Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006389.1 Kokia drynarioides strain JFW-HI SEQ_120966, 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: 5185
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:134 original size:29 final size:30
Alignment explanation
Indices: 102--231 Score: 123
Period size: 28 Copynumber: 4.5 Consensus size: 30
92 TGAACTTTCC
*
102 AAAATTACCATTTTTACCTCGAA-TGTCTA
1 AAAATTACCATTTTTACCCCGAACTGTCTA
* * *
131 AAAATT-CCATTTTAACCCCTAACCT-TCCA
1 AAAATTACCATTTTTACCCCGAA-CTGTCTA
160 AAAATTACCA-TTTTACCCTCGAA-TGTCT-
1 AAAATTACCATTTTTACCC-CGAACTGTCTA
*
188 AAAATT-CCATTTTTAACCCCGAACCTTTC-A
1 AAAATTACCATTTTT-ACCCCGAA-CTGTCTA
218 AAAATTACCATTTT
1 AAAATTACCATTTT
232 GTTCCCGAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.04
28 28 0.34
29 28 0.34
30 16 0.20
31 7 0.09
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCCGAACTGTCTA
Found at i:137 original size:58 final size:57
Alignment explanation
Indices: 18--231 Score: 197
Period size: 58 Copynumber: 3.7 Consensus size: 57
8 CTTTCCAAAC
* ** * * *
18 TTCCATATTTAACCCTAAACTCTTTAAAAATTA-CATTTTTACCAC-CAAACTTTCTAGAA
1 TTCCAT-TTTAACCCTGAACT-TTCCAAAATTACCATTTTTACC-CTCGAA-TGTCTAAAA
*
77 TTCCGTTTCTGAA-CCTGAACTTTCCAAAATTACCATTTTTA-CCTCGAATGTCTAAAAA
1 TTCCATTT-T-AACCCTGAACTTTCCAAAATTACCATTTTTACCCTCGAATGTCT-AAAA
*
135 TTCCATTTTAACCCCT-AACCTTCCAAAAATTACCA-TTTTACCCTCGAATGTCTAAAA
1 TTCCATTTTAA-CCCTGAACTTTCC-AAAATTACCATTTTTACCCTCGAATGTCTAAAA
* *
192 TTCCATTTTTAACCCCGAACCTTTCAAAAATTACCATTTT
1 TTCCA-TTTTAACCCTGAA-CTTTCCAAAATTACCATTTT
232 GTTCCCGAAG
Statistics
Matches: 130, Mismatches: 12, Indels: 26
0.77 0.07 0.15
Matches are distributed among these distances:
56 2 0.02
57 30 0.23
58 68 0.52
59 28 0.22
60 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.36
Consensus pattern (57 bp):
TTCCATTTTAACCCTGAACTTTCCAAAATTACCATTTTTACCCTCGAATGTCTAAAA
Found at i:173 original size:30 final size:28
Alignment explanation
Indices: 130--231 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 28
120 TCGAATGTCT
*
130 AAAAATTCCATTTTAACCCCTAACCTTCC
1 AAAAATTCCATTTTAACCCCGAACCTT-C
159 AAAAATTACCATTTT-ACCCTCGAA--TGTC
1 AAAAATT-CCATTTTAACCC-CGAACCT-TC
*
187 TAAAATTCCATTTTTAACCCCGAACCTTTC
1 AAAAATTCCA-TTTTAACCCCGAACC-TTC
217 AAAAATTACCATTTT
1 AAAAATT-CCATTTT
232 GTTCCCGAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
27 3 0.05
28 16 0.26
29 16 0.26
30 22 0.36
31 4 0.07
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCCCGAACCTTC
Found at i:192 original size:57 final size:58
Alignment explanation
Indices: 93--231 Score: 212
Period size: 58 Copynumber: 2.4 Consensus size: 58
83 TTCTGAACCT
*
93 GAACTTTCC-AAAATTACCATTTTTACCTCGAATGTCTAAAAATTCCA-TTTTAACCCC
1 GAACCTTCCAAAAATTACCA-TTTTACCTCGAATGTCTAAAAATTCCATTTTTAACCCC
*
150 TAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCT-AAAATTCCATTTTTAACCCC
1 GAACCTTCCAAAAATTACCATTTTA-CCTCGAATGTCTAAAAATTCCATTTTTAACCCC
*
208 GAACCTTTCAAAAATTACCATTTT
1 GAACCTTCCAAAAATTACCATTTT
232 GTTCCCGAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
57 21 0.28
58 54 0.72
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
GAACCTTCCAAAAATTACCATTTTACCTCGAATGTCTAAAAATTCCATTTTTAACCCC
Found at i:4949 original size:6 final size:6
Alignment explanation
Indices: 4933--5036 Score: 75
Period size: 6 Copynumber: 16.3 Consensus size: 6
4923 TTCAATGAAT
*
4933 AAAGAAA AAAGAA AAAGAAGA AGAAGAA AATGAA AAAGAA AAAGAA AAAGAAA
1 AAAG-AA AAAGAA AAAG-A-A A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-AA
* * * * **
4986 AAAGAGGA AAACAA AAAGAA AAACAA AAA-TA GAAGAA ATGGAA AAAGAA
1 AAAGA--A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
5035 AA
1 AA
5037 GGAGAGGTCG
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
5 3 0.04
6 50 0.65
7 13 0.17
8 8 0.10
9 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:4967 original size:21 final size:19
Alignment explanation
Indices: 4933--5036 Score: 84
Period size: 21 Copynumber: 5.1 Consensus size: 19
4923 TTCAATGAAT
4933 AAAGAAAAAAGAAAAAGAAGA
1 AAAG-AAAAAGAAAAAGAA-A
*
4954 AGAAGAAAATGAAAAAG-AA
1 A-AAGAAAAAGAAAAAGAAA
*
4973 AAAGAAAAAGAAAAAAGAGGA
1 AAAGAAAAAG-AAAAAGA-AA
* *
4994 AAACAAAAAGAAAAACAAA
1 AAAGAAAAAGAAAAAGAAA
5013 AATAGAAGAAATGGAAAAAGAAA
1 AA-AGAA-AAA--GAAAAAGAAA
5036 A
1 A
5037 GGAGAGGTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.12
19 11 0.16
20 10 0.15
21 25 0.37
22 3 0.04
23 10 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAGAAA
Found at i:4975 original size:27 final size:25
Alignment explanation
Indices: 4933--5036 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 25
4923 TTCAATGAAT
*
4933 AAAGAAAAAAGAAAAAGAAGAAGAAGA
1 AAAG-AAAAAGAAAAAGAAAAAGAA-A
4960 AAATGAAAAAGAAAAAGAAAAAGAAA
1 AAA-GAAAAAGAAAAAGAAAAAGAAA
* *
4986 AAAGAGGAAAACAAAAAGAAAAACAAA
1 AAAGA--AAAAGAAAAAGAAAAAGAAA
5013 AATAGAAGAAATGGAAAAAGAAAA
1 AA-AGAA-AAA--GAAAAAGAAAA
5037 GGAGAGGTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.03
26 5 0.08
27 45 0.68
28 4 0.06
29 10 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAAAAGAAA
Found at i:4979 original size:33 final size:33
Alignment explanation
Indices: 4926--5022 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
4916 ACTCGGATTC
4926 AATGAATAAAGAAAAAAGAAAAAGAAGAAGAAGAA
1 AATGAA-AAAG-AAAAAGAAAAAGAAGAAGAAGAA
* *
4961 AATGAAAAAGAAAAAGAAAAAGAAAAAAGAGGAA
1 AATGAAAAAGAAAAAGAAAAAG-AAGAAGAAGAA
* * *
4995 AA-CAAAAAGAAAAACAAAAA-TAGAAGAA
1 AATGAAAAAGAAAAAGAAAAAGAAGAAGAA
5023 ATGGAAAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 5 0.09
33 28 0.52
34 15 0.28
35 6 0.11
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (33 bp):
AATGAAAAAGAAAAAGAAAAAGAAGAAGAAGAA
Done.