Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010032.1 Kokia drynarioides strain JFW-HI SEQ_124800, 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: 43126
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:72 original size:16 final size:16
Alignment explanation
Indices: 27--76 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17 TAAACCTAGC
*
27 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
43 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
57 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
73 TAAT
1 TAAT
77 ATCCCCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:2035 original size:2 final size:2
Alignment explanation
Indices: 2028--2055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2018 TAAAGCAATA
2028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2056 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7011 original size:30 final size:30
Alignment explanation
Indices: 6979--7035 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6969 TCTTTATCAT
* *
6979 TTTTAAAA-GATTAAATTAAAATTTTATAA
1 TTTTAAAAGGATCAAAGTAAAATTTTATAA
*
7008 TTTTAAAAGGATCAAAGTACAATTTTAT
1 TTTTAAAAGGATCAAAGTAAAATTTTAT
7036 TTTTATTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTTAAAAGGATCAAAGTAAAATTTTATAA
Found at i:8704 original size:17 final size:17
Alignment explanation
Indices: 8682--8716 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8672 TTGAGTTAGT
8682 TTTAATATATGGTCGGC
1 TTTAATATATGGTCGGC
8699 TTTAATATATGGTCGGC
1 TTTAATATATGGTCGGC
8716 T
1 T
8717 CTGTCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (17 bp):
TTTAATATATGGTCGGC
Found at i:16896 original size:109 final size:109
Alignment explanation
Indices: 16705--16934 Score: 426
Period size: 109 Copynumber: 2.1 Consensus size: 109
16695 TTTACTTAGA
*
16705 GTTTCGTGGTAATTATGGAGATGATTTTATATCCCTTTTGTAAGTGTCTTATGAGATTTATGGTT
1 GTTTCGTGGTAATTATGGAGATAATTTTATATCCCTTTTGTAAGTGTCTTATGAGATTTATGGTT
16770 TTGTTTATTGGTTTGCTCTTCGAGATTTTGAACTTTGTATTTGG
66 TTGTTTATTGGTTTGCTCTTCGAGATTTTGAACTTTGTATTTGG
*
16814 GTTTCGTGGTAATTATGGAGATAATTTTATATCCCTTTTGTGAGTGTCTTATGAGATTTATGGTT
1 GTTTCGTGGTAATTATGGAGATAATTTTATATCCCTTTTGTAAGTGTCTTATGAGATTTATGGTT
16879 TTGTTTATTGGTTTGCTCTTCGAGATTTTGAACTTTGTATTTGG
66 TTGTTTATTGGTTTGCTCTTCGAGATTTTGAACTTTGTATTTGG
*
16923 GTTTTG-GGTAAT
1 GTTTCGTGGTAAT
16935 GTACGTTTAG
Statistics
Matches: 118, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 6 0.05
109 112 0.95
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.50
Consensus pattern (109 bp):
GTTTCGTGGTAATTATGGAGATAATTTTATATCCCTTTTGTAAGTGTCTTATGAGATTTATGGTT
TTGTTTATTGGTTTGCTCTTCGAGATTTTGAACTTTGTATTTGG
Found at i:17791 original size:21 final size:21
Alignment explanation
Indices: 17743--17799 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
17733 TAGTGCAGAC
*
17743 TTCTACCGATACAAGAGATAG
1 TTCTACCAATACAAGAGATAG
* * *
17764 TTTTACCTATACAAGAGACTCG
1 TTCTACCAATACAAGAGA-TAG
17786 -TCTACCAATACAAG
1 TTCTACCAATACAAG
17800 TCATGTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCAATACAAGAGATAG
Found at i:18944 original size:196 final size:190
Alignment explanation
Indices: 18520--18953 Score: 609
Period size: 190 Copynumber: 2.3 Consensus size: 190
18510 TACCAGTACT
* * * *
18520 CGATACTGCTCACATGAGCTGTCGAGAACTCGCAACATATGCAGTACCCCAGCCATCGGTACTGT
1 CGATGCTGCTCACACGAGCTGTCGAGAACTCGCAACATATGCAGTACCCCAGCCATCGATACAGT
* * *
18585 GTCTGTCTGTAATTGTTCCCTAACGATGCTACTCACACGAGCTATCGAGAATGTGCATTTTAAGC
66 GTCTGTCTATAACTGTTCCCTAACGATGCTACTCACACGAGCTATCGAAAATGTGCATTTTAAGC
* * * *
18650 ACATCACAGCCATCGTAGGGCCTATAATCCATTTATGATTCATATATTTTTTCCGATGCA
131 ACATCACAACCATCGAAGGGCCTATAATCCATTTAGGATTCATATATCTTTTCCGATGCA
*
18710 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATG-AGGTACCCCAGCCATCGATACAG
1 CGATGCTGCTCACACGAGCTGTCGAGAACTCGCAACATATGCA-GTACCCCAGCCATCGATACAG
* * * *
18774 TGTTTGTCTATAACTGTTCCCTAACGATGCTGCTCGCACGAGCTATCGAAAAGGTGCATNCATTT
65 TGTCTGTCTATAACTGTTCCCTAACGATGCTACTCACACGAGCTATCGAAAA--TG--TGCATTT
* * *
18839 TAAGCATCAATCCCAACCATCGAAGGGCCTATAATCCATTTAGGATTTATATCTCTTTTCCGATG
126 TAAGCA-C-ATCACAACCATCGAAGGGCCTATAATCCATTTAGGATTCATATATCTTTTCCGATG
18904 CA
189 CA
* *
18906 TGATGCTGCTCACACGAGCTGTCGAGAACTCACAACATATGCAGTACC
1 CGATGCTGCTCACACGAGCTGTCGAGAACTCGCAACATATGCAGTACC
18954 TTTAGCCATC
Statistics
Matches: 214, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
189 1 0.00
190 103 0.48
192 2 0.01
194 12 0.06
195 1 0.00
196 94 0.44
197 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (190 bp):
CGATGCTGCTCACACGAGCTGTCGAGAACTCGCAACATATGCAGTACCCCAGCCATCGATACAGT
GTCTGTCTATAACTGTTCCCTAACGATGCTACTCACACGAGCTATCGAAAATGTGCATTTTAAGC
ACATCACAACCATCGAAGGGCCTATAATCCATTTAGGATTCATATATCTTTTCCGATGCA
Found at i:28642 original size:22 final size:22
Alignment explanation
Indices: 28598--28642 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28588 TTAAAATGGA
*
28598 AATTTATAAATGTTGATGAGAT
1 AATTTATAAATGTTGAAGAGAT
* * *
28620 AATTTATCAATTTTGAAGTGAT
1 AATTTATAAATGTTGAAGAGAT
28642 A
1 A
28643 GATCTTAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (22 bp):
AATTTATAAATGTTGAAGAGAT
Found at i:28896 original size:14 final size:15
Alignment explanation
Indices: 28874--28906 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28864 CAAAAATATT
*
28874 AATGTAATT-TCTAA
1 AATGCAATTGTCTAA
28888 AATGCAATTGTCTAA
1 AATGCAATTGTCTAA
28903 AATG
1 AATG
28907 TAATGGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (15 bp):
AATGCAATTGTCTAA
Found at i:29063 original size:18 final size:18
Alignment explanation
Indices: 29040--29074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29030 TTATTGATCG
*
29040 AATCGATTTAATTCGATT
1 AATCGATCTAATTCGATT
*
29058 AATCGATCTAGTTCGAT
1 AATCGATCTAATTCGAT
29075 CGAATGTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (18 bp):
AATCGATCTAATTCGATT
Found at i:34964 original size:48 final size:48
Alignment explanation
Indices: 34893--34993 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 48
34883 ACAATCCACT
34893 AAAATAAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
1 AAAATAAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
*
34941 AAAATCAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
1 AAAATAAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
34989 AAAAT
1 AAAAT
34994 TAAGATAAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (48 bp):
AAAATAAAAATTAAGTTCATAAAAACTTTCATTTCAACTAAAGAGAGG
Done.