Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013203.1 Kokia drynarioides strain JFW-HI SEQ_128222, 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: 26869
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:15080 original size:39 final size:39
Alignment explanation
Indices: 15037--15124 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
15027 CATCATGTGT
* *
15037 TGTGGATTCTCTGAAGCTTGTGTGAGTAGAATTGAATGA
1 TGTGGATTCTCTGAAGCTCGTGTGAGCAGAATTGAATGA
* **
15076 TGTGGATTCTTTGAAGCTCGTGTGAGCATCATTGAATGA
1 TGTGGATTCTCTGAAGCTCGTGTGAGCAGAATTGAATGA
*
15115 TGCGGATTCT
1 TGTGGATTCT
15125 TTAAAGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (39 bp):
TGTGGATTCTCTGAAGCTCGTGTGAGCAGAATTGAATGA
Found at i:15337 original size:17 final size:17
Alignment explanation
Indices: 15313--15369 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
15303 TTGGAAATCG
15313 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
15330 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
15347 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
15364 AATTTA
1 AATTTA
15370 GAAAAGTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:16317 original size:21 final size:21
Alignment explanation
Indices: 16276--16317 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16266 AAACCGTTCA
* *
16276 GATCTAGGCTAGATCTGGTTT
1 GATCTAGCCTAGATCTCGTTT
16297 GATCTAGACCTAGATC-CGTTT
1 GATCTAG-CCTAGATCTCGTTT
16318 TTTAAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
GATCTAGCCTAGATCTCGTTT
Found at i:17190 original size:30 final size:29
Alignment explanation
Indices: 17144--17526 Score: 275
Period size: 30 Copynumber: 12.9 Consensus size: 29
17134 ACTATTTTAC
17144 CCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
17173 CCCCAAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
* * * *
17202 CCCTCAAACTTCAAAAAATCTCATTTTTTTA
1 CCC-CGAACTTCCAAAAATCCCA-TTTTTGA
* * *
17233 TCCCGAAACTTCCAAAAATTACCA-TGTT-A
1 CCCCG-AACTTCCAAAAA-TCCCATTTTTGA
17262 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATCCCATTTTTGA
17292 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATCCCATTTTTGA
* *
17322 CCCCGAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
* *
17351 TCCTCGAACTTCCAAAAATCCCAATTTTGA
1 -CCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
17381 CCTCGAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
* *
17410 CCCCCAAATTTCCAAAAATCCCATTTTCTGA
1 -CCCCGAACTTCCAAAAATCCCATTTT-TGA
** * *
17441 TTCTGAACCTTTCTAAAAATCACCA-TTTT-A
1 CCCCGAA-C-TTCCAAAAATC-CCATTTTTGA
17471 CCCTCGAACTTCC-AAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATCCCATTTTTGA
* * *
17500 CTCCGAACCTTCCAAAACTACCATTTT
1 CCCCGAA-CTTCCAAAAATCCCATTTT
17527 ACCCCCCCGT
Statistics
Matches: 284, Mismatches: 40, Indels: 59
0.74 0.10 0.15
Matches are distributed among these distances:
27 3 0.01
28 29 0.10
29 85 0.30
30 117 0.41
31 31 0.11
32 16 0.06
33 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:17212 original size:59 final size:59
Alignment explanation
Indices: 17119--17294 Score: 246
Period size: 59 Copynumber: 3.0 Consensus size: 59
17109 AAGGTCCTTG
* *
17119 AACCTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
17178 AACCTTCTAAAAATTACCATTTTACCCTCAAACTTCAAAAAATCTCATTTTTTTATCCCGA
1 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGA-CCCCA
* *
17239 AA-CTTCCAAAAATTACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
1 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
17295 TCGAACTTCC
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 3 0.03
59 48 0.47
60 45 0.44
61 6 0.06
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:17329 original size:59 final size:59
Alignment explanation
Indices: 17144--17530 Score: 307
Period size: 59 Copynumber: 6.5 Consensus size: 59
17134 ACTATTTTAC
* * *
17144 CCCCGAA-CTTCCAAAAATCCCATTTTTGACCC-CAAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAATCCCATTTTT-ACCCTCGAA-CTTCCAAAAA-TCCCATTTTTGA
* * * * * *
17202 CCCTC-AAACTTCAAAAAATCTCATTTTTTTATCC-CGAAACTTCCAAAAATTACCA-TGTT-A
1 CCC-CGAACCTTCCAAAAATCCCA--TTTTTACCCTCG-AACTTCCAAAAA-TCCCATTTTTGA
17262 CCCTCGAA-CTTCCAAAAATCCCATTTTTGACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCC-CGAACCTTCCAAAAATCCCATTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * *
17322 CCCCGAACCTTCTAAAAATTACCA-TTTTATCCTCGAACTTCCAAAAATCCCAATTTTGA
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * * *
17381 CCTCGAACCTTCTAAAAATTACCA-TTTTACCCCCAAATTTCCAAAAATCCCATTTTCTGA
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTT-TGA
** * *
17441 TTCTGAACCTTTCTAAAAATCACCA-TTTTACCCTCGAACTTCC-AAAATCCCATTTTTGA
1 CCCCGAACC-TTCCAAAAATC-CCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
17500 CTCCGAACCTTCCAAAACTACCA-TTTTACCC
1 CCCCGAACCTTCCAAAAATCCCATTTTTACCC
17531 CCCCGTGCAT
Statistics
Matches: 280, Mismatches: 34, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
57 11 0.04
58 22 0.08
59 125 0.45
60 82 0.29
61 40 0.14
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:17343 original size:89 final size:87
Alignment explanation
Indices: 17144--17530 Score: 335
Period size: 89 Copynumber: 4.4 Consensus size: 87
17134 ACTATTTTAC
* * * *
17144 CCCCG-AACTTCCAAAAA-TCCCATTTTTGACCC-CAAACCTTCTAAAAATTACCATTTTACCCT
1 CCCCGAAACTTCCAAAAATTACCA-TTTT-ACCCTCGAA-CTTCCAAAAA-TCCCATTTTACCCT
* * * *
17206 CAAACTTCAAAAAATCTCATTTTTTTA
62 CGAACTTCCAAAAATCCCA-TTTTTGA
* *
17233 TCCCGAAACTTCCAAAAATTACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTCG
1 CCCCGAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTT-ACCCTCG
17298 AACTTCCAAAAATCCCATTTTTGA
64 AACTTCCAAAAATCCCATTTTTGA
* * *
17322 CCCCGAACCTTCTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCAATTTTGA-CCTCG
1 CCCCGAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCC-ATTTT-ACCCTCG
* *
17386 AACCTTCTAAAAATTACCA-TTTT-A
64 AA-CTTCCAAAAA-TCCCATTTTTGA
* * * ** *
17410 CCCCCAAATTTCCAAAAA-TCCCATTTT-CTGATTCTGAACCTTTCTAAAAATCACCATTTTACC
1 CCCCGAAACTTCCAAAAATTACCATTTTAC--CCTC-GAA-C-TTCCAAAAATC-CCATTTTACC
17473 CTCGAACTTCC-AAAATCCCATTTTTGA
60 CTCGAACTTCCAAAAATCCCATTTTTGA
* * *
17500 CTCCGAACCTTCC-AAAACTACCATTTTACCC
1 CCCCGAAACTTCCAAAAATTACCATTTTACCC
17531 CCCCGTGCAT
Statistics
Matches: 244, Mismatches: 35, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
87 8 0.03
88 32 0.13
89 107 0.44
90 68 0.28
91 27 0.11
92 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (87 bp):
CCCCGAAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTACCCTCGAA
CTTCCAAAAATCCCATTTTTGA
Found at i:17490 original size:208 final size:208
Alignment explanation
Indices: 17118--17526 Score: 597
Period size: 208 Copynumber: 2.0 Consensus size: 208
17108 GAAGGTCCTT
* *
17118 GAACCTTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCAAACCT
* * * *
17183 TCTAAAAATTACCATTTTACCCTCAAACTTCAAAAAATCTCATTTTTTTATCCCGAAACTTCCAA
66 TCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTCTGATCCCGAAACTTCCAA
* *
17248 AAATTACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTCGAA-CTTCCAAAAATC
131 AAATCACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACCTTCCAAAAATA
17312 CCATTTTTGACCCC
195 CCATTTTTGACCCC
* * * *
17326 GAACCTTCTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCAATTTTGACCTCGAACCT
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCAAACCT
* * * * * *
17391 TCTAAAAATTACCATTTTACCCCCAAATTTCCAAAAATCCCATTTTCTGATTCTGAACCTTTCTA
66 TCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTCTGATCCCGAAAC-TTCCA
* * *
17456 AAAATCACCATTTTACCCTCGAACTTCC-AAAATCCCATTTTTGACTCCGAACCTTCCAAAACTA
130 AAAATCACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATA
17520 CCATTTT
195 CCATTTT
17527 ACCCCCCCGT
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
207 4 0.02
208 144 0.81
209 30 0.17
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (208 bp):
GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCAAACCT
TCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTCTGATCCCGAAACTTCCAA
AAATCACCATGTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATAC
CATTTTTGACCCC
Found at i:21386 original size:12 final size:12
Alignment explanation
Indices: 21371--21401 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21361 AGACCAGATG
21371 CAAGAGCGTATC
1 CAAGAGCGTATC
21383 CAAGAGCGTATC
1 CAAGAGCGTATC
21395 CAAGAGC
1 CAAGAGC
21402 AAATGAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.13
Consensus pattern (12 bp):
CAAGAGCGTATC
Done.