Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002367.1 Kokia drynarioides strain JFW-HI SEQ_114444, 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: 9922
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:6968 original size:98 final size:96
Alignment explanation
Indices: 6866--7167 Score: 270
Period size: 97 Copynumber: 3.1 Consensus size: 96
6856 GGAAAGATTA
* ** *
6866 AAGCCACAATGACAGATTTAACACTCTAAAA-CCAAAGAGGAAAAGATTAAAG-C-T-ATAACAG
1 AAGCCATAATGACAGACCTAACAC-CCAAAATCCAAA-AGGAAAAGATTAAAGTCGTAATAAC-G
6927 TAGATCTTACACCTTAAAACTGAAGAGAGATAGGTTG
63 --GATCTTACACCTTAAAACTGAAGAGAGA-AGGTTG
* * * * *
6964 AAGCCGTAATGACAGACCTAACACCCAAAATTCGAAAAGGGAAAGATTTAAGTCGTAATGACGGA
1 AAGCCATAATGACAGACCTAACACCCAAAA-TCCAAAAGGAAAAGATTAAAGTCGTAATAACGGA
* *
7029 TCTTACACTTTAAAACTGAAGAGTGAAGGTTG
65 TCTTACACCTTAAAACTGAAGAGAGAAGGTTG
* * * * * * * * ** *
7061 AAGTCATAATGATATACCTAACACCCTAAAATCGAAAAGGGATAGATTGAAGTTGTAATGGCGAA
1 AAGCCATAATGACAGACCTAACACCC-AAAATCCAAAAGGAAAAGATTAAAGTCGTAATAACGGA
* * *
7126 TCTAACACCTTAAAATTGAAGAGAGAAAGATTG
65 TCTTACACCTTAAAACTGAAGAGAG-AAGGTTG
7159 AAGCCATAA
1 AAGCCATAA
7168 CGGAGGATCT
Statistics
Matches: 171, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
97 83 0.49
98 77 0.45
99 5 0.03
100 2 0.01
101 4 0.02
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (96 bp):
AAGCCATAATGACAGACCTAACACCCAAAATCCAAAAGGAAAAGATTAAAGTCGTAATAACGGAT
CTTACACCTTAAAACTGAAGAGAGAAGGTTG
Found at i:6988 original size:49 final size:49
Alignment explanation
Indices: 6935--7553 Score: 346
Period size: 49 Copynumber: 12.7 Consensus size: 49
6925 AGTAGATCTT
* * * *
6935 ACACCTTAAAACTGAAGAGAGATAGGTTGAAGCCGTAATGACAGACCTA
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * * * *
6984 ACACC-CAAAATTCGAAAAGGGAAAGATTTAAGTCGTAATGACGGATCTT
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * ***
7033 ACACTTTAAAACTGAAGAGTGA-AGGTTGAAGTCATAATGATATACCTA
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * * *
7081 ACACCCTAAAA-TCGAAAAGGGATAGATTGAAGTTGTAATGGCGAATCTA
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * * * * *
7130 ACACCTTAAAATTGAAGAGAGAAAGATTGAAGCCATAACGGA-GGATCTT
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAA-TGACGGACCTA
* * * * *
7179 ACACCTTAAAATTGAAGAGGGATAGGTTGAAGCCGCAA-CAGCGGACCTA
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGA-CGGACCTA
* * ** * ** * * * *
7228 ACGCC-AAAAACCAAAGAGGGAAAGATTGAAGTCACAACGACGAATCTT
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * **
7276 ACACCTTAAAA-TCAAAGAGGGATAGGTTCAAGTCGTAACGGTGGACCTA
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* *
7325 ACATCC-TAAAA-TAGAAGAGGGATAGGTTGAAGTCGTAA-GATGGACCTA
1 ACA-CCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
** * * * * * *
7373 ACACCTTAAAACCAAAGAGGGATAGATTTAAGCCGTAACGATGGATCTT
1 ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* ** * * * *
7422 ACACCTTAAAA-TCGAAGAGGGAAAGATTGAAGTCACAACGATGGATCTT
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * * * *
7471 ACACCTTAAAA-TCGAAGAGGGATAGGTTGAAGTTGGAATGGCTGACCTA
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
* * *
7520 ATACCATAAAA-TCGAAGAGGGATAGAATGAAGTC
1 ACACCTTAAAACT-GAAGAGGGATAGATTGAAGTC
7554 ACGACGGTGG
Statistics
Matches: 439, Mismatches: 115, Indels: 32
0.75 0.20 0.05
Matches are distributed among these distances:
47 4 0.01
48 110 0.25
49 316 0.72
50 9 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (49 bp):
ACACCTTAAAACTGAAGAGGGATAGATTGAAGTCGTAATGACGGACCTA
Found at i:7101 original size:97 final size:97
Alignment explanation
Indices: 6929--7167 Score: 318
Period size: 97 Copynumber: 2.4 Consensus size: 97
6919 TATAACAGTA
*
6929 GATCTTACACCTTAAAACTGAAGAGAGATAGGTTGAAGCCGTAATGACAGACCTAACACCCAAAA
1 GATCTTACACCTTAAAACTGAAGAGAGA-AGGTTGAAGCCATAATGACAGACCTAACACCCAAAA
*
6994 TTCGAAAAGGGAAAGATTTAAGTCGTAATGACG
65 TTCGAAAAGGGAAAGATTGAAGTCGTAATGACG
* * * * *
7027 GATCTTACACTTTAAAACTGAAGAGTGAAGGTTGAAGTCATAATGATATACCTAACACCCTAAAA
1 GATCTTACACCTTAAAACTGAAGAGAGAAGGTTGAAGCCATAATGACAGACCTAACACCC-AAAA
* * *
7092 -TCGAAAAGGGATAGATTGAAGTTGTAATGGCG
65 TTCGAAAAGGGAAAGATTGAAGTCGTAATGACG
* * * *
7124 AATCTAACACCTTAAAATTGAAGAGAGAAAGATTGAAGCCATAA
1 GATCTTACACCTTAAAACTGAAGAGAG-AAGGTTGAAGCCATAA
7168 CGGAGGATCT
Statistics
Matches: 122, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
97 78 0.64
98 44 0.36
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (97 bp):
GATCTTACACCTTAAAACTGAAGAGAGAAGGTTGAAGCCATAATGACAGACCTAACACCCAAAAT
TCGAAAAGGGAAAGATTGAAGTCGTAATGACG
Found at i:7281 original size:97 final size:95
Alignment explanation
Indices: 7144--7590 Score: 396
Period size: 97 Copynumber: 4.6 Consensus size: 95
7134 CTTAAAATTG
* * * **
7144 AAGAGAGAAAGATTGAAGCCATAACGGA-GGATCTTACACCTTAAAATTGAAGAGGGATAGGTTG
1 AAGAGGGAAAGATTGAAGTCACAAC-GATGGATCTTACACCTTAAAATCAAAGAGGGATAGGTTG
* * * *
7208 AAGCCGCAACAGCGGACCTAACGCCAAAAACCA
65 AAGCCGTAAC-GTGGACCTAACACCTAAAA-CA
* * *
7241 AAGAGGGAAAGATTGAAGTCACAACGACGAATCTTACACCTTAAAATCAAAGAGGGATAGGTTCA
1 AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCAAAGAGGGATAGGTTGA
* *
7306 AGTCGTAACGGTGGACCTAACATCCTAAAATA
66 AGCCGTAAC-GTGGACCTAACA-CCTAAAACA
* * ** * * * * *
7338 GAAGAGGGATAGGTTGAAGTCGTAA-GATGGACCTAACACCTTAAAACCAAAGAGGGATAGATTT
1 -AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCAAAGAGGGATAGGTTG
* * *
7402 AAGCCGTAACGATGGATCTTACACCTTAAAATCG
65 AAGCCGTAACG-TGGACCTAACACC-TAAAA-CA
*
7436 AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGA
1 AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCAAAGAGGGATAGGTTGA
** * * * *
7501 AGTTGGAATG-GCTGACCTAATACCATAAAATCG
66 AGCCGTAACGTG--GACCTAACACC-TAAAA-CA
* * * * * * *
7534 AAGAGGGATAGAATGAAGTCACGACGGTGGATCTAACACCTTGAAACCAAAGAGGGA
1 AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCAAAGAGGGA
7591 ACAAATTGAA
Statistics
Matches: 285, Mismatches: 56, Indels: 17
0.80 0.16 0.05
Matches are distributed among these distances:
96 6 0.02
97 148 0.52
98 131 0.46
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (95 bp):
AAGAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCAAAGAGGGATAGGTTGA
AGCCGTAACGTGGACCTAACACCTAAAACA
Found at i:7445 original size:195 final size:194
Alignment explanation
Indices: 6935--7590 Score: 564
Period size: 195 Copynumber: 3.4 Consensus size: 194
6925 AGTAGATCTT
* * * ** * *
6935 ACACCTTAAAACT-GAAGAGAGATAGGTTGAAGCCGTAATGACAGACCTAACACC-CAAAATTCG
1 ACACCATAAAA-TAGAAGAGAGATAGATTGAAGCCGTAACGATGGACCTAACACCTTAAAA--CC
* * * * * *
6998 AAA-AGGGAAAGATTTAAGTCGTAATGACGGATCTTACACTTTAAAACTGAAGAGTG-AAGGTTG
63 AAAGAGGGATAGATTTAAGCCGTAACGACGGATCTTACACCTTAAAAC-GAAGAGGGAAAGATTG
* * * * * * * * *
7061 AAGTCATAATGATATACCTAACACCCTAAAATCGAAA-AGGGATAGATTGAAGTTGTAATGGCGA
127 AAGTCACAACGAGA-ATCTTACACCTTAAAATC-AAAGAGGGATAGGTTGAAGTTGTAATGGTGG
*
7125 ATCTA
190 ACCTA
* * * * * * ***
7130 ACACCTTAAAATTGAAGAGAGAAAGATTGAAGCCATAACGGA-GGATCTTACACCTTAAAATTGA
1 ACACCATAAAATAGAAGAGAGATAGATTGAAGCCGTAAC-GATGGACCTAACACCTTAAAACCAA
* * * * * * * *
7194 AGAGGGATAGGTTGAAGCCGCAAC-AGCGGACCTAACGCC-AAAAACCAAAGAGGGAAAGATTGA
65 AGAGGGATAGATTTAAGCCGTAACGA-CGGATCTTACACCTTAAAA-CGAAGAGGGAAAGATTGA
* * *
7257 AGTCACAACGACGAATCTTACACCTTAAAATCAAAGAGGGATAGGTTCAAGTCGTAACGGTGGAC
128 AGTCACAACGA-GAATCTTACACCTTAAAATCAAAGAGGGATAGGTTGAAGTTGTAATGGTGGAC
7322 CTA
192 CTA
* * *
7325 ACATCC-TAAAATAGAAGAGGGATAGGTTGAAGTCGTAA-GATGGACCTAACACCTTAAAACCAA
1 ACA-CCATAAAATAGAAGAGAGATAGATTGAAGCCGTAACGATGGACCTAACACCTTAAAACCAA
*
7388 AGAGGGATAGATTTAAGCCGTAACGATGGATCTTACACCTTAAAATCGAAGAGGGAAAGATTGAA
65 AGAGGGATAGATTTAAGCCGTAACGACGGATCTTACACCTTAAAA-CGAAGAGGGAAAGATTGAA
* * *
7453 GTCACAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTTGGAATGGCT-GAC
129 GTCACAACGA-GAATCTTACACCTTAAAATCAAAGAGGGATAGGTTGAAGTTGTAATGG-TGGAC
7517 CTA
192 CTA
* * * * * * *
7520 ATACCATAAAATCGAAGAGGGATAGAATGAAGTCACG--ACGGTGGATCTAACACCTTGAAACCA
1 ACACCATAAAATAGAAGAGAGATAGATTGAAG-C-CGTAACGATGGACCTAACACCTTAAAACCA
7583 AAGAGGGA
64 AAGAGGGA
7591 ACAAATTGAA
Statistics
Matches: 369, Mismatches: 74, Indels: 35
0.77 0.15 0.07
Matches are distributed among these distances:
193 2 0.01
194 66 0.18
195 260 0.70
196 39 0.11
197 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (194 bp):
ACACCATAAAATAGAAGAGAGATAGATTGAAGCCGTAACGATGGACCTAACACCTTAAAACCAAA
GAGGGATAGATTTAAGCCGTAACGACGGATCTTACACCTTAAAACGAAGAGGGAAAGATTGAAGT
CACAACGAGAATCTTACACCTTAAAATCAAAGAGGGATAGGTTGAAGTTGTAATGGTGGACCTA
Found at i:7503 original size:146 final size:146
Alignment explanation
Indices: 6935--7503 Score: 542
Period size: 146 Copynumber: 3.9 Consensus size: 146
6925 AGTAGATCTT
** * * * * *
6935 ACACCTTAAAACTGAAGAGAGATAGGTTGAAGCCGTAATGAC-AGACCTAACACC-CAAAATTCG
1 ACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTAACGACGA-ATCTAACACCTTAAAA-TCG
* * * * * * *
6998 AAAAGGGAAAGATTTAAGTCGTAATGACGGATCTTACACTTTAAAA-CTGAAGAGTGA-AGGTTG
64 AAGAGGGAAAGATTGAAGTCATAACGATGGATCTTACACCTTAAAATC-GAAGAGGGATAGGTTG
* **
7061 AAGTCATAATGATATACCTA
128 AAGTCGTAA-GATGGACCTA
* * ** * * *
7081 ACACCCTAAAATCGAAA-AGGGATAGATTGAAGTTGTAATGGCGAATCTAACACCTTAAAATTGA
1 ACACCTTAAAA-CCAAAGAGGGATAGATTGAAGCCGTAACGACGAATCTAACACCTTAAAATCGA
* * *
7145 AGAGAGAAAGATTGAAGCCATAACGGA-GGATCTTACACCTTAAAATTGAAGAGGGATAGGTTGA
65 AGAGGGAAAGATTGAAGTCATAAC-GATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGA
* * * *
7209 AGCCGCAACAGCGGACCTA
129 AGTCGTAAGA-TGGACCTA
* * * * ** * *
7228 ACGCC-AAAAACCAAAGAGGGAAAGATTGAAGTCACAACGACGAATCTTACACCTTAAAATCAAA
1 ACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTAACGACGAATCTAACACCTTAAAATCGAA
* * * * * * * *
7292 GAGGGATAGGTTCAAGTCGTAACGGTGGACCTAACATCC-TAAAATAGAAGAGGGATAGGTTGAA
66 GAGGGAAAGATTGAAGTCATAACGATGGATCTTACA-CCTTAAAATCGAAGAGGGATAGGTTGAA
7356 GTCGTAAGATGGACCTA
130 GTCGTAAGATGGACCTA
* * * *
7373 ACACCTTAAAACCAAAGAGGGATAGATTTAAGCCGTAACGATGGATCTTACACCTTAAAATCGAA
1 ACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTAACGACGAATCTAACACCTTAAAATCGAA
*
7438 GAGGGAAAGATTGAAGTCACAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
66 GAGGGAAAGATTGAAGTCATAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
7503 T
131 T
7504 TGGAATGGCT
Statistics
Matches: 339, Mismatches: 72, Indels: 24
0.78 0.17 0.06
Matches are distributed among these distances:
145 18 0.05
146 288 0.85
147 33 0.10
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (146 bp):
ACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTAACGACGAATCTAACACCTTAAAATCGAA
GAGGGAAAGATTGAAGTCATAACGATGGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
TCGTAAGATGGACCTA
Done.