Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012146.1 Kokia drynarioides strain JFW-HI SEQ_127145, 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: 4016
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Found at i:838 original size:9 final size:9
Alignment explanation
Indices: 826--865 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
816 AAAAATAAGG
826 AAAAAGAAA
1 AAAAAGAAA
*
835 AAAAAGAAG
1 AAAAAGAAA
*
844 AAAAAGAGGA
1 AAAAAGA-AA
854 AAAAAGAAA
1 AAAAAGAAA
863 AAA
1 AAA
866 GAGAGCTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:846 original size:18 final size:18
Alignment explanation
Indices: 813--865 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
803 TTCACCCCAA
*
813 AAAAAAAATAAGGAAAAAG
1 AAAAAAAAGAA-GAAAAAG
832 AAAAAAAAGAAGAAAAAG
1 AAAAAAAAGAAGAAAAAG
*
850 AGGAAAAAAGAA-AAAA
1 A-AAAAAAAGAAGAAAA
866 GAGAGCTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAGAAAAAG
Found at i:1919 original size:49 final size:48
Alignment explanation
Indices: 1824--2592 Score: 407
Period size: 49 Copynumber: 15.7 Consensus size: 48
1814 CATTGAATCC
* * * * * *
1824 TATACTCTAGAGATGTGAAGGGAAAGATTGAAGACACAATGACGAATT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAATT
* * * *
1872 TAATACCCTAAAGATGTGAAGGGAGAGATTAAAGCCGCAACGGCGAATCT
1 T-ATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAAT-T
* * * ** ** *
1922 CATACCCTAGAGATATGAAGGGAAAGGTTAAAGTTGCAACGGAAAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * *
1971 TATACCCTGGGGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAAT-T
* * * * * * *
2020 CATACCGTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACAAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * ** *
2069 TGTACCTTAGAGATATGAAGGGAGAGATTGAAGCCGCAATAGCAAATCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAAT-T
* * * * * * * * * * *
2118 CATACCCCAAAAATATGGAGGGAAAGGTTAAAGCCACAATGGTGAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * * * * * **
2167 TGTACCTTAGAGATATGGAGGGAGAGATTGAAGTCGTAATGATGAATCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAAT-T
* * * * * ** * *
2216 CATACCTTAGAGATATGGAGGGAAAGGTTGACGCTACAACGGTGAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * * * * ** * *
2265 TGTGCCTTAGAGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * * *
2314 TGTACCATAGAGATATGGAGGGAAAGGTTGAAGACC-CAACGGCGAACCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAG-CCGCAACGGCGAA-TT
* * * *
2363 TATACCCTAGAGATATGGAGGGAAAGTTTGAAGCCGTAACGACGAATCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAAT-T
* * * **
2412 TTTACCCTAAAGATATGAAGGGAAAGGTT-ACA-CCGCAACGATGAATCT
1 TATACCCTAGAGATATGAAGGGAAAGATTGA-AGCCGCAACGGCGAAT-T
* * * *
2460 TATACCCTAAAGATAT-AGAGGGAAAGGTTGAAGCCGCAACGACGAACCT
1 TATACCCTAGAGATATGA-AGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * ** *
2509 TATACCCTA-AGGATGTGGAA-GGCAAGGTTGAAGCCGCAATAGCGAACCT
1 TATACCCTAGA-GATAT-GAAGGGAAAGATTGAAGCCGCAACGGCGAA-TT
* * * *
2558 TATAGCCTAGAAATGTGGAGGGAAAGATTGAAGCC
1 TATACCCTAGAGATATGAAGGGAAAGATTGAAGCC
2593 ACAGAGGCAA
Statistics
Matches: 571, Mismatches: 128, Indels: 43
0.77 0.17 0.06
Matches are distributed among these distances:
47 1 0.00
48 48 0.08
49 516 0.90
50 5 0.01
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (48 bp):
TATACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGCGAATT
Found at i:1990 original size:98 final size:98
Alignment explanation
Indices: 1883--2610 Score: 572
Period size: 98 Copynumber: 7.4 Consensus size: 98
1873 AATACCCTAA
* * *
1883 AGATGTGAAGGGAGAGATTAAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGAAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
*** * * * *
1948 GTTAAAGTTGCAACGGAAAACCTTATACCCTGG
66 GTTAAAGCCACAACGGAGAACCTTGTACCTTAG
* *
1981 GGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCGTAGAGATATGGAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * *
2046 GTTGAAGCCGCAAC-GACAAACCTTGTACCTTAG
66 GTTAAAGCCACAACGGA-GAACCTTGTACCTTAG
** * * * *
2079 AGATATGAAGGGAGAGATTGAAGCCGCAATAGCAAATCTCATACCCCAAAAATATGGAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* *
2144 GTTAAAGCCACAATGGTGAACCTTGTACCTTAG
66 GTTAAAGCCACAACGGAGAACCTTGTACCTTAG
* * * * ** *
2177 AGATATGGAGGGAGAGATTGAAGTCGTAATGATGAATCTCATACCTTAGAGATATGGAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * * * *
2242 GTTGACGCTACAACGGTGAACCTTGTGCCTTAG
66 GTTAAAGCCACAACGGAGAACCTTGTACCTTAG
* * * * ** * * ** *
2275 AGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTTGTACCATAGAGATATGGAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * * *
2340 GTTGAAGACC-CAACGGCGAACCTTATACCCTAG
66 GTTAAAG-CCACAACGGAGAACCTTGTACCTTAG
* * * * * ** * *
2373 AGATATGGAGGGAAAGTTTGAAGCCGTAACGACGAATCTTTTACCCTAAAGATATGAAGGGAAAG
1 AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * * * * *
2438 GTTACA-CCGCAAC-GATGAATCTTATACCCTAA
66 GTTAAAGCCACAACGGA-GAACCTTGTACCTTAG
* * * * * * * *
2470 AGATAT-AGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTA-AGGATGTGGAAGGCA
1 AGATATGA-AGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGA-GATATGGAGGGAA
* * ** * *
2533 AGGTTGAAGCCGCAATAGCGAACCTTATAGCC-TAG
64 AGGTTAAAGCCACAACGGAGAACCTTGTA-CCTTAG
* * * * * *
2568 AAATGTGGAGGGAAAGATTGAAGCCACAGA-GGCAAATCTCATA
1 AGATATGAAGGGAGAGATTGAAGCCGCA-ACGGCGAATCTCATA
2611 GCGTGAAGAT
Statistics
Matches: 520, Mismatches: 98, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
96 4 0.01
97 77 0.15
98 433 0.83
99 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (98 bp):
AGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
GTTAAAGCCACAACGGAGAACCTTGTACCTTAG
Found at i:2091 original size:147 final size:147
Alignment explanation
Indices: 1824--2595 Score: 561
Period size: 147 Copynumber: 5.3 Consensus size: 147
1814 CATTGAATCC
* * * * * * * * * * *
1824 TATACTCTAGAGATGTGAAGGGAAAGATTGAAGACACAATGACGAA-TTTAATACCCTAAAGATG
1 TATACCCTAAAGATATGAAGGGAAAGGTTGAAGCCACAACGGCGAACCTT-ATACCATAGAGATA
* * * * * * * *
1888 TGAAGGGAGAGATTAAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGAAGGGAAAGGTTAA
65 TGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGA
**
1953 AGTTGCAACGGAAAACCT
130 AGCCGCAACGGAAAACCT
*** * * * * * *
1971 TATACCCTGGGGATATGAAGGGAGAGATTGAAGCCGCAACGGCGAATCTCATACCGTAGAGATAT
1 TATACCCTAAAGATATGAAGGGAAAGGTTGAAGCCACAACGGCGAACCTTATACCATAGAGATAT
* * * * *
2036 GGAGGGAAAGGTTGAAGCCGCAACGACAAACCTTGTACCTTAGAGATATGAAGGGAGAGATTGAA
66 GGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAA
** * *
2101 GCCGCAATAGCAAATCT
131 GCCGCAACGGAAAACCT
* * * * * * * * *
2118 CATACCCCAAAAATATGGAGGGAAAGGTTAAAGCCACAATGGTGAACCTTGTACCTTAGAGATAT
1 TATACCCTAAAGATATGAAGGGAAAGGTTGAAGCCACAACGGCGAACCTTATACCATAGAGATAT
* * * * * * * * * * *
2183 GGAGGGAGAGATTGAAGTCGTAATGATGAATCTCATACCTTAGAGATATGGAGGGAAAGGTTGAC
66 GGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAA
** **
2248 GCTACAACGGTGAACCT
131 GCCGCAACGGAAAACCT
* * * * * * * * *
2265 TGTGCCTTAGAGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTTGTACCATAGAGATAT
1 TATACCCTAAAGATATGAAGGGAAAGGTTGAAGCCACAACGGCGAACCTTATACCATAGAGATAT
* * *
2330 GGAGGGAAAGGTTGAAGACC-CAACGGCGAACCTTATACCCTAGAGATATGGAGGGAAAGTTTGA
66 GGAGGGAAAGGTTGAAG-CCGCAACGACGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGA
* * *
2394 AGCCGTAAC-GACGAATCT
130 AGCCGCAACGGA-AAACCT
* * ** * * *
2412 TTTACCCTAAAGATATGAAGGGAAAGGTT-ACA-CCGCAACGATGAATCTTATACCCTAAAGATA
1 TATACCCTAAAGATATGAAGGGAAAGGTTGA-AGCCACAACGGCGAACCTTATACCATAGAGATA
* * *
2475 TAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTA-AGGATGTGGAA-GGCAAGGTT
65 TGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTAGA-GATAT-GAAGGGAAAGGTT
** **
2538 GAAGCCGCAATAGCGAACCT
128 GAAGCCGCAACGGAAAACCT
* * * *
2558 TATAGCCTAGAA-ATGTGGAGGGAAAGATTGAAGCCACA
1 TATACCCTA-AAGATATGAAGGGAAAGGTTGAAGCCACA
2596 GAGGCAAATC
Statistics
Matches: 483, Mismatches: 131, Indels: 22
0.76 0.21 0.03
Matches are distributed among these distances:
145 3 0.01
146 109 0.23
147 369 0.76
148 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (147 bp):
TATACCCTAAAGATATGAAGGGAAAGGTTGAAGCCACAACGGCGAACCTTATACCATAGAGATAT
GGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTAGAGATATGAAGGGAAAGGTTGAA
GCCGCAACGGAAAACCT
Found at i:2191 original size:196 final size:195
Alignment explanation
Indices: 1883--2592 Score: 681
Period size: 196 Copynumber: 3.6 Consensus size: 195
1873 AATACCCTAA
* * * * *
1883 AGATGTGAAGGGAGAGATTAAAGCCGCAACGGCGAATCTCATACCCTAGAGATATGAAGGGAAAG
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
** * * * * * *
1948 GTTAAAGTTGCAACGGAAAACCTTATACCCTGGGGATATGAAGGGAGAGATTGAAGCCGCAACGG
66 GTTAAAG-CCCAACGGAGAACCTTATACCCTAGAGATATGGAGGGAGAGATTGAAGCCGTAACGA
* **
2013 CGAATCTCATACCGTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGACAAACCTTGTACCTTA
130 CGAATCTCATACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGATGAACCTTGTACCTTA
2078 G
195 G
* * * * * *
2079 AGATATGAAGGGAGAGATTGAAGCCGCAATAGCAAATCTCATACCCCAAAAATATGGAGGGAAAG
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * * * * *
2144 GTTAAAGCCACAATGGTGAACCTTGTACCTTAGAGATATGGAGGGAGAGATTGAAGTCGTAATGA
66 GTTAAAGCC-CAACGGAGAACCTTATACCCTAGAGATATGGAGGGAGAGATTGAAGCCGTAACGA
* * * ** * *
2209 TGAATCTCATACCTTAGAGATATGGAGGGAAAGGTTGACGCTACAACGGTGAACCTTGTGCCTTA
130 CGAATCTCATACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGATGAACCTTGTACCTTA
2274 G
195 G
* * * ** * ** *
2275 AGATATGGAGGGAAAGGTTGATGCCAAAATGGCGAACCTTGTACCATAGAGATATGGAGGGAAAG
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
* * * *
2340 GTTGAAGACCCAACGGCGAACCTTATACCCTAGAGATATGGAGGGAAAGTTTGAAGCCGTAACGA
66 GTTAAAG-CCCAACGGAGAACCTTATACCCTAGAGATATGGAGGGAGAGATTGAAGCCGTAACGA
** * * * * *
2405 CGAATCTTTTACCCTAAAGATATGAAGGGAAAGGTT-ACA-CCGCAACGATGAATCTTATACCCT
130 CGAATCTCATACCCTAGAGATATGGAGGGAAAGGTTGA-AGCCGCAACGATGAACCTTGTACCTT
*
2468 AA
194 AG
* * * * * * * *
2470 AGATAT-AGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCCTA-AGGATGTGGAAGGCA
1 AGATATGA-AGGGAAAGATTGAAGCCGCAATGGCGAATCTCATACCCTAGA-GATATGGAGGGAA
* ** * * * * *
2533 AGGTTGAAGCCGCAATAGCGAACCTTATAGCCTAGAAATGTGGAGGGAAAGATTGAAGCC
64 AGGTTAAAGCC-CAACGGAGAACCTTATACCCTAGAGATATGGAGGGAGAGATTGAAGCC
2593 ACAGAGGCAA
Statistics
Matches: 420, Mismatches: 88, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
194 3 0.01
195 119 0.28
196 296 0.70
197 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (195 bp):
AGATATGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTCATACCCTAGAGATATGGAGGGAAAG
GTTAAAGCCCAACGGAGAACCTTATACCCTAGAGATATGGAGGGAGAGATTGAAGCCGTAACGAC
GAATCTCATACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACGATGAACCTTGTACCTTAG
Found at i:2818 original size:45 final size:44
Alignment explanation
Indices: 2751--3010 Score: 234
Period size: 45 Copynumber: 5.9 Consensus size: 44
2741 TACATCACCT
*
2751 CATCCAATCTTTTACCCCTAGTCAAGAGAGGCAGATTGAAGCCAC
1 CATCCAATCTTTTA-CCCTAATCAAGAGAGGCAGATTGAAGCCAC
* * *
2796 CATCCAATCTTTTACCCTTAGTCAAGAGGGGCAGATTGAAGCTAC
1 CATCCAATCTTTTACCC-TAATCAAGAGAGGCAGATTGAAGCCAC
* * * * *
2841 CATCTAATCTTTTATCCCTAATAAAAAAAGGCAGATTGAAACCAC
1 CATCCAATCTTTTA-CCCTAATCAAGAGAGGCAGATTGAAGCCAC
* *
2886 CATCCAATCTTTTATCCCTAATCTAA-AGGGGAAGATTGAAG---C
1 CATCCAATCTTTTA-CCCTAATC-AAGAGAGGCAGATTGAAGCCAC
* * *
2928 TATCCAATCTTTTACCCCTAATCCAGATG-GGCAGATTAAAG-CA-
1 CATCCAATCTTTTA-CCCTAATCAAGA-GAGGCAGATTGAAGCCAC
2971 -ATCCAATCTTTTACCTCTAATTC-AGA-AGGGCAGATTGAAG
1 CATCCAATCTTTTACC-CTAA-TCAAGAGA-GGCAGATTGAAG
3011 TCACATACAA
Statistics
Matches: 182, Mismatches: 22, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
41 3 0.02
42 64 0.35
43 3 0.02
44 3 0.02
45 104 0.57
46 5 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (44 bp):
CATCCAATCTTTTACCCTAATCAAGAGAGGCAGATTGAAGCCAC
Found at i:2916 original size:90 final size:88
Alignment explanation
Indices: 2749--2949 Score: 264
Period size: 90 Copynumber: 2.3 Consensus size: 88
2739 GCTACATCAC
* * * * *
2749 CTCATCCAATCTTTTACCCCTAGTCAAGAGAGGCAGATTGAAGCCACCATCCAATCTTTTACCCT
1 CTCATCCAATCTTTTACCCCTAATAAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTACCCT
* *
2814 TAGTCAAGAGGGGCAGATTGAAG
66 TAATCAAGAGGGGAAGATTGAAG
* *
2837 CTACCATCTAATCTTTTATCCCTAATAAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTATC
1 CT--CATCCAATCTTTTACCCCTAATAAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTA-C
2902 CC-TAATCTAA-AGGGGAAGATTGAAG
63 CCTTAATC-AAGAGGGGAAGATTGAAG
2927 CT-ATCCAATCTTTTACCCCTAAT
1 CTCATCCAATCTTTTACCCCTAAT
2950 CCAGATGGGC
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
87 19 0.19
88 2 0.02
90 72 0.73
91 5 0.05
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (88 bp):
CTCATCCAATCTTTTACCCCTAATAAAAAAAGGCAGATTGAAACCACCATCCAATCTTTTACCCT
TAATCAAGAGGGGAAGATTGAAG
Done.