Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001852.1 Kokia drynarioides strain JFW-HI SEQ_113608, 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: 14085
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Found at i:294 original size:86 final size:86
Alignment explanation
Indices: 76--457 Score: 339
Period size: 86 Copynumber: 4.5 Consensus size: 86
66 GCATCGACTT
* * * * ** * *
76 CTTGGTGTCTTGGATGTGCGGGAGAATCGAACACCATCGACAACTTAGGTCGATGGTGGTGCGAG
1 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACTTAGACCGATGGTCGTGCGGG
** **
141 ACCAT-TTGAAGCACGGGCAC
66 ACCATCAGGAAGCATTGGCAC
** * * * * *
161 CTACGTGCC------GTGCGGGAGCATCGGACTCCATTGGCAACTTAGCCCGATAGTGGTGCGGG
1 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACTTAGACCGATGGTCGTGCGGG
* *
220 ACCATCAAGAAGCATTAGCAC
66 ACCATCAGGAAGCATTGGCAC
* * * * * * *
241 TTTGGTGCCTTGGATTTGGGGGTGCATCGGACACCATCGGCAACATAGACCGATGGTTGTGCTGG
1 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACTTAGACCGATGGTCGTGCGGG
* *
306 ACCACCAGGAAGCATTGGTAC
66 ACCATCAGGAAGCATTGGCAC
** *
327 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGAAAACTTA-AGCCGATGGTCGTGTGG
1 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACTTAGA-CCGATGGTCGTGCGG
*
391 GACCATCAGGAAGCATCGGCAC
65 GACCATCAGGAAGCATTGGCAC
*** * * *
413 CTTGGTGCCTTGGATGTGTAAGAGCATCGGAAACTATCAGCAACT
1 CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACT
458 GATAGCATTA
Statistics
Matches: 234, Mismatches: 55, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
79 46 0.20
80 16 0.07
85 7 0.03
86 165 0.71
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.22
Consensus pattern (86 bp):
CTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGGCAACTTAGACCGATGGTCGTGCGGG
ACCATCAGGAAGCATTGGCAC
Found at i:12115 original size:86 final size:85
Alignment explanation
Indices: 12025--12485 Score: 313
Period size: 86 Copynumber: 5.4 Consensus size: 85
12015 TAACTTAAAT
* *
12025 CGATAGTGGTGCTGGACCATCGAGAAGCATGGGCACTTTGGTGCCTTAGATGTGCGGGAGCATCG
1 CGATGGTGGTGCTGGACCATCGAGAAGCATGGGCACCTTGGTGCCTT-GATGTGCGGGAGCATCG
*
12090 GACACCATCAACAACTTAGGC
65 GACACCATCCACAACTTAGGC
* * ** * * * * * *
12111 CGATAGTGGCGCAAGACCATCGGGAAGCATGGGTACCTTGGTGCCTTGAATATGCGAGATCATCT
1 CGATGGTGGTGCTGGACCATCGAGAAGCATGGGCACCTTGGTGCCTTG-ATGTGCGGGAGCATCG
* ** *
12176 TACACCATCCGTAACTTAGGT
65 GACACCATCCACAACTTAGGC
* * * *
12197 CGATGGTGGTAC-GAGACCATCGAGAAGAATGGGCAGCTTGGTGCCTTTCATGTGCGGGAGCATC
1 CGATGGTGGTGCTG-GACCATCGAGAAGCATGGGCACCTTGGTGCC-TTGATGTGCGGGAGCATC
* ** *
12261 GGACACTATCCGTAACTTA-AC
64 GGACACCATCCACAACTTAGGC
** * * *
12282 CAGATGGTGGTG-TGAGACCATCGAGAAGCATCCGTACCTTGGTACCTTGGATGTGTGGGAGCAT
1 C-GATGGTGGTGCTG-GACCATCGAGAAGCATGGGCACCTTGGTGCCTT-GATGTGCGGGAGCAT
** * *
12346 CAAACACCAT-TACTAACATAGGC
63 CGGACACCATCCAC-AACTTAGGC
* * * **** * * * *
12369 CGATGGTGGTACGGGACCATCGAAAAGCACT-AATTCCTTGGTGCCTTGTATTTACGAGAGTATC
1 CGATGGTGGTGCTGGACCATCGAGAAGCA-TGGGCACCTTGGTGCCTTG-ATGTGCGGGAGCATC
** * * *
12433 AAACACCATCAACAACTTTGGT
64 GGACACCATCCACAACTTAGGC
* *
12455 CGATGGTGGTACGGGACCATC-AGCAAGCATG
1 CGATGGTGGTGCTGGACCATCGAG-AAGCATG
12486 AAAACATTCG
Statistics
Matches: 295, Mismatches: 66, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
85 7 0.02
86 280 0.95
87 8 0.03
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (85 bp):
CGATGGTGGTGCTGGACCATCGAGAAGCATGGGCACCTTGGTGCCTTGATGTGCGGGAGCATCGG
ACACCATCCACAACTTAGGC
Found at i:12302 original size:172 final size:172
Alignment explanation
Indices: 12039--12391 Score: 415
Period size: 172 Copynumber: 2.1 Consensus size: 172
12029 AGTGGTGCTG
* *
12039 GACCATCGAGAAGCATGGGCACTTTGGTGCCTTAGATGTGCGGGAGCATCGGACACCATCAACAA
1 GACCATCGAGAAGAATGGGCACTTTGGTGCCTTACATGTGCGGGAGCATCGGACACCATCAACAA
* * ** *
12104 CTTAGGCCGATAGTGGCGCAAGACCATCGGGAAGCATGGGTACCTTGGTGCCTTGAATATGCGAG
66 CTTAGACCGATAGTGGCGCAAGACCATCGAGAAGCATCCGTACCTTGGTACCTTGAATATGCGAG
* ** * * *
12169 ATCATCTTACACCA-TCCGTAACTTAGGTCGATGGTGGTACGA
131 AGCATCAAACACCATTAC-TAACATAGGCCGATGGTGGTACGA
* * ***
12211 GACCATCGAGAAGAATGGGCAGC-TTGGTGCCTTTCATGTGCGGGAGCATCGGACACTATCCGTA
1 GACCATCGAGAAGAATGGGCA-CTTTGGTGCCTTACATGTGCGGGAGCATCGGACACCATCAACA
* * ** * * *
12275 ACTTA-ACCAGATGGTGGTGTGAGACCATCGAGAAGCATCCGTACCTTGGTACCTTGGATGTGTG
65 ACTTAGACC-GATAGTGGCGCAAGACCATCGAGAAGCATCCGTACCTTGGTACCTTGAATATGCG
* *
12339 GGAGCATCAAACACCATTACTAACATAGGCCGATGGTGGTACGG
129 AGAGCATCAAACACCATTACTAACATAGGCCGATGGTGGTACGA
12383 GACCATCGA
1 GACCATCGA
12392 AAAGCACTAA
Statistics
Matches: 151, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
171 2 0.01
172 146 0.97
173 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (172 bp):
GACCATCGAGAAGAATGGGCACTTTGGTGCCTTACATGTGCGGGAGCATCGGACACCATCAACAA
CTTAGACCGATAGTGGCGCAAGACCATCGAGAAGCATCCGTACCTTGGTACCTTGAATATGCGAG
AGCATCAAACACCATTACTAACATAGGCCGATGGTGGTACGA
Found at i:12994 original size:43 final size:43
Alignment explanation
Indices: 12870--12996 Score: 116
Period size: 43 Copynumber: 3.0 Consensus size: 43
12860 CATTACCGAA
* * * *
12870 ACCTTGGTGCCTTGAATTTAC-GAGAGCATCAGAA-AGTATCGAC
1 ACCTTGGTGCCTTGGATCTGCTG-GAGCATC-GAACAGCATCGAC
* * *
12913 ACTTTGGTGCCTTGGATCTGCTGGAGCATTGGACAGCATCGAC
1 ACCTTGGTGCCTTGGATCTGCTGGAGCATCGAACAGCATCGAC
* * *
12956 ACCTTGGTGCCTTGGATGTGC-GGAATCATCGAATAGCATCG
1 ACCTTGGTGCCTTGGATCTGCTGG-AGCATCGAACAGCATCG
12997 GTAAATAGGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 4 0.06
43 63 0.93
44 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (43 bp):
ACCTTGGTGCCTTGGATCTGCTGGAGCATCGAACAGCATCGAC
Found at i:13054 original size:82 final size:84
Alignment explanation
Indices: 12955--13162 Score: 228
Period size: 82 Copynumber: 2.5 Consensus size: 84
12945 ACAGCATCGA
* * * * *
12955 CACCTTGGTGCCTTGGATGTGCGGAATCATC-GAATAGCATCGGTAA-ATAGGTCGATGGTGGTA
1 CACCTTGGTGCCTTGGATGTGCGGAAGCATCTG-ACACCATCGGTAACATAGGCCGATGGTGATA
13018 CAAGACCATCTGA-AAGCAT-
65 CAAGACCATC-GAGAAGCATG
* * *
13037 CACTTTGGTGCCTTGGATGTGCGGGAGCATCTGACACCATCGGTAACATAGGCCGATGGTGATGC
1 CACCTTGGTGCCTTGGATGTGCGGAAGCATCTGACACCATCGGTAACATAGGCCGATGGTGATAC
**
13102 GGGACCATCGAGAAGCATGGG
66 AAGACCATCGAGAAGCAT--G
* *
13123 CACCTTGGTGCCTTGGATGTGCAGG-AGCTTCGGACACCAT
1 CACCTTGGTGCCTTGGATGTGC-GGAAGCATCTGACACCAT
13163 TCGCAACTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
82 41 0.39
83 29 0.27
86 34 0.32
87 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (84 bp):
CACCTTGGTGCCTTGGATGTGCGGAAGCATCTGACACCATCGGTAACATAGGCCGATGGTGATAC
AAGACCATCGAGAAGCATG
Found at i:13159 original size:86 final size:83
Alignment explanation
Indices: 12955--13283 Score: 283
Period size: 86 Copynumber: 3.9 Consensus size: 83
12945 ACAGCATCGA
* * * * * *
12955 CACCTTGGTGCCTTGGATGTGCGGAATCATCGAATAGCATCGGTAA-ATAGGTCGATGGTGGTAC
1 CACCTTGGTGCCTTGGATGTGCGG-AGCATCGGACACCATCGGTAACATAGGCCGATGGTGGTGC
*
13019 AAGACCATCTGA-AAGCAT-
65 GAGACCATC-GAGAAGCATG
* * *
13037 CACTTTGGTGCCTTGGATGTGCGGGAGCATCTGACACCATCGGTAACATAGGCCGATGGTGATGC
1 CACCTTGGTGCCTTGGATGTGC-GGAGCATCGGACACCATCGGTAACATAGGCCGATGGTGGTGC
*
13102 GGGACCATCGAGAAGCATGGG
65 GAGACCATCGAGAAGCAT--G
* * *
13123 CACCTTGGTGCCTTGGATGTGCAGGAGCTTCGGACACCATTC-GCAACTTA-GCTCGATGGTGGT
1 CACCTTGGTGCCTTGGATGTGC-GGAGCATCGGACACCA-TCGGTAACATAGGC-CGATGGTGGT
* * *
13186 GTGGGACCATC-AGTAAGTATTG
63 GCGAGACCATCGAG-AAGCA-TG
* * * * * * * *
13208 ACACCATGGTGACTTAGATGTGCGGATGCATCAGACACTATTGGTAACATATGCCAATGGTGGTG
1 -CACCTTGGTGCCTTGGATGTGCGGA-GCATCGGACACCATCGGTAACATAGGCCGATGGTGGTG
13273 CGAGACCATCG
64 CGAGACCATCG
13284 GTAAGTACCG
Statistics
Matches: 200, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
82 39 0.19
83 30 0.15
85 9 0.05
86 117 0.58
87 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (83 bp):
CACCTTGGTGCCTTGGATGTGCGGAGCATCGGACACCATCGGTAACATAGGCCGATGGTGGTGCG
AGACCATCGAGAAGCATG
Done.