Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011784.1 Kokia drynarioides strain JFW-HI SEQ_126779, 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: 22843
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2009 original size:15 final size:15
Alignment explanation
Indices: 1991--2042 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1981 CTTTATTTTC
1991 TTATATTTTATAATA
1 TTATATTTTATAATA
** *
2006 TTATATAATAAAATA
1 TTATATTTTATAATA
2021 TTATTATTTATTATAATA
1 TTA-TA-TT-TTATAATA
2039 TTAT
1 TTAT
2043 TATTAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 15 0.54
16 2 0.07
17 2 0.07
18 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATTTTATAATA
Found at i:2051 original size:18 final size:18
Alignment explanation
Indices: 1998--2051 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
1988 TTCTTATATT
1998 TTATAATATTA-TA-TAA
1 TTATAATATTATTATTAA
* *
2014 -TAAAATATTATTATTTA
1 TTATAATATTATTATTAA
2031 TTATAATATTATTATTAA
1 TTATAATATTATTATTAA
2049 TTA
1 TTA
2052 ATATATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.29
16 2 0.06
17 2 0.06
18 18 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATATTATTATTAA
Found at i:2057 original size:18 final size:18
Alignment explanation
Indices: 1999--2057 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1989 TCTTATATTT
*
1999 TATAATATTATATAA-TAA
1 TATATTATTAT-TAATTAA
* *
2017 AATATTATTATTTATT-A
1 TATATTATTATTAATTAA
2034 TAATATTATTATTAATTAA
1 T-ATATTATTATTAATTAA
2053 TATAT
1 TATAT
2058 CATTTGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATTATTAATTAA
Found at i:8720 original size:32 final size:32
Alignment explanation
Indices: 8674--8741 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
8664 TATGGTTGAA
*
8674 TTTTAAAGGAAAATGGTGAAAGAAATTTTTCT
1 TTTTAAAGGAAAATGGTGAAAGAAAATTTTCT
*
8706 TTTTGAAGGAAAATGGTGAAAGAAAATTTTCT
1 TTTTAAAGGAAAATGGTGAAAGAAAATTTTCT
8738 TTTT
1 TTTT
8742 CCGCTTTCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (32 bp):
TTTTAAAGGAAAATGGTGAAAGAAAATTTTCT
Found at i:8878 original size:18 final size:18
Alignment explanation
Indices: 8825--8878 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
8815 TTCTTATAGT
8825 TTATAATATTA-TA-TAA
1 TTATAATATTATTATTAA
* *
8841 -TAAAATATTATTATTTA
1 TTATAATATTATTATTAA
8858 TTATAATATTATTATTAA
1 TTATAATATTATTATTAA
8876 TTA
1 TTA
8879 ATATATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.29
16 2 0.06
17 2 0.06
18 18 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATATTATTATTAA
Found at i:8884 original size:18 final size:18
Alignment explanation
Indices: 8826--8884 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
8816 TCTTATAGTT
*
8826 TATAATATTATATAA-TAA
1 TATATTATTAT-TAATTAA
* *
8844 AATATTATTATTTATT-A
1 TATATTATTATTAATTAA
8861 TAATATTATTATTAATTAA
1 T-ATATTATTATTAATTAA
8880 TATAT
1 TATAT
8885 CTTTTGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATTATTAATTAA
Found at i:9963 original size:24 final size:24
Alignment explanation
Indices: 9918--9973 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
9908 TCAAGTGAGA
* * *
9918 CTTTATTTTCATCATTTCCATTGT
1 CTTTAATTTCAACAATTCCATTGT
*
9942 CTTTAATTTCAACAATTGCATTGT
1 CTTTAATTTCAACAATTCCATTGT
*
9966 -TTTCATTT
1 CTTTAATTT
9974 GAAACCAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (24 bp):
CTTTAATTTCAACAATTCCATTGT
Found at i:16007 original size:26 final size:25
Alignment explanation
Indices: 15947--16007 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
15937 TTAGGATTGC
* *
15947 TTTTGAGAAATGCTTTTAAAAAGTG
1 TTTTGAAAAATGATTTTAAAAAGTG
* * *
15972 CTTTGAAAAAATGATTTTGAAAAGTAT
1 TTTTG-AAAAATGATTTTAAAAAGT-G
15999 TTTTGAAAA
1 TTTTGAAAA
16008 GCTTGGTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.14
26 20 0.71
27 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.39
Consensus pattern (25 bp):
TTTTGAAAAATGATTTTAAAAAGTG
Found at i:17142 original size:23 final size:23
Alignment explanation
Indices: 17116--17160 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17106 TTATGACACA
* *
17116 GTTATGTTTGCTTTTATAGCATG
1 GTTATGTCTGCTTCTATAGCATG
17139 GTTATGTCTGCTTCTATAGCAT
1 GTTATGTCTGCTTCTATAGCAT
17161 ATTAGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (23 bp):
GTTATGTCTGCTTCTATAGCATG
Found at i:17964 original size:41 final size:41
Alignment explanation
Indices: 17907--18029 Score: 183
Period size: 41 Copynumber: 3.0 Consensus size: 41
17897 AGAGATATAG
* *
17907 TTACGGATGCAAACATGATATAGATACAGTTACAGATGCAA
1 TTACGGATGCAGACATGATACAGATACAGTTACAGATGCAA
* * * *
17948 TTACGGATACAGACATGATACAGATACAGTCACAAATACAA
1 TTACGGATGCAGACATGATACAGATACAGTTACAGATGCAA
*
17989 TTACGGATGTAGACATGATACAGATACAGTTACAGATGCAA
1 TTACGGATGCAGACATGATACAGATACAGTTACAGATGCAA
18030 ACGTGATACC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (41 bp):
TTACGGATGCAGACATGATACAGATACAGTTACAGATGCAA
Found at i:18754 original size:41 final size:41
Alignment explanation
Indices: 18624--18758 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 41
18614 CCATGTGTCA
* *
18624 GCCCGTGTGCCCCCAGAATAGTATACACACTCCCTGACCCAC
1 GCCCGTGTG-CCTCAGAATAGTATACACACACCCTGACCCAC
* *
18666 GCTCATGTGCCTCAGAATAGTATACACACACCCTGACCCAC
1 GCCCGTGTGCCTCAGAATAGTATACACACACCCTGACCCAC
* * * **
18707 GTCCGTGTGCCTCACAATAGTATACATACACCCTGACTTAC
1 GCCCGTGTGCCTCAGAATAGTATACACACACCCTGACCCAC
*
18748 CCCCGTGTGCC
1 GCCCGTGTGCC
18759 AGCTCGTGTG
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 73 0.91
42 7 0.09
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (41 bp):
GCCCGTGTGCCTCAGAATAGTATACACACACCCTGACCCAC
Found at i:18824 original size:55 final size:53
Alignment explanation
Indices: 18712--18825 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 53
18702 CCCACGTCCG
* ** * * *
18712 TGTGCCTCACAATAGTATACATACACCCTGACTTACCCCCGTGTGCCAGCTCG
1 TGTGCCTCACAATAGTATACACACACCCTGACACACCCCCGTATGCCAGCCCC
* *
18765 TGTGCCTC-CAAATAGTATAGACACACACCCTGACACACGCCCGTATGCTAGCCCC
1 TGTGCCTCAC-AATAGTAT--ACACACACCCTGACACACCCCCGTATGCCAGCCCC
18820 TGTGCC
1 TGTGCC
18826 CCCTGTACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.02
53 16 0.32
55 33 0.66
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.22
Consensus pattern (53 bp):
TGTGCCTCACAATAGTATACACACACCCTGACACACCCCCGTATGCCAGCCCC
Found at i:20221 original size:27 final size:27
Alignment explanation
Indices: 20183--20235 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
20173 AACAACGACT
20183 GGATGCGCATGGATCTTTCCTTTGACA
1 GGATGCGCATGGATCTTTCCTTTGACA
*
20210 GGATGTGCATGGATCTTTCCTTTGAC
1 GGATGCGCATGGATCTTTCCTTTGAC
20236 GAACGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (27 bp):
GGATGCGCATGGATCTTTCCTTTGACA
Found at i:21219 original size:17 final size:17
Alignment explanation
Indices: 21199--21232 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21189 TAAAAATTAT
*
21199 AAAAATCTTAAAACACA
1 AAAAATATTAAAACACA
*
21216 AAAATTATTAAAACACA
1 AAAAATATTAAAACACA
21233 CAATTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATATTAAAACACA
Done.