bp):
CATCACCACCTGTATCAG
Found at i:25873 original size:9 final size:9
Alignment explanation
Indices: 25835--25908 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
25825 TTCACTCTCT
25835 TCTTCCTCC
1 TCTTCCTCC
*
25844 TCCTCC-CC
1 TCTTCCTCC
25852 -CTTCTCTTCC
1 TCTTC-C-TCC
25862 TCTTCCTCC
1 TCTTCCTCC
* *
25871 TCTTCTTCT
1 TCTTCCTCC
* *
25880 TCTTCTTCT
1 TCTTCCTCC
* *
25889 TCTTCTTCT
1 TCTTCCTCC
25898 TCTTCCTCC
1 TCTTCCTCC
25907 TC
1 TC
25909 CTCTTTCTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 42 0.76
10 3 0.05
11 4 0.07
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (9 bp):
TCTTCCTCC
Found at i:25877 original size:3 final size:3
Alignment explanation
Indices: 25852--25902 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
25842 CCTCCTCCCC
* * *
25852 CTT C-T CTT CCT CTT CCT CCT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
25899 CTT C
1 CTT C
25903 CTCCTCCTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:28881 original size:17 final size:17
Alignment explanation
Indices: 28849--28881 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28839 TAAATAAATC
28849 TAAATAAAACTCTTAAG
1 TAAATAAAACTCTTAAG
28866 TAAACTAAAACT-TTAA
1 TAAA-TAAAACTCTTAA
28882 TTCATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAATAAAACTCTTAAG
Found at i:39610 original size:19 final size:20
Alignment explanation
Indices: 39588--39629 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
39578 CTTTTAAAAA
39588 ATAT-TTAA-TTAA-TTAAT
1 ATATATTAATTTAATTTAAT
39605 ATATATTAATTTTAATTTAAT
1 ATATATTAA-TTTAATTTAAT
39626 ATAT
1 ATAT
39630 TCTATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
20 4 0.19
21 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTAATTTAATTTAAT
Found at i:39694 original size:17 final size:17
Alignment explanation
Indices: 39653--39694 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
39643 TAAACATAGA
39653 AAAATTAATATATAAAAT
1 AAAA-TAATATATAAAAT
* *
39671 CACATAATATATAAAAT
1 AAAATAATATATAAAAT
39688 AAAATAA
1 AAAATAA
39695 AACAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAATATATAAAAT
Found at i:41849 original size:16 final size:16
Alignment explanation
Indices: 41828--41862 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41818 TGGAAATATC
41828 TCCAAAGTTCAACAAA
1 TCCAAAGTTCAACAAA
41844 TCCAAAGTTCAACAAA
1 TCCAAAGTTCAACAAA
41860 TCC
1 TCC
41863 CCCTTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (16 bp):
TCCAAAGTTCAACAAA
Done.