Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011635.1 Kokia drynarioides strain JFW-HI SEQ_126626, 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, 779
Length: 1299
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Found at i:199 original size:49 final size:49
Alignment explanation
Indices: 117--822 Score: 283
Period size: 49 Copynumber: 14.4 Consensus size: 49
107 ATTGAATCCG
* * * *
117 ATACTCTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGACGAATTTA
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * *
166 ATACCCTAAAGATGTGAAGGGAGAGATTAAAGCCGCAACGGCGAATCTC
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * *
215 ATACCCTAGAGATATGAAGGGAAAGGTTAAAGTCGCAACG--GAAAGCCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACG-AA-TCTA
* * * * * * *
264 ATACCCTAGGGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTC
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * *
313 ATACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * * * *
362 GTACCTTAGAGATATGAAGGGAGAGATTGAAGCCGCAA-TAGCAAATCTC
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGA-CGAATCTA
* * * * * * * * * *
411 ATACCCCAAAAATATGGAGGGAAAGGTTAAAGCCACAATGATGAACCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * * ** * *
460 GTACCTTAGAGATATGGAGGGAGAGATTGAAGTCGTAATGACGAATCTC
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * ** * * *
509 ATACCTTAGAGATATGGAGGGAAAGGTTGAAGCTGCAACGGCGAACCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * * * * * * * *
558 GTGCCTTAGAGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * * * *
607 GTACCATAGAGATATGGAGGGAAAGGTTGAAGACC-CAACGGCGAACCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAG-CCACAACGACGAATCTA
* * * * ** *
656 ATACCCTAGAGATATGGAGGGAAAGTTTGAAGCCGTAACGACGAATCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * *
705 ATACCCTAAAGATATGAAGGGAAAGGTTACA-CCGCAACGATGAATCTT
1 ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
* * * * * * * *
753 ATACCCTAAAGATAT-AGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTT
1 ATACCCTAGAGATGTGA-AGGGAAAGATTAAAGCCACAACGACGAATCTA
802 ATACCCTA-AGGATGTGGAAGG
1 ATACCCTAGA-GATGT-GAAGG
823 CAAGGTTGAA
Statistics
Matches: 535, Mismatches: 109, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
47 2 0.00
48 48 0.09
49 475 0.89
50 8 0.01
51 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.19
Consensus pattern (49 bp):
ATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACGACGAATCTA
Found at i:282 original size:98 final size:98
Alignment explanation
Indices: 166--902 Score: 675
Period size: 98 Copynumber: 7.5 Consensus size: 98
156 GACGAATTTA
* * *
166 ATACCCTAAAGATGTGAAGGGAGAGATTAAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
* *
231 AAGGGAAAGGTTAAAGTCGCAACGGA-AAGCCTT
66 GAGGGAAAGGTTAAAGCCGCAACGGAGAA-CCTT
*
264 ATACCCTAGGGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
*
329 GAGGGAAAGGTTGAAGCCGCAAC-GACGAACCTT
66 GAGGGAAAGGTTAAAGCCGCAACGGA-GAACCTT
* * ** * * * *
362 GTACCTTAGAGATATGAAGGGAGAGATTGAAGCCGCAATAGCAAATCTCATACCCCAAAAATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
* *
427 GAGGGAAAGGTTAAAGCCACAA-TGATGAACCTT
66 GAGGGAAAGGTTAAAGCCGCAACGGA-GAACCTT
* * * * * * * *
460 GTACCTTAGAGATATGGAGGGAGAGATTGAAGTCGTAATGACGAATCTCATACCTTAGAGATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
* * *
525 GAGGGAAAGGTTGAAGCTGCAACGGCGAACCTT
66 GAGGGAAAGGTTAAAGCCGCAACGGAGAACCTT
* * * * * * * ** * * ** *
558 GTGCCTTAGAGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTTGTACCATAGAGATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
* *
623 GAGGGAAAGGTTGAAGACC-CAACGGCGAACCTT
66 GAGGGAAAGGTTAAAG-CCGCAACGGAGAACCTT
* * * * * * *
656 ATACCCTAGAGATATGGAGGGAAAGTTTGAAGCCGTAACGACGAATCTTATACCCTAAAGATATG
1 ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
* * *
721 AAGGGAAAGGTTACA-CCGCAAC-GATGAATCTT
66 GAGGGAAAGGTTAAAGCCGCAACGGA-GAACCTT
* * * * * *
753 ATACCCTAAAGATAT-AGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTA-AGGATG
1 ATACCCTAGAGATATGA-AGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGA-GATA
* * * ** *
816 TGGAAGGCAAGGTTGAAGCCGCAATAGCGAACCTT
64 TGGAGGGAAAGGTTAAAGCCGCAACGGAGAACCTT
* * * * **
851 ATAGCCTAGAAATGAGGAA-GGAAAGATTGAAGCCATAGA-GGCGAATCTCATA
1 ATACCCTAGAGAT-ATGAAGGGAGAGATTGAAGCCGCA-ACGGCGAATCTCATA
903 GCGTGAAGAT
Statistics
Matches: 536, Mismatches: 89, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
96 4 0.01
97 77 0.14
98 446 0.83
99 8 0.01
100 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.19
Consensus pattern (98 bp):
ATACCCTAGAGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
GAGGGAAAGGTTAAAGCCGCAACGGAGAACCTT
Found at i:399 original size:147 final size:146
Alignment explanation
Indices: 117--885 Score: 665
Period size: 147 Copynumber: 5.2 Consensus size: 146
107 ATTGAATCCG
* * * * *
117 ATACTCTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGACGAAT-TTAATACCCTAAAGATGT
1 ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCACAATGACGAATCTT-ATACCCTAGAGATAT
* * * * * * *
181 GAAGGGAGAGATTAAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGAAGGGAAAGGTTAAA
65 GGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAA
*
246 GTCGCAACGGAAAGCCTT
130 GCCGCAACGGAAA-CCTT
* * * * * * *
264 ATACCCTAGGGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATG
1 ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCACAATGACGAATCTTATACCCTAGAGATATG
* * * * *
329 GAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATATGAAGGGAGAGATTGAAG
66 GAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAAG
* * * *
394 CCGCAATAGCAAATCTC
131 CCGCAA-CGGAAACCTT
* * * * * * * * *
411 ATACCCCAAAAATATGGAGGGAAAGGTTAAAGCCACAATGATGAACCTTGTACCTTAGAGATATG
1 ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCACAATGACGAATCTTATACCCTAGAGATATG
* * * * * * * * * *
476 GAGGGAGAGATTGAAGTCGTAATGACGAATCTCATACCTTAGAGATATGGAGGGAAAGGTTGAAG
66 GAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAAG
* *
541 CTGCAACGGCGAACCTT
131 CCGCAACGG-AAACCTT
* * * * * * * * * *
558 GTGCCTTAGAGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTTGTACCATAGAGATATG
1 ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCACAATGACGAATCTTATACCCTAGAGATATG
* *
623 GAGGGAAAGGTTGAAGACC-CAACGGCGAACCTTATACCCTAGAGATATGGAGGGAAAGTTTGAA
66 GAGGGAAAGGTTGAAG-CCGCAACGGCGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAA
* *
687 GCCGTAAC-GACGAATCTT
130 GCCGCAACGGA--AACCTT
* * * * *
705 ATACCCTAAAGATATGAAGGGAAAGGTT-ACA-CCGCAACGATGAATCTTATACCCTAAAGATAT
1 ATACCCTAGAGATATGAAGGGAAAGGTTGA-AGCCACAATGACGAATCTTATACCCTAGAGATAT
* * *
768 AGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTA-AGGATGTGGAA-GGCAAGGTTG
65 GGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAGA-GATAT-GAAGGGAAAGGTTG
*
831 AAGCCGCAATAGCG-AACCTT
128 AAGCCGCAA-CG-GAAACCTT
* * * *
851 ATAGCCTAGAAATGAGGAA-GGAAAGATTGAAGCCA
1 ATACCCTAGAGAT-ATGAAGGGAAAGGTTGAAGCCA
886 TAGAGGCGAA
Statistics
Matches: 491, Mismatches: 115, Indels: 32
0.77 0.18 0.05
Matches are distributed among these distances:
145 3 0.01
146 108 0.22
147 373 0.76
148 6 0.01
149 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.19
Consensus pattern (146 bp):
ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCACAATGACGAATCTTATACCCTAGAGATATG
GAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAAG
CCGCAACGGAAACCTT
Found at i:828 original size:49 final size:50
Alignment explanation
Indices: 195--884 Score: 508
Period size: 49 Copynumber: 14.1 Consensus size: 50
185 GGAGAGATTA
* * *
195 AAGCCGCAACGGCGAATCTCATACCCT-AGAGATAT-GAAGGGAAAGGTTA
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAA-GGAAAGGTTG
* * * * *
244 AAGTCGCAACGG-AAAGCCTTATACCCT-AGGGATAT-GAAGGGAGAGATTG
1 AAGCCGCAACGGCGAA-CCTTATACCCTAAGAGATATGGAA-GGAAAGGTTG
* * *
293 AAGCCGCAACGGCGAATCTCATACCCT-AGAGATATGGAGGGAAAGGTTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* * * * *
342 AAGCCGCAACGACGAACCTTGTA-CCTTAGAGATAT-GAAGGGAGAGATTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAA-GGAAAGGTTG
** * * * * * * *
391 AAGCCGCAATAGCAAATCTCATACCCCAA-AAATATGGAGGGAAAGGTTA
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* * ** * * * * *
440 AAGCCACAATGATGAACCTTGTA-CCTTAGAGATATGGAGGGAGAGATTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* * * * * * * *
489 AAGTCGTAATGACGAATCTCATA-CCTTAGAGATATGGAGGGAAAGGTTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* * * * *
538 AAGCTGCAACGGCGAACCTTGT-GCCTTAGAGATATGGAGGGAAAGGTTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* ** * * * *
587 ATGCCAAAATGGCGAACCTTGTACCAT-AGAGATATGGAGGGAAAGGTTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* *
636 AAGACC-CAACGGCGAACCTTATACCCT-AGAGATATGGAGGGAAAGTTTG
1 AAG-CCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* * *
685 AAGCCGTAACGACGAATCTTATACCCTAA-AGATAT-GAAGGGAAAGGTT-
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAA-GGAAAGGTTG
** * * *
733 ACA-CCGCAACGATGAATCTTATACCCTAA-AGATATAGAGGGAAAGGTTG
1 A-AGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
* *
782 AAGCCGCAACGGCGAACCTTATACCCTAAG-GATGTGGAAGGCAAGGTTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
** * * *
831 AAGCCGCAATAGCGAACCTTATAGCCT-AGAAATGA-GGAAGGAAAGATTG
1 AAGCCGCAACGGCGAACCTTATACCCTAAGAGAT-ATGGAAGGAAAGGTTG
880 AAGCC
1 AAGCC
885 ATAGAGGCGA
Statistics
Matches: 517, Mismatches: 103, Indels: 42
0.78 0.16 0.06
Matches are distributed among these distances:
48 57 0.11
49 446 0.86
50 14 0.03
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.19
Consensus pattern (50 bp):
AAGCCGCAACGGCGAACCTTATACCCTAAGAGATATGGAAGGAAAGGTTG
Found at i:1110 original size:45 final size:45
Alignment explanation
Indices: 1043--1299 Score: 248
Period size: 45 Copynumber: 5.8 Consensus size: 45
1033 TACATCACCT
*
1043 CATCCAATCTTTTACCCCTAGTCAAGAGAGGCAGATTGAAGCCAC
1 CATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAGCCAC
* * * *
1088 CATCCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGCTAC
1 CATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAGCCAC
* * * *
1133 CATCTAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCAC
1 CATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAGCCAC
* * * *
1178 CATTCAATCTTTTATCCCTAATCTAA-AGGGGAAGATTGAAG---C
1 CATCCAATCTTTTACCCCTAATC-AAGAGAGGCAGATTGAAGCCAC
* *
1220 TATCCAATCTTTTACCCCTAATCCAA-ATG-GGCAGATTAAAG---C
1 CATCCAATCTTTTACCCCTAAT-CAAGA-GAGGCAGATTGAAGCCAC
*
1262 GATCCAATCTTTTACCCCTAATTC-AGA-AGGGCAGATTG
1 CATCCAATCTTTTACCCCTAA-TCAAGAGA-GGCAGATTG
Statistics
Matches: 180, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 64 0.36
43 3 0.02
45 110 0.61
46 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (45 bp):
CATCCAATCTTTTACCCCTAATCAAGAGAGGCAGATTGAAGCCAC
Found at i:1208 original size:90 final size:88
Alignment explanation
Indices: 1041--1283 Score: 282
Period size: 90 Copynumber: 2.8 Consensus size: 88
1031 GCTACATCAC
* * * *
1041 CTCATCCAATCTTTTACCCCTAGTCAAGAGAGGCAGATTGAAGCCACCATCCAATCTTTTACCCT
1 CTCATCCAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTACCCT
* *
1106 TAGTCAAGAGGGGCAGATTGAAG
66 TAATCAAGAGGGGAAGATTGAAG
* *
1129 CTACCATCTAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCACCATTCAATCTTTTATC
1 CT--CATCCAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTA-C
1194 CC-TAATCTAA-AGGGGAAGATTGAAG
63 CCTTAATC-AAGAGGGGAAGATTGAAG
* ** * * *
1219 CT-ATCCAATCTTTTACCCCTAATCCAAATGGGCAGATT-AAA--GCGATCCAATCTTTTACCCC
1 CTCATCCAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTACCCT
1280 TAAT
66 TAAT
1284 TCAGAAGGGC
Statistics
Matches: 135, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
83 3 0.02
84 17 0.13
86 3 0.02
87 32 0.24
88 2 0.01
90 73 0.54
91 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (88 bp):
CTCATCCAATCTTTTACCCCTAATCAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTACCCT
TAATCAAGAGGGGAAGATTGAAG
Done.