Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011370.1 Kokia drynarioides strain JFW-HI SEQ_126351, 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: 2469
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:272 original size:17 final size:18
Alignment explanation
Indices: 236--328 Score: 84
Period size: 17 Copynumber: 5.3 Consensus size: 18
226 TAATAATTTT
*
236 TTTAAATTTGAAAATAAA
1 TTTAAATTTCAAAATAAA
* *
254 TTTAAACTT-AAATTAAA
1 TTTAAATTTCAAAATAAA
* *
271 TTTAAA-TTCAAGACAAA
1 TTTAAATTTCAAAATAAA
288 TTTAAATTT-AAAATAAA
1 TTTAAATTTCAAAATAAA
* ** *
305 TTCAAATTTTTAAACAAA
1 TTTAAATTTCAAAATAAA
323 TTTAAA
1 TTTAAA
329 AGGGAGTTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.03
17 38 0.62
18 21 0.34
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
TTTAAATTTCAAAATAAA
Found at i:310 original size:23 final size:23
Alignment explanation
Indices: 266--313 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
256 TAAACTTAAA
* *
266 TTAAATTTAAATTCAAGACAAAT
1 TTAAATTTAAAATAAAGACAAAT
**
289 TTAAATTTAAAATAAATTCAAAT
1 TTAAATTTAAAATAAAGACAAAT
312 TT
1 TT
314 TTAAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATTTAAAATAAAGACAAAT
Found at i:941 original size:204 final size:204
Alignment explanation
Indices: 591--966 Score: 576
Period size: 204 Copynumber: 1.8 Consensus size: 204
581 ACTTGGCCTT
* * * * *
591 CTTCTCAGTATCTCATCGGGGAGCTAACCACTTTATGGCTTCGACTTGCTTCTCCGCGTCTCATC
1 CTTCTCAGTACCTCATCAGGAAGCTAACCACTTTATGGCTTCGACCTGCTTCTCAGCGTCTCATC
* * * *
656 AGGAAGCTGGGGTTCGAAGATTTGCTCATTTTAAGCCTCGTTTGGGTCTTCTGTTCAGCACCTCC
66 AGGAAGCTGGGGTTCAAAGATTTCCTCACTTTAAGCCTCGTTTGGGTCTTCTGTTCAGCACCTCA
721 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACGAA
131 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACGAA
786 TTTGGTTCA
196 TTTGGTTCA
* *
795 CTTCTCAGTACCTCATCAGGAAGCTAA-C-CTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
1 CTTCTCAGTACCTCATCAGGAAGCTAACCACTT-TATGGCTTCGACCTGCTTCTCAGCGTCTCAT
* * * *
858 CAGGAAGCTGGGGTTTAAAGACTTTCCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCGGCACCT
65 CAGGAAGCTGGGGTTCAAAGA-TTTCCTCACTTTAAGCCTCGTTTGGGTCTTCTGTTCAGCACCT
*
923 CATTAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCT
129 CATCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCT
967 CNNNNNNNNN
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
202 3 0.02
203 47 0.31
204 104 0.68
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (204 bp):
CTTCTCAGTACCTCATCAGGAAGCTAACCACTTTATGGCTTCGACCTGCTTCTCAGCGTCTCATC
AGGAAGCTGGGGTTCAAAGATTTCCTCACTTTAAGCCTCGTTTGGGTCTTCTGTTCAGCACCTCA
TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACGAA
TTTGGTTCA
Found at i:1456 original size:204 final size:204
Alignment explanation
Indices: 1106--2202 Score: 925
Period size: 204 Copynumber: 5.5 Consensus size: 204
1096 ACTTGGTCTT
* * * * * * *
1106 CTTCTCAGTATCTCATCGGGGAGCTAACCACTT-TATGGCTTCGACTTGCTTCTCCGCGTCTCAT
1 CTTCTCAGTACCTCATCAGGAAGCTAA-C-CTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCAT
* * ** * *
1170 CGGGAAGCTGGGGTTCGAAGA-TTTGCTCGTTTTAAGCCTCGTTTGGGTCTTCTGTTCAGCACCT
64 CAGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCAGCACCT
*
1234 CCTCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACG
129 CATCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACG
1299 AATTTGGTTCA
194 AATTTGGTTCA
*
1310 CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTACTTCTCAGTGTCTCATCA
1 CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
* * *
1375 GGAAGCTGGGCTTTAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCGGCACCTCA
66 GGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCAGCACCTCA
* * *
1440 TTAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTCCGTATTTCATCCGGAAGACGAA
131 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACGAA
* *
1505 TTTCGTTAA
196 TTTGGTTCA
*
1514 CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCAACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
* * ***
1579 GGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCAGCACCTCA
* * * *
1644 TCAAGAAGATG---AC--CGC-----G--TC-GTTCGCTTC-TCTGTATCTCAT-CAGGAAGGCG
131 TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTC-GTATTTCATCCA-GAAGACG
*
1694 GATTTGGTTCA
194 AATTTGGTTCA
* * *
1705 CTTCTC-GATATCTCATCAGGAAGCTGACCTTCTATTGTTTCGACCTGCTTCTCAGTGTCTCATC
1 CTTCTCAG-TACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
* * * *
1769 AGGAAGCTGGGGTTCAAAGACTTTGCTCGCTTTGAGCGTGGGTTCGATTT-GGTCTTCTTCTCAA
65 AGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGC-----CTCG-TTTGGGTCTTCTTTTCAG
* * * * * * * *
1833 TATCTCATTAGGAAGATG---AC--CGCGTCGTTTGTTTTAATCCACTTC-TCTGTATCTCAT-T
124 CACCTCATCAGGAAGATGATTACATCGC-T-GTTTGTTTCAATTCGCTTCTTC-GTATTTCATCC
*
1891 AGGAAGATGAATTTGG-TCTA
186 A-GAAGACGAATTTGGTTC-A
* * *
1911 CTTCTCCGTATCTCATCAGGAAGCTAA---T-TA---CTTCGACAC-GCTTCTCAGTATCTCATC
1 CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGAC-CTGCTTCTCAGTGTCTCATC
* * * * *
1968 AGGGAGCTGTGGTTCAAAGA-TTTGCTCA-TGTTGAGCATGGGTTTGGTTTGGGTCTTCTTCTCA
65 AGGAAGCTGGGGTTCAAAGACTTTGCTCACT-TTGAGC------CTCGTTTGGGTCTTCTTTTCA
* * ** * * * *
2031 GTATCTCATCAGGAAGATG---ACCGCGTTGTTCGTTTCAATCCGCTTC-TCTGTATCTCA-CCA
123 GCACCTCATCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTC-GTATTTCATCCA
*
2091 GGAATACGAATTTGG-TCTA
187 -GAAGACGAATTTGGTTC-A
* * * * ** * *
2110 CTTCTCCGTATCTCATCAGGAAGTTAACCGTT-TATTGCTCCGATATGCTTCTCGGTGTGTCATC
1 CTTCTCAGTACCTCATCAGGAAGCTAACC-TTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATC
* * *
2174 AGGAAGTTGGGTTTCGAAGAC-TTGCTCAC
65 AGGAAGCTGGGGTTCAAAGACTTTGCTCAC
2203 ATCGTGCGTG
Statistics
Matches: 761, Mismatches: 92, Indels: 77
0.82 0.10 0.08
Matches are distributed among these distances:
190 3 0.00
191 124 0.16
192 2 0.00
194 1 0.00
196 36 0.05
197 4 0.01
198 16 0.02
199 152 0.20
200 2 0.00
201 4 0.01
202 5 0.01
203 49 0.06
204 261 0.34
205 3 0.00
206 98 0.13
207 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (204 bp):
CTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
GGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTTTCAGCACCTCA
TCAGGAAGATGATTACATCGCTGTTTGTTTCAATTCGCTTCTTCGTATTTCATCCAGAAGACGAA
TTTGGTTCA
Found at i:2024 original size:395 final size:393
Alignment explanation
Indices: 1269--2266 Score: 1032
Period size: 395 Copynumber: 2.5 Consensus size: 393
1259 TTTGTTTCAA
* *
1269 TTCGCTTCT-TCGTATTTCATCCA-GAAGACGAATTTGGTTCACTTCTC-AGTACCTCATCAGGA
1 TTCGCTTCTCT-GTATCTCAT-CAGGAAGACGAATTTGGTTCACTTCTCGA-TATCTCATCAGGA
* *
1331 AGCTAACCTTCTATTGCTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGGGCTTTAAAGACT
63 AGCTAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGCTTCAAAGACT
* * *** *
1396 TTGCTCACTTTGAGC----CTCGTTTGGGTCTTCTTTTCGGCACCTCATTAGGAAGATGATTACA
128 TTGCTCACTTTGAGCGTGGTTCGTTT-GGTCTTCTTCTCAATATCTCATTAGGAAGATG---AC-
* * * *
1457 TCGC-TGTTTGTTTCAATTCGCTTCTCCGTATTTCATCCGGAAGACGAATTTCGTTAACTTCTCA
188 -CGCGTGTTTGTTTCAATCCACTTCTCCGTATCTCATCAGGAAGACGAATTTCGTTAACTTCTCA
*
1521 GTACCTCATCAGGAAGCTAACCTTCTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCT
252 GTACCTCATCAGGAAGCTAA-C-TCTA-T-CTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCT
*
1586 GGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCTCAGTGTCTCATCAAGAA
313 GGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCTCAGTATCTCATCAAGAA
1651 GATGACCGC-G-TCG-
378 GATGACCGCTGTTCGT
* *
1664 TTCGCTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTTCACTTCTCGATATCTCATCAGGAAGC
1 TTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCGATATCTCATCAGGAAGC
* * *
1729 TGACCTTCTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGACTTTG
66 TAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGCTTCAAAGACTTTG
*
1794 CTCGCTTTGAGCGTGGGTTCGATTTGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTC
131 CTCACTTTGAGCGT-GGTTCG-TTTGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGT-
* * * * * * *
1859 GTTTGTTTTAATCCACTTCTCTGTATCTCATTAGGAAGATGAATTTGGTCT-ACTTCTCCGTATC
193 GTTTGTTTCAATCCACTTCTCCGTATCTCATCAGGAAGACGAATTTCGT-TAACTTCTCAGTACC
* * *
1923 TCATCAGGAAGCTAA-T-TA-CTTCGACAC-GCTTCTCAGTATCTCATCAGGGAGCTGTGGTTCA
257 TCATCAGGAAGCTAACTCTATCTTCAAC-CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCA
* * * *
1984 AAGA-TTTGCTCA-TGTTGAGCATGGGTTTGGTTTGGGTCTTCTTCTCAGTATCTCATCAGGAAG
321 AAGACTTTGCTCACT-TTGAGC------CTCGTTTAGGTCTTCTTCTCAGTATCTCATCAAGAAG
2047 ATGACCGCGTTGTTCGTT
379 ATGACCGC--TGTTCG-T
* *
2065 TCAATCCGCTTCTCTGTATCTCACCAGGAATACGAATTTGG-TCTACTTCTCCG-TATCTCATCA
1 T---T-CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTC-ACTTCT-CGATATCTCATCA
* * ** * * * * *
2128 GGAAGTTAACCGTT-TATTGCTCCGATATGCTTCTCGGTGTGTCATCAGGAAGTTGGGTTTCGAA
60 GGAAGCTAACC-TTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGCTTCAAA
* * * * *
2192 GAC-TTGCTCACATCGTGCGTGGTCTTGGTTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGA
124 GACTTTGCTCACTTTGAGCGTGG--TTCGTTTGGTCTTCTTCTCAATATCTCATTAGGAAGATGA
2256 CCGCGTTGTTT
187 CCGCG-TGTTT
2267 TATGGGTATC
Statistics
Matches: 510, Mismatches: 57, Indels: 63
0.81 0.09 0.10
Matches are distributed among these distances:
388 1 0.00
389 14 0.03
390 41 0.08
391 1 0.00
393 2 0.00
394 3 0.01
395 168 0.33
396 3 0.01
397 68 0.13
398 2 0.00
399 3 0.01
400 30 0.06
401 4 0.01
403 2 0.00
404 60 0.12
405 104 0.20
406 4 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (393 bp):
TTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCGATATCTCATCAGGAAGC
TAACCTTCTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGCTTCAAAGACTTTG
CTCACTTTGAGCGTGGTTCGTTTGGTCTTCTTCTCAATATCTCATTAGGAAGATGACCGCGTGTT
TGTTTCAATCCACTTCTCCGTATCTCATCAGGAAGACGAATTTCGTTAACTTCTCAGTACCTCAT
CAGGAAGCTAACTCTATCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGAC
TTTGCTCACTTTGAGCCTCGTTTAGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCTGTT
CGT
Done.