Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011568.1 Kokia drynarioides strain JFW-HI SEQ_126557, 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: 28387
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:5909 original size:35 final size:36
Alignment explanation
Indices: 5868--5962 Score: 131
Period size: 35 Copynumber: 2.6 Consensus size: 36
5858 CGTTTGTTTA
*
5868 ATGTTCACGAACATGTTCATTTAAC-T-TAATCGAAC
1 ATGTTCACGAACATGTTCA-TGAACATATAATCGAAC
*
5903 ATGTTCACGAACATGTTCATGAACATATAATTGAAC
1 ATGTTCACGAACATGTTCATGAACATATAATCGAAC
*
5939 ATGTTCACGAACAATGTTAATGAA
1 ATGTTCACGAAC-ATGTTCATGAA
5963 TACATACACA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
34 4 0.07
35 20 0.37
36 20 0.37
37 10 0.19
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (36 bp):
ATGTTCACGAACATGTTCATGAACATATAATCGAAC
Found at i:5915 original size:12 final size:12
Alignment explanation
Indices: 5898--5956 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
5888 TTAACTTAAT
5898 CGAACATGTTCA
1 CGAACATGTTCA
5910 CGAACATGTTCA
1 CGAACATGTTCA
* * *
5922 TGAACAT-ATAA
1 CGAACATGTTCA
*
5933 TTGAACATGTTCA
1 -CGAACATGTTCA
5946 CGAACAATGTT
1 CGAAC-ATGTT
5957 AATGAATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 2 0.05
12 29 0.76
13 7 0.18
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:8854 original size:41 final size:41
Alignment explanation
Indices: 8806--8886 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
8796 AAATATCATA
*
8806 ATTTAAATATTTAATTGTACTCTTTTATCAAAATTTGTATG
1 ATTTAAATATTTAATTGTACTATTTTATCAAAATTTGTATG
8847 ATTTAAATATTTAATTGTACTATTTTATCAAAATTTGTAT
1 ATTTAAATATTTAATTGTACTATTTTATCAAAATTTGTAT
8887 TTTATTGACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (41 bp):
ATTTAAATATTTAATTGTACTATTTTATCAAAATTTGTATG
Found at i:8871 original size:21 final size:21
Alignment explanation
Indices: 8806--8871 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
8796 AAATATCATA
8806 ATTTAAATATTTAATTGTACT
1 ATTTAAATATTTAATTGTACT
* **
8827 CTTT---TATCAAAATTTGTA-T
1 ATTTAAATAT-TTAA-TTGTACT
8846 GATTTAAATATTTAATTGTACT
1 -ATTTAAATATTTAATTGTACT
8868 ATTT
1 ATTT
8872 TATCAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 8 0.25
21 12 0.38
22 3 0.09
23 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (21 bp):
ATTTAAATATTTAATTGTACT
Found at i:9167 original size:22 final size:23
Alignment explanation
Indices: 9135--9179 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
9125 ATATATATTA
*
9135 TATTAAAAAAATCAAA-TTAAAT
1 TATTAAAAAAATAAAATTTAAAT
*
9157 TATTAATAAAATAAAATTTAAAT
1 TATTAAAAAAATAAAATTTAAAT
9180 ACTTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TATTAAAAAAATAAAATTTAAAT
Found at i:9193 original size:23 final size:23
Alignment explanation
Indices: 9167--9210 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9157 TATTAATAAA
*
9167 ATAAAATT-TAAATACTTAAATAC
1 ATAAAATTAAAAATA-TTAAATAC
*
9190 ATAATATTAAAAATATTAAAT
1 ATAAAATTAAAAATATTAAAT
9211 GTACTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
ATAAAATTAAAAATATTAAATAC
Found at i:16905 original size:20 final size:21
Alignment explanation
Indices: 16869--16907 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16859 TCAGTAAAAT
*
16869 AAATAATTGTTAAAATATATC
1 AAATAATTGTAAAAATATATC
16890 AAATAATT-TAAAAATATA
1 AAATAATTGTAAAAATATA
16908 AATTCAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATAATTGTAAAAATATATC
Found at i:18989 original size:160 final size:159
Alignment explanation
Indices: 18660--19274 Score: 744
Period size: 160 Copynumber: 3.9 Consensus size: 159
18650 GAAAAATAAC
* * * *
18660 CGAACTTTTCGAGTTTCAACCTCACCGTATAAGTCTTTTTTTTATCTCACAATCGAGTTCGGAGG
1 CGAACTTTTCGGGTTTCAACCTCACC-TATAAGGCTTTCTTTTATCTGACAATCGAGTTCGGAGG
* * * ** *
18725 CTAGGCATGTTGGTTTCTTATCTGAAATTTTCGGGGCAAGTTGTGGGGCAGTTCTAGATAGAATC
65 CTAGGCATGTTGGTTTCTTAGCTGAAATTTTCAGGGCAGGTTG-GGGGTGGTTCTAGATAAAATC
*
18790 CACCTTGCCCAAACTTATATGGGAGAAACAGT
129 CACCTTGCCC-AACTTATATGGGAGAAACAAT
* * *
18822 CGAACTTTTTGGGTTTCAACCTCATCCTATAAGGCTTTCTTTTATCTGACAATCGAGTTTGGAAG
1 CGAACTTTTCGGGTTTCAACCTCA-CCTATAAGGCTTTCTTTTATCTGACAATCGAGTTCGGAGG
* *
18887 CTA-GCGTGTTGGTTTCTTAGCTGAAATTTTCAGGGCAGGTTGGGGGTGGTTCTACATAAAATCC
65 CTAGGCATGTTGGTTTCTTAGCTGAAATTTTCAGGGCAGGTTGGGGGTGGTTCTAGATAAAATCC
18951 ACCTTGCCCAAGCTTATATGGGAGAAACAAT
130 ACCTTGCCCAA-CTTATATGGGAGAAACAAT
* * * * *
18982 AGAACTTTTTGGGTTTCAACCTTACACTATAGGGCTTTCTTTTATCTGACAATCGAGTTTGGAGG
1 CGAACTTTTCGGGTTTCAACCTCAC-CTATAAGGCTTTCTTTTATCTGACAATCGAGTTCGGAGG
* *
19047 CTA-GCATGTTGGCTTCTTAGCTGAAATTTTCAGGGCAGGTTGCGGGTGGTTCTAGATAAAATCC
65 CTAGGCATGTTGGTTTCTTAGCTGAAATTTTCAGGGCAGGTTGGGGGTGGTTCTAGATAAAATCC
* * * * *
19111 ACCCTGCCC--C---GATGAGGAAAAATAAC
130 ACCTTGCCCAACTTATATG-GGAGAAACAAT
* * * *
19137 CCAACTTTTCAGGTTTCAACCTCACCT-TATAGGTCTTTCTTTTATCTGACAATCGAGTTCAGCG
1 CGAACTTTTCGGGTTTCAACCTCACCTATA-AGG-CTTTCTTTTATCTGACAATCGAGTTCGGAG
* * ** *
19201 GCTAGGCATGTTAGTTAT-TTAGCTGAAACTTTCAGGGCATATTGGGGGTGGTTTTAGATAAAAT
64 GCTAGGCATGTTGGTT-TCTTAGCTGAAATTTTCAGGGCAGGTTGGGGGTGGTTCTAGATAAAAT
19265 CCACCTTGCC
128 CCACCTTGCC
19275 TCGACTCAAT
Statistics
Matches: 399, Mismatches: 46, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
153 2 0.01
154 7 0.02
155 59 0.15
156 59 0.15
157 2 0.01
159 3 0.01
160 172 0.43
161 35 0.09
162 58 0.15
163 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (159 bp):
CGAACTTTTCGGGTTTCAACCTCACCTATAAGGCTTTCTTTTATCTGACAATCGAGTTCGGAGGC
TAGGCATGTTGGTTTCTTAGCTGAAATTTTCAGGGCAGGTTGGGGGTGGTTCTAGATAAAATCCA
CCTTGCCCAACTTATATGGGAGAAACAAT
Found at i:24307 original size:29 final size:30
Alignment explanation
Indices: 24275--24335 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
24265 TTCATTAAAA
*
24275 AATAAC-AATTCGAT-TCTTTTTAAAAGGTT
1 AATAACAAATTCGATCT-TTTTTAAAAGATT
*
24304 AATATCAAATTCGATCTTTTTTAAAAGATT
1 AATAACAAATTCGATCTTTTTTAAAAGATT
24334 AA
1 AA
24336 GGGTCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 22 0.79
31 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (30 bp):
AATAACAAATTCGATCTTTTTTAAAAGATT
Found at i:26716 original size:6 final size:6
Alignment explanation
Indices: 26705--26733 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
26695 CCAATTTTAC
26705 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
26734 CATTTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:27665 original size:23 final size:24
Alignment explanation
Indices: 27639--27686 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
27629 GGAGAAGCAT
27639 AAGAA-AAAAA-AAAAAAAAGTTAA
1 AAGAATAAAAATAAAAAAAA-TTAA
*
27662 AAGAATAAAAATGAAAAAAATTAA
1 AAGAATAAAAATAAAAAAAATTAA
27686 A
1 A
27687 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.12
Consensus pattern (24 bp):
AAGAATAAAAATAAAAAAAATTAA
Found at i:27678 original size:24 final size:24
Alignment explanation
Indices: 27650--27706 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
27640 AGAAAAAAAA
27650 AAAAAAAGTTAAAAGAATAAAAATG
1 AAAAAAA-TTAAAAGAATAAAAATG
****
27675 AAAAAAATTAAATTTTTAAAAATG
1 AAAAAAATTAAAAGAATAAAAATG
27699 AAAAAAAT
1 AAAAAAAT
27707 ATTAGGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (24 bp):
AAAAAAATTAAAAGAATAAAAATG
Found at i:28132 original size:16 final size:16
Alignment explanation
Indices: 28111--28141 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28101 TTTAATCTTT
*
28111 TTTATTTTATTATTTA
1 TTTATTTAATTATTTA
28127 TTTATTTAATTATTT
1 TTTATTTAATTATTT
28142 TTCAAAGGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTAATTATTTA
Done.