Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010322.1 Kokia drynarioides strain JFW-HI SEQ_125186, 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: 30218
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Found at i:13485 original size:49 final size:49
Alignment explanation
Indices: 13422--14279 Score: 516
Period size: 49 Copynumber: 17.6 Consensus size: 49
13412 TTAAGGTGTT
** * *
13422 AGGTTCGCTATTGCGGCCTCAACCTTTCCCTTCATGTTTCTGAGGTACA
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTTTCTGAGGTACA
* * * * *
13471 AGGTTCGCCGTTGCGACTTAAACATTTCCCTTCATATCTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGT-TTCTGAGGTACA
* * ** *
13520 AGATTC-CTCGTTGAGGCTTAAATATTT-TCTATCATGTTTCTGAGGTACA
1 AGGTTCGC-CGTTGCGGCTTAAACCTTTCCCT-TCATGTTTCTGAGGTACA
* * * * * * *
13569 AGGTTGGCCGTTGCGACTTAATCCTTTCCCTCCATAGCTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-GTTTCTGAGGTACA
* * * *
13618 AGATTCGCCGTTGCGGCTTAAATCTTCCCCTTCATGTTTCTGAGGTGCA
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTTTCTGAGGTACA
* * * * * *
13667 AGGTTTGTCGTTGCGACTTAAACCTTTCCC-TCAATAGCTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTC-AT-GTTTCTGAGGTACA
* ** * * *
13716 AGATTCGTTGTTGCGGCTTAAATCTTTCCCTCCATGTTTCTAAGGTACA
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTTTCTGAGGTACA
* * * * **
13765 AGGTTCGCCGTTGTGACTTAAACATTTCCCTT-ATATCTTC-GTTGTAGCA
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGT-TTCTGAGGTA-CA
* *
13814 A-ATTC-CTCGTTGCAGCTTAAATCC-TTCCCTTCATGTTTCTGAGGTACA
1 AGGTTCGC-CGTTGCGGCTTAAA-CCTTTCCCTTCATGTTTCTGAGGTACA
** * * ** * * * *
13862 AGGTTCATCGTTTCGACTTAAACCTTTTTCTCCATATCTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGT-TTCTGAGGTACA
* * * *
13911 AGATTCACCGTTACGGCTTAAATCC-TTCCCTTCATGTTTTTGAGGTACA
1 AGGTTCGCCGTTGCGGCTTAAA-CCTTTCCCTTCATGTTTCTGAGGTACA
* * ** * ** * *
13960 AGGTTCACTGTTATGACTTAAACCTTTCCCTTCATAACTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-GTTTCTGAGGTACA
* * * * *
14009 AGATTCGTCGTTGCGGCTTAAATCTTTCCCTTTATGTTTCTAAGGTACA
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTTTCTGAGGTACA
** * * * **
14058 AGGTTCATCGTTGCGACTTAAACCTTTCCC-TCATATCTTC-GTGGTAGT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGT-TTCTGAGGTACA
* *
14106 AGATTC-CTCGTTGTGGCTTAAATCC-TTCCCTTCATGTTTCTGAGGTACA
1 AGGTTCGC-CGTTGCGGCTTAAA-CCTTTCCCTTCATGTTTCTGAGGTACA
* * * ** * * * * *
14155 AGGCTCACCGTTACAACTTAAACCTTTCTCTCCATATCTTC-GTGGTACT
1 AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGT-TTCTGAGGTACA
* ** *
14204 AGATTCATCGTTACGGCTTAAATCC-TTCCCTTCATGTTTCTGAGGTACA
1 AGGTTCGCCGTTGCGGCTTAAA-CCTTTCCCTTCATGTTTCTGAGGTACA
* *
14253 AGGTTTC-CCGTTGCGACTTAATCCTTT
1 AGG-TTCGCCGTTGCGGCTTAAACCTTT
14280 TCCTCCATAT
Statistics
Matches: 601, Mismatches: 169, Indels: 78
0.71 0.20 0.09
Matches are distributed among these distances:
47 1 0.00
48 98 0.16
49 471 0.78
50 31 0.05
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
AGGTTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTTTCTGAGGTACA
Found at i:13579 original size:98 final size:98
Alignment explanation
Indices: 13447--14301 Score: 1050
Period size: 98 Copynumber: 8.7 Consensus size: 98
13437 GCCTCAACCT
* *
13447 TTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTCATATCTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
*
13512 GTGGTACTAGATTCCTCGTTGAGGCTTAAAT-A
66 GTGGTACTAGATTCCTCGTTGAGGCTTAAATCC
** ** * * *
13544 TTTTCTATCATGTTTCTGAGGTACAAGGTTGGCCGTTGCGACTTAATCCTTTCCCTCCATAGCTT
1 TTCCCT-TCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTT
*
13609 CGTGGTACTAGATTCGC-CGTTGCGGCTTAAAT-C
65 CGTGGTACTAGATTC-CTCGTTGAGGCTTAAATCC
* *** *
13642 TTCCCCTTCATGTTTCTGAGGTGCAAGGTTTGTCGTTGCGACTTAAACCTTTCCC-TCAATAGCT
1 TT-CCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTC-ATATCT
* * * *
13706 TCGTGGTACTAGATTCGTTGTTGCGGCTTAAATCT
64 TCGTGGTACTAGATTCCTCGTTGAGGCTTAAATCC
* * * * *
13741 TTCCCTCCATGTTTCTAAGGTACAAGGTTCGCCGTTGTGACTTAAACATTTCCCTT-ATATCTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
* *
13805 GTTGTAGC-AAATTCCTCGTTGCA-GCTTAAATCC
66 GTGGTA-CTAGATTCCTCGTTG-AGGCTTAAATCC
* * ** *
13838 TTCCCTTCATGTTTCTGAGGTACAAGGTTCATCGTTTCGACTTAAACCTTTTTCTCCATATCTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
13903 GTGGTACTAGATTCAC-CGTT-ACGGCTTAAATCC
66 GTGGTACTAGATTC-CTCGTTGA-GGCTTAAATCC
* * ** *
13936 TTCCCTTCATGTTTTTGAGGTACAAGGTTCACTGTTATGACTTAAACCTTTCCCTTCATAACTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
* * *
14001 GTGGTACTAGATTCGTCGTTGCGGCTTAAATCT
66 GTGGTACTAGATTCCTCGTTGAGGCTTAAATCC
* * *
14034 TTCCCTTTATGTTTCTAAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCC-TCATATCTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
* *
14098 GTGGTAGTAGATTCCTCGTTGTGGCTTAAATCC
66 GTGGTACTAGATTCCTCGTTGAGGCTTAAATCC
* * * * *
14131 TTCCCTTCATGTTTCTGAGGTACAAGGCTCACCGTTACAACTTAAACCTTTCTCTCCATATCTTC
1 TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
*
14196 GTGGTACTAGATTCATCGTT-ACGGCTTAAATCC
66 GTGGTACTAGATTCCTCGTTGA-GGCTTAAATCC
* * *
14229 TTCCCTTCATGTTTCTGAGGTACAAGGTTTC-CCGTTGCGACTTAATCCTTTTCCTCCATATCTT
1 TTCCCTTCATGTTTCTGAGGTACAAGG-TTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTT
14293 CGTGGTACT
65 CGTGGTACT
14302 GAAACTTGTA
Statistics
Matches: 653, Mismatches: 86, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.00
97 168 0.26
98 475 0.73
99 9 0.01
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
TTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
GTGGTACTAGATTCCTCGTTGAGGCTTAAATCC
Found at i:13964 original size:293 final size:291
Alignment explanation
Indices: 13445--14301 Score: 1218
Period size: 293 Copynumber: 2.9 Consensus size: 291
13435 CGGCCTCAAC
*
13445 CTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTCATATCT
1 CTTTCCCTTCATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTT-ATATCT
* **
13510 TCGTGGTA-CTAGATTCCTCGTTGAGGCTTAAAT-ATTTTCTATCATGTTTCTGAGGTACAAGGT
65 TCGTGGTAGC-AGATTCCTCGTTGA-GCTTAAATCCTTCCCT-TCATGTTTCTGAGGTACAAGGT
** * * * * * *
13573 TGGCCGTTGCGACTTAATCCTTTCCCTCCATAGCTTCGTGGTACTAGATTCGCCGTTGCGGCTTA
127 TCACCGTTACGACTTAAACCTTTCTCTCCATATCTTCGTGGTACTAGATTCACCGTTACGGCTTA
* **
13638 AAT-CTTCCCCTTCATGTTTCTGAGGTGCAAGGTTTGTCGTTGCGACTTAAACCTTTCCCTCAAT
192 AATCCTT-CCCTTCATGTTTCTGAGGTACAAGGTTTCACGTTGCGACTTAAACCTTTCCCTC-AT
* *
13702 AGCTTCGTGGTACTAGATTCGTTGTTGCGGCTTAAAT
255 AACTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAAT
* *
13739 CTTTCCCTCCATGTTTCTAAGGTACAAGGTTCGCCGTTGTGACTTAAACATTTCCCTTATATCTT
1 CTTTCCCTTCATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTATATCTT
* *
13804 CGTTGTAGCAAATTCCTCGTTGCAGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACAAGGTTCA
66 CGTGGTAGCAGATTCCTCGTTG-AGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACAAGGTTCA
* * *
13869 TCGTTTCGACTTAAACCTTTTTCTCCATATCTTCGTGGTACTAGATTCACCGTTACGGCTTAAAT
130 CCGTTACGACTTAAACCTTTCTCTCCATATCTTCGTGGTACTAGATTCACCGTTACGGCTTAAAT
* **
13934 CCTTCCCTTCATGTTTTTGAGGTACAAGG-TTCACTGTTATGACTTAAACCTTTCCCTTCATAAC
195 CCTTCCCTTCATGTTTCTGAGGTACAAGGTTTCAC-GTTGCGACTTAAACCTTTCCC-TCATAAC
13998 TTCGTGGTACTAGATTCGTCGTTGCGGCTTAAAT
258 TTCGTGGTACTAGATTCGTCGTTGCGGCTTAAAT
* ** * *
14032 CTTTCCCTTTATGTTTCTAAGGTACAAGGTTCATCGTTGCGACTTAAACCTTTCCCTCATATCTT
1 CTTTCCCTTCATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTATATCTT
* * *
14097 CGTGGTAGTAGATTCCTCGTTGTGGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACAAGGCTCA
66 CGTGGTAGCAGATTCCTCGTTG-AGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACAAGGTTCA
* *
14162 CCGTTACAACTTAAACCTTTCTCTCCATATCTTCGTGGTACTAGATTCATCGTTACGGCTTAAAT
130 CCGTTACGACTTAAACCTTTCTCTCCATATCTTCGTGGTACTAGATTCACCGTTACGGCTTAAAT
* * * *
14227 CCTTCCCTTCATGTTTCTGAGGTACAAGGTTTCCCGTTGCGACTTAATCCTTTTCCTCCATATCT
195 CCTTCCCTTCATGTTTCTGAGGTACAAGGTTTCACGTTGCGACTTAAACCTTTCCCT-CATAACT
14292 TCGTGGTACT
259 TCGTGGTACT
14302 GAAACTTGTA
Statistics
Matches: 504, Mismatches: 51, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
292 4 0.01
293 430 0.85
294 70 0.14
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (291 bp):
CTTTCCCTTCATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTATATCTT
CGTGGTAGCAGATTCCTCGTTGAGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACAAGGTTCAC
CGTTACGACTTAAACCTTTCTCTCCATATCTTCGTGGTACTAGATTCACCGTTACGGCTTAAATC
CTTCCCTTCATGTTTCTGAGGTACAAGGTTTCACGTTGCGACTTAAACCTTTCCCTCATAACTTC
GTGGTACTAGATTCGTCGTTGCGGCTTAAAT
Found at i:14486 original size:35 final size:35
Alignment explanation
Indices: 14447--14518 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
14437 CTCTGGGATC
14447 ATCATGGTTTGTCACTTCTTGCAGTTTTATTAACA
1 ATCATGGTTTGTCACTTCTTGCAGTTTTATTAACA
14482 ATCATGGTTTGTCACTTCTTGCAGTTTTATTAACA
1 ATCATGGTTTGTCACTTCTTGCAGTTTTATTAACA
14517 AT
1 AT
14519 GTACCATCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.46
Consensus pattern (35 bp):
ATCATGGTTTGTCACTTCTTGCAGTTTTATTAACA
Found at i:22398 original size:114 final size:114
Alignment explanation
Indices: 22192--22420 Score: 395
Period size: 114 Copynumber: 2.0 Consensus size: 114
22182 ACTTAATTAG
* *
22192 AGTTATTGTGTTAAAATGTAATGCGAATGAATGCGTGTATGCAATGTATGAGAAGATATTGATTC
1 AGTTATTGTGTTAAAATGTAATGCGAATGAATGCATGTATGCAATGTATGAGAAGACATTGATTC
*
22257 TGAATTCAATACCATTAGATGAACTTTACTAGAAGATAAATTTCTTTAC
66 TGAATTCAATACCATTAGATCAACTTTACTAGAAGATAAATTTCTTTAC
* *
22306 AGTTGTTGTGTTAAAATGTAATGCGAATGAATGCATGTATTCAATGTATGAGAAGACATTGATTC
1 AGTTATTGTGTTAAAATGTAATGCGAATGAATGCATGTATGCAATGTATGAGAAGACATTGATTC
* *
22371 TGAATTCAATTCCATTAGATCAGCTTTACTAGAAGATAAATTTCTTTAC
66 TGAATTCAATACCATTAGATCAACTTTACTAGAAGATAAATTTCTTTAC
22420 A
1 A
22421 AAGAATGAGT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (114 bp):
AGTTATTGTGTTAAAATGTAATGCGAATGAATGCATGTATGCAATGTATGAGAAGACATTGATTC
TGAATTCAATACCATTAGATCAACTTTACTAGAAGATAAATTTCTTTAC
Found at i:28898 original size:88 final size:88
Alignment explanation
Indices: 28749--28924 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
28739 ACACTTCCCA
*
28749 TGTCAATACATCCCTCAATATAGAGAACTTGTTACCCCAAATATGCAACATACATTCAAGCGTGT
1 TGTCAATACATCCCTCAATATAGAGAACTTGTTACCCCAAATATACAACATACATTCAAGCGTGT
28814 ACACATCGTCAATATATTATTCG
66 ACACATCGTCAATATATTATTCG
28837 TGTCAATACATCCCTCAATATAGAGAACTTGTTACCCCAAATATACAACATACATTCAAGCGTGT
1 TGTCAATACATCCCTCAATATAGAGAACTTGTTACCCCAAATATACAACATACATTCAAGCGTGT
*
28902 ACACATCGTCAATATATTGTTCG
66 ACACATCGTCAATATATTATTCG
28925 ACATTCAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (88 bp):
TGTCAATACATCCCTCAATATAGAGAACTTGTTACCCCAAATATACAACATACATTCAAGCGTGT
ACACATCGTCAATATATTATTCG
Found at i:29139 original size:63 final size:63
Alignment explanation
Indices: 29060--29181 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
29050 TTGACAGTCG
*
29060 ATGTATTCTATCACTCGAAAAGTTTCCAAGTTCCAGGAATATAATTTTGCATTCATCGACCTA
1 ATGTATTCTATCACTCGAAAAGTTTCCAAGTTCCAGGAATATAATTCTGCATTCATCGACCTA
*
29123 ATGTATTCTTTCACTCGAAAAGTTTCCAAGTTCCAGGAATATAATTCTGCATTCATCGA
1 ATGTATTCTATCACTCGAAAAGTTTCCAAGTTCCAGGAATATAATTCTGCATTCATCGA
29182 TCTAGCCCTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (63 bp):
ATGTATTCTATCACTCGAAAAGTTTCCAAGTTCCAGGAATATAATTCTGCATTCATCGACCTA
Done.