Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002050.1 Kokia drynarioides strain JFW-HI SEQ_113938, 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: 71462
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:15951 original size:18 final size:18
Alignment explanation
Indices: 15930--15971 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
15920 CCAAATGCGA
15930 TCACAGAATCAGATGCAG
1 TCACAGAATCAGATGCAG
* *
15948 TCACATACTCAGATGCAG
1 TCACAGAATCAGATGCAG
*
15966 CCACAG
1 TCACAG
15972 GTTTGAATGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (18 bp):
TCACAGAATCAGATGCAG
Found at i:29241 original size:21 final size:20
Alignment explanation
Indices: 29202--29267 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
29192 TTACAATCAG
* *
29202 CAAACTCAGATGCATCCACAA
1 CAAA-TCAGATGTAGCCACAA
*
29223 CAAAGTCAGATGTAGCCACAC
1 CAAA-TCAGATGTAGCCACAA
**
29244 CAGAATTGGATGTAGCCACAA
1 CA-AATCAGATGTAGCCACAA
29265 CAA
1 CAA
29268 TCTTCAATCC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.03
21 34 0.92
22 2 0.05
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (20 bp):
CAAATCAGATGTAGCCACAA
Found at i:35109 original size:18 final size:18
Alignment explanation
Indices: 35086--35134 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
35076 ATGCAAATGT
35086 TGCTAAAGGGGAAATCCC
1 TGCTAAAGGGGAAATCCC
*
35104 TGCTAAAAGGGAAATCCC
1 TGCTAAAGGGGAAATCCC
* *
35122 TACTGAAGGGGAA
1 TGCTAAAGGGGAA
35135 GAAACCCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (18 bp):
TGCTAAAGGGGAAATCCC
Found at i:36741 original size:26 final size:26
Alignment explanation
Indices: 36705--36761 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
36695 TTTTACTATT
*
36705 AATTGTCACTGCATGAACATGTCCAG
1 AATTGTCACTGCATGAACATGTCCAA
*
36731 AATTGTCACTGCATGAGCATGTCCAA
1 AATTGTCACTGCATGAACATGTCCAA
36757 AATTG
1 AATTG
36762 CGCCCATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (26 bp):
AATTGTCACTGCATGAACATGTCCAA
Found at i:44700 original size:36 final size:36
Alignment explanation
Indices: 44655--44724 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
44645 CCAAGATAAA
44655 AAAAAAAGCATGAAGTCAGCGTGTTTATCTCGGTAT
1 AAAAAAAGCATGAAGTCAGCGTGTTTATCTCGGTAT
44691 AAAAAAAGCATGAAGTCAGCGTGTTTATCTCGGT
1 AAAAAAAGCATGAAGTCAGCGTGTTTATCTCGGT
44725 GATATTGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (36 bp):
AAAAAAAGCATGAAGTCAGCGTGTTTATCTCGGTAT
Found at i:55982 original size:52 final size:52
Alignment explanation
Indices: 55866--56048 Score: 253
Period size: 52 Copynumber: 3.5 Consensus size: 52
55856 TTCCCATTTA
* * * *
55866 ATACTCACGATGACACAAAGTCATC-GAAC-CTTAGATCCGTAAAAGATCCAT
1 ATACTCACGATGACACATAGTCATCGGAACTCATA-ATCCGTAAAGGATTCAT
* *
55917 ATGCTCACAATGACACATAGTCATCGGAACTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGAACTCATAATCCGTAAAGGATTCAT
* * * *
55969 ATACTCATGATGACACATAGTCATTGGATCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGAACTCATAATCCGTAAAGGATTCAT
56021 ATACTCACGATGACACATAGTCATCGGA
1 ATACTCACGATGACACATAGTCATCGGA
56049 CCTTTTTGCA
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
51 22 0.19
52 91 0.78
53 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGAACTCATAATCCGTAAAGGATTCAT
Found at i:56027 original size:26 final size:26
Alignment explanation
Indices: 55945--56027 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
55935 AGTCATCGGA
*
55945 ACTCATAATCCGTAAAGGATTCATAT
1 ACTCATAATCCATAAAGGATTCATAT
* * * * * **
55971 ACTCATGATGACACATAGTCATT-GGAT
1 ACTCATAAT-CCATAAAG-GATTCATAT
55998 -CTCATAATCCATAAAGGATTCATAT
1 ACTCATAATCCATAAAGGATTCATAT
56023 ACTCA
1 ACTCA
56028 CGATGACACA
Statistics
Matches: 38, Mismatches: 15, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
24 3 0.08
25 7 0.18
26 19 0.50
27 6 0.16
28 3 0.08
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.30
Consensus pattern (26 bp):
ACTCATAATCCATAAAGGATTCATAT
Found at i:58898 original size:21 final size:21
Alignment explanation
Indices: 58809--58898 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
58799 CCAACCATGG
58809 CCGTGTGGCTATTCCACACGC
1 CCGTGTGGCTATTCCACACGC
* * *
58830 TCGCGTGGCTATCCCACACGC
1 CCGTGTGGCTATTCCACACGC
** * *
58851 CCGCATGGCTATTCTACATGC
1 CCGTGTGGCTATTCCACACGC
* *
58872 CTGTGTGGCTATTCTACACGC
1 CCGTGTGGCTATTCCACACGC
58893 CCGTGT
1 CCGTGT
58899 AACTCACTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.14, C:0.36, G:0.23, T:0.27
Consensus pattern (21 bp):
CCGTGTGGCTATTCCACACGC
Found at i:65297 original size:16 final size:16
Alignment explanation
Indices: 65258--65299 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
65248 TTTATGCTTA
*
65258 TTTCATCTTTATTTAT
1 TTTCATGTTTATTTAT
65274 TTTCATGTTTATTTAT
1 TTTCATGTTTATTTAT
65290 ATTT-ATGTTT
1 -TTTCATGTTT
65300 TTTCACACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTCATGTTTATTTAT
Done.