Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002760.1 Kokia drynarioides strain JFW-HI SEQ_115082, 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: 2087
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Found at i:521 original size:49 final size:50
Alignment explanation
Indices: 436--619 Score: 168
Period size: 49 Copynumber: 3.8 Consensus size: 50
426 GGAGATATAG
* * * *
436 AGGGAAAGGTTTAAGTCGCAATGACGAA-CCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCCTGGTACCTCAGAAGCATAA
*
485 AGGGAAAGATTTAAGTCGCAACGGCGAATCC-GGTA-C-CATGAAG-ATTTGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCCTGGTACCTCA-GAAGCA--TAA
** * **
534 AGGGAAA-AGTTTAAGTCGCAAC-GATAAACCTTTTACCTCAGAAGCATAA
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAATCCTGGTACCTCAGAAGCATAA
* *
583 AGGGAAAGATTTAAGCCACAACGGCGAATCC-GGTACC
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCCTGGTACC
620 ACGAAGATTT
Statistics
Matches: 106, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
47 3 0.03
48 11 0.10
49 76 0.72
50 13 0.12
51 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (50 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAATCCTGGTACCTCAGAAGCATAA
Found at i:605 original size:98 final size:98
Alignment explanation
Indices: 436--646 Score: 350
Period size: 98 Copynumber: 2.2 Consensus size: 98
426 GGAGATATAG
* * *
436 AGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGT
1 AGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGC
* *
501 CGCAACGGCGAATCCGGTACCATGAAGATTTGA
66 CACAACGGCGAATCCGGTACCACGAAGATTTGA
* * *
534 AGGGAAAAGTTTAAGTCGCAACGATAAACCTTTTACCTCAGAAGCATAAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGC
599 CACAACGGCGAATCCGGTACCACGAAGATTTGA
66 CACAACGGCGAATCCGGTACCACGAAGATTTGA
632 AGGGAAAGGTTTAAG
1 AGGGAAAGGTTTAAG
647 CCATATGGAG
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGC
CACAACGGCGAATCCGGTACCACGAAGATTTGA
Found at i:635 original size:49 final size:49
Alignment explanation
Indices: 484--649 Score: 151
Period size: 49 Copynumber: 3.4 Consensus size: 49
474 CAGAAGCATA
* * *
484 AAGGGAAAGATTTAAGTCGCAACGGCGAATCCGGTACCATGAAGATTTG
1 AAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAAGATTTG
* * ** * ** * *
533 AAGGGAAA-AGTTTAAGTCGCAAC-GATAAACCTTTTACCTCAGAAGCA--TA
1 AAGGGAAAGA-TTTAAGCCACAACGGCGAATCC-GGTACCAC-GAAG-ATTTG
582 AAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAAGATTTG
1 AAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAAGATTTG
*
631 AAGGGAAAGGTTTAAGCCA
1 AAGGGAAAGATTTAAGCCA
650 TATGGAGGGA
Statistics
Matches: 91, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
47 1 0.01
48 10 0.11
49 69 0.76
50 10 0.11
51 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAAGATTTG
Found at i:814 original size:219 final size:219
Alignment explanation
Indices: 430--840 Score: 504
Period size: 219 Copynumber: 1.9 Consensus size: 219
420 TATCATGGAG
* * *
430 ATATAGAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATAAAGGGAAAGAT
1 ATATAGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGAT
* * * * ** * * * * *
495 TTAAGTCGCAACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAAGTTTAAGTCGCAACGATA
66 TTAAGCCACAACGACAAATCCAATACCATCAAGATATGAAGAGAAAAGTTTAAGTCACAACGACA
* * * * *
560 AACCTTTTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAA
131 AACCTTGTACCTCAAAAGCATAAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAA
625 GATTTGAAGGGAAAGGTTTAAGCC
196 GATTTGAAGGGAAAGGTTTAAGCC
* * * **
649 ATATGGAGGGAAAGGTTT-AGCTCACAACGACGAATCTTGTACCTCAGAACCATGAAGGGGGAGA
1 ATATAGAGGGAAAGGTTTAAG-TCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGA
* * * *
713 TTTAAGCCACTACGACAAATCCAATACCA-CAAGGATATGAAGAGAAAGGTTTAAGTCACAATGG
65 TTTAAGCCACAACGACAAATCCAATACCATCAA-GATATGAAGAGAAAAGTTTAAGTCACAACGA
* *
777 CAAACCTTGTACCTCAAAAGCATGAAA-AGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC
129 CAAACCTTGTACCTCAAAAGCAT-AAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCAC
841 AGGGATATAA
Statistics
Matches: 159, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
218 4 0.03
219 152 0.96
220 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (219 bp):
ATATAGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGAT
TTAAGCCACAACGACAAATCCAATACCATCAAGATATGAAGAGAAAAGTTTAAGTCACAACGACA
AACCTTGTACCTCAAAAGCATAAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAA
GATTTGAAGGGAAAGGTTTAAGCC
Found at i:838 original size:49 final size:49
Alignment explanation
Indices: 749--930 Score: 127
Period size: 49 Copynumber: 3.7 Consensus size: 49
739 CCACAAGGAT
* * * * * * * *
749 ATGAAGAGAAAGGTTTAAGTCACAATGGCAAACCTTGTACCTCAAAAGC
1 ATGAAAAGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAAGC
* * * *
798 ATGAAAAGAAAGATTTAAGCCGCAACGACGAATCTAGTA-C-CACAGGG
1 ATGAAAAGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAAGC
* * * * * *
845 ATATAAAAGGGAAATG-TTTAAGTCGCAACGGCGGACCTTGTACCTCGAAAGC
1 AT-GAAAA--GAAA-GATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAAGC
**
897 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 ATGAAAAGAAAGATTTAAGCCGCAACGGCGAATC
931 CAATACCACG
Statistics
Matches: 98, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
47 6 0.06
48 6 0.06
49 52 0.53
50 25 0.26
51 4 0.04
52 5 0.05
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (49 bp):
ATGAAAAGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAAAAGC
Found at i:950 original size:49 final size:49
Alignment explanation
Indices: 805--957 Score: 143
Period size: 49 Copynumber: 3.1 Consensus size: 49
795 AGCATGAAAA
* * * *
805 GAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-AGGGATATAAAAGG
1 GAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGA-AGATAT-GAAGG
* * * * *
855 GAAATG-TTTAAGTCGCAACGGCGGA-CCTTGTACCTCGAA-AGCATGAAGG
1 GAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAGA-TATGAAGG
*
904 GAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGG
1 GAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGG
953 GAAAG
1 GAAAG
958 GTTACAACTG
Statistics
Matches: 81, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
48 1 0.01
49 47 0.58
50 31 0.38
51 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (49 bp):
GAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGG
Found at i:1007 original size:98 final size:98
Alignment explanation
Indices: 649--1008 Score: 363
Period size: 98 Copynumber: 3.7 Consensus size: 98
639 GGTTTAAGCC
* * * * * * **
649 ATATGGAGGGAAAGGTTT-AGCTCACAACGACGAATCTTGTACCTCAG-AACCATGAAGGGGGAG
1 ATATGAAGGGAAAGGTTTAAG-TCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAAGAGAAAG
* * *
712 ATTTAAGCCACTACGACAAATCCAATACCACAAGG
65 ATTTAAGCCGCAACGACGAATCCAATACCACAA-G
* * * * *
747 ATATGAAGAGAAAGGTTTAAGTCACAATGGCAAACCTTGTACCTCA-AAAGCATGAAAAGAAAGA
1 ATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAAGAGAAAGA
* * *
811 TTTAAGCCGCAACGACGAATCTAGTACCACAGGG
66 TTTAAGCCGCAACGACGAATCCAATACCACA-AG
* * * *
845 ATATAAAAGGGAAATGTTTAAGTCGCAACGGCGGACCTTGTACCTC-GAAAGCATGAAGGGAAAG
1 ATAT-GAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAAGAGAAAG
*
909 ATTTAAGCCGCAACGGCGAATCCAATACCACGAAG
65 ATTTAAGCCGCAACGACGAATCCAATACCAC-AAG
* * * * *
944 ATATGAAGGGAAAGGTTACAACT-GTAACGGCGAACCTTGTACCTTAGAAA-CATGACGAGAAAG
1 ATATGAAGGGAAAGGTT-TAAGTCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAAGAGAAAG
1007 AT
65 AT
1009 CGAACCCACG
Statistics
Matches: 215, Mismatches: 39, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
98 123 0.57
99 91 0.42
100 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
ATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAGCATGAAGAGAAAGA
TTTAAGCCGCAACGACGAATCCAATACCACAAG
Found at i:1279 original size:39 final size:39
Alignment explanation
Indices: 1233--1350 Score: 152
Period size: 39 Copynumber: 3.0 Consensus size: 39
1223 CACCATCAAC
1233 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
*
1272 CAATCTCTTACCCCGAGCTTAGGGTAGA-T-C-ACCATT
1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
* * *
1308 AGCCAATCTCCTACCCCGAGCCTGGGGCAGATTGCAACCATT
1 ---CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
1350 C
1 C
1351 GGTCTTTTAC
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
36 6 0.09
37 1 0.01
38 1 0.01
39 52 0.76
40 1 0.01
41 1 0.01
42 6 0.09
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
Found at i:1350 original size:78 final size:78
Alignment explanation
Indices: 1221--1414 Score: 246
Period size: 78 Copynumber: 2.5 Consensus size: 78
1211 GTGAAGTTAC
* * *
1221 ATCACCATCAACCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCC
1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC
* * *
1286 GAG-CTTAGGGTAG
66 AAGCCTGA-GGCAG
* * ** * *
1299 ATCACCATTAGCCAATCTCCTACCCCGAGCCTGGGGCAGATTGCAACCATTCGGTCTTTTACCTC
1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC
1364 AAGCCTGAGGCAG
66 AAGCCTGAGGCAG
* *
1377 ATCACTATCAGCCAATCTCTTACCTCGAGCCTGGGGCA
1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCA
1415 AATCATCATC
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
78 96 0.97
79 3 0.03
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (78 bp):
ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC
AAGCCTGAGGCAG
Found at i:1400 original size:39 final size:39
Alignment explanation
Indices: 1357--1439 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
1347 ATTCGGTCTT
* *
1357 TTACCTCAAGCCTGAGGCAGATCA-CTATCAGCCAATCTC
1 TTACCTCAAGCCTGAGGCAAATCATC-ATCAACCAATCTC
* *
1396 TTACCTCGAGCCTGGGGCAAATCATCATCAACCAATCTC
1 TTACCTCAAGCCTGAGGCAAATCATCATCAACCAATCTC
*
1435 CTACC
1 TTACC
1440 CCGAGTCTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 37 0.97
40 1 0.03
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (39 bp):
TTACCTCAAGCCTGAGGCAAATCATCATCAACCAATCTC
Done.