Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002759.1 Kokia drynarioides strain JFW-HI SEQ_115081, 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:0.35, 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: 522
Period size: 219 Copynumber: 1.9 Consensus size: 219
420 TATCATGGAG
* * *
430 ATATAGAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCATAAAGGGAAAGAT
1 ATATAGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGAT
* * * * * * * * * *
495 TTAAGTCGCAACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAAAGTTTAAGTCGCAACGATA
66 TTAAGCCACAACGACAAATCCAGTACCATCAAGATATGAAGAGAAAAGTTTAAGTCACAACGACA
* * * *
560 AACCTTTTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCACAACGGCGAATCCGGTACCACGAA
131 AACCTTGTACCTCAGAAGCATAAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAA
625 GATTTGAAGGGAAAGGTTTAAGCC
196 GATTTGAAGGGAAAGGTTTAAGCC
* * * **
649 ATATGGAGGGAAAGGTTT-AGCTCACAACGACGAATCTTGTACCTCAGAACCATGAAGGGGGAGA
1 ATATAGAGGGAAAGGTTTAAG-TCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGA
* * * *
713 TTTAAGCCACTACGACAAATCCAGTACCA-CAAGGATATGAAGAGAAAGGTTTAAGTCACAATGG
65 TTTAAGCCACAACGACAAATCCAGTACCATCAA-GATATGAAGAGAAAAGTTTAAGTCACAACGA
* *
777 CAAACCTTGTACCTCAGAAGCATGAAA-AGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC
129 CAAACCTTGTACCTCAGAAGCAT-AAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCAC
841 AGGGATATAA
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
218 4 0.02
219 154 0.96
220 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (219 bp):
ATATAGAGGGAAAGGTTTAAGTCACAACGACGAACCTTGTACCTCAGAACCATAAAGGGAAAGAT
TTAAGCCACAACGACAAATCCAGTACCATCAAGATATGAAGAGAAAAGTTTAAGTCACAACGACA
AACCTTGTACCTCAGAAGCATAAAGAGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAA
GATTTGAAGGGAAAGGTTTAAGCC
Found at i:818 original size:98 final size:98
Alignment explanation
Indices: 649--960 Score: 351
Period size: 98 Copynumber: 3.2 Consensus size: 98
639 GGTTTAAGCC
* * * * **
649 ATATGGAGGGAAAGGTTT-AGCTCACAACGACGAATCTTGTACCTCAGAACCATGAAGGGGGAGA
1 ATATGAAGGGAAAGGTTTAAG-TCACAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGA
* * *
713 TTTAAGCCACTACGACAAATCCAGTACCACAAGG
65 TTTAAGCCGCAACGACGAATCCAGTACCACAAGG
* * * **
747 ATATGAAGAGAAAGGTTTAAGTCACAATGGCAAACCTTGTACCTCAGAAGCATGAAAAGAAAGAT
1 ATATGAAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGAT
* *
812 TTAAGCCGCAACGACGAATCTAGTACCACAGGG
66 TTAAGCCGCAACGACGAATCCAGTACCACAAGG
* * ** *
845 ATATAAAAGGGAAATGTTTAAGTTGCAACGGCGGACCTTGTACCTC-GAAAGCATGAAGGGAAAG
1 ATAT-GAAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAG-AAGCATGAAGGGAAAG
* *
909 ATTTAAGCCGCAACGGCGAATCCAATACCACGAA-G
64 ATTTAAGCCGCAACGACGAATCCAGTACCAC-AAGG
*
944 ACATGAAGGGAAAGGTT
1 ATATGAAGGGAAAGGTT
961 ACAACTGTAA
Statistics
Matches: 177, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
98 95 0.54
99 81 0.46
100 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (98 bp):
ATATGAAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGAT
TTAAGCCGCAACGACGAATCCAGTACCACAAGG
Found at i:838 original size:49 final size:49
Alignment explanation
Indices: 673--930 Score: 146
Period size: 49 Copynumber: 5.2 Consensus size: 49
663 GTTTAGCTCA
* * ** *
673 CAACGACGAATCTTGTACCTCAGAACCATGAAGGGGGAGATTTAAGCCA
1 CAACGACGAATCTTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCG
* * ** * * * * * *
722 CTACGACAAATCCAGTACCACA-AGGATATGAAGAGAAAGGTTTAAGTCA
1 CAACGACGAATCTTGTACCTCAGAAG-CATGAAGAGAAAGATTTAAGCCG
* * * * *
771 CAATGGCAAACCTTGTACCTCAGAAGCATGAAAAGAAAGATTTAAGCCG
1 CAACGACGAATCTTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCG
* * * * * * **
820 CAACGACGAATCTAGTACCACAG-GGATATAAAAGGGAAATG-TTTAAGTTG
1 CAACGACGAATCTTGTACCTCAGAAG-CAT-GAAGAGAAA-GATTTAAGCCG
* * * *
870 CAACGGCGGACCTTGTACCTC-GAAAGCATGAAGGGAAAGATTTAAGCCG
1 CAACGACGAATCTTGTACCTCAG-AAGCATGAAGAGAAAGATTTAAGCCG
*
919 CAACGGCGAATC
1 CAACGACGAATC
931 CAATACCACG
Statistics
Matches: 150, Mismatches: 51, Indels: 16
0.69 0.24 0.07
Matches are distributed among these distances:
48 3 0.02
49 112 0.75
50 33 0.22
51 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (49 bp):
CAACGACGAATCTTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCG
Found at i:949 original size:49 final size:49
Alignment explanation
Indices: 699--957 Score: 145
Period size: 49 Copynumber: 5.3 Consensus size: 49
689 ACCTCAGAAC
** * * * *
699 CATGAAGGGGGAGATTTAAGCCACTACGACAAATCCAGTACCAC-AAGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GA
* * * * * * * * *
748 TATGAAGAGAAAGGTTTAAGTCACAATGGC-AAACCTTGTACCTCAGAAG-
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGA
** * * *
797 CATGAAAAGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-AGGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGA-AGA
* * ** * * *
846 TATAAAAGGGAAATG-TTTAAGTTGCAACGGCGGA-CCTTGTACCTCGAA-A
1 CAT-GAAGGGAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAGA
*
895 GCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGA
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
945 CATGAAGGGAAAG
1 CATGAAGGGAAAG
958 GTTACAACTG
Statistics
Matches: 152, Mismatches: 44, Indels: 28
0.68 0.20 0.12
Matches are distributed among these distances:
47 1 0.01
48 6 0.04
49 105 0.69
50 36 0.24
51 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
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.