Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002531.1 Kokia drynarioides strain JFW-HI SEQ_114705, 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: 23210
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:1962 original size:5 final size:5
Alignment explanation
Indices: 1954--1979 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1944 ATAAACGAAG
1954 TGATT TGATT TGATT TGATT TGATT T
1 TGATT TGATT TGATT TGATT TGATT T
1980 TATAAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TGATT
Found at i:3110 original size:2 final size:2
Alignment explanation
Indices: 3103--3134 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3093 TCACATATCC
3103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3135 GGTTCAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7060 original size:6 final size:6
Alignment explanation
Indices: 7049--7082 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
7039 CCTCAACCAG
*
7049 AGCCTC AGCCTC AGCCTC AGCCTC AGCCTG AGCC
1 AGCCTC AGCCTC AGCCTC AGCCTC AGCCTC AGCC
7083 AGAGAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.15
Consensus pattern (6 bp):
AGCCTC
Found at i:7061 original size:18 final size:18
Alignment explanation
Indices: 7038--7077 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7028 CAAGGATCGT
*
7038 GCCTCAACCAGAGCCTCA
1 GCCTCAACCACAGCCTCA
* *
7056 GCCTCAGCCTCAGCCTCA
1 GCCTCAACCACAGCCTCA
7074 GCCT
1 GCCT
7078 GAGCCAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.47, G:0.17, T:0.15
Consensus pattern (18 bp):
GCCTCAACCACAGCCTCA
Found at i:17099 original size:161 final size:159
Alignment explanation
Indices: 16728--17207 Score: 852
Period size: 161 Copynumber: 3.0 Consensus size: 159
16718 CTTGATTCCT
* * * * *
16728 AAGTTCTTGCATGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAACGAGTAAAATT
1 AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
*
16793 AAATGGAGTTAGTATTTTGAGTTGCAAGTTTGTAATTGTATAAATTGTGATTGATTTGTATGTAT
66 AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTGTATAAATTGTGATTGATTTGTATGTAT
*
16858 TTAAAAAAAAGACTCGAAAAGTTCTTTAA
131 TTAAAAAAAAGACTCGAAAAGTTCTATAA
16887 AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
1 AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
*
16952 AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTGTATAAATTATGATTGATTTGTATGTAT
66 AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTGTATAAATTGTGATTGATTTGTATGTA-
17017 TTTAAAAAAAAAGACTCGAAAAGTTCTATAA
130 TTT-AAAAAAAAGACTCGAAAAGTTCTATAA
17048 AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
1 AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
*
17113 AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTATATAAATTGTGATTGATTTGTATGTAT
66 AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTGTATAAATTGTGATTGATTTGTATGTAT
*
17178 TTAAAAAAAAGACTCGAAAAGTTCTGTAA
131 TTAAAAAAAAGACTCGAAAAGTTCTATAA
17207 A
1 A
17208 CCTTGAGACC
Statistics
Matches: 308, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
159 149 0.48
160 6 0.02
161 153 0.50
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (159 bp):
AAGTTCTCGCGTGATTGAATTTGATTCTTGATTGATTGAAAGGTTATAAATGAATGTGTAAGATT
AAATGGAGTTAGTATTCTGAGTTGCAAGTTTGTAATTGTATAAATTGTGATTGATTTGTATGTAT
TTAAAAAAAAGACTCGAAAAGTTCTATAA
Found at i:17946 original size:12 final size:12
Alignment explanation
Indices: 17929--17964 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
17919 CACAATCCAC
*
17929 CATTTCATATTT
1 CATTTCACATTT
17941 CATTTCACATTT
1 CATTTCACATTT
17953 CATTTC-CATTT
1 CATTTCACATTT
17964 C
1 C
17965 TCATCTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTTCACATTT
Found at i:18832 original size:52 final size:52
Alignment explanation
Indices: 18768--18944 Score: 255
Period size: 52 Copynumber: 3.4 Consensus size: 52
18758 ATTTCATTTA
* * * ** *
18768 ATACTCACGATGACTCATAGTCATCAGACCTCTTGTTCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
* * *
18820 ACACTCACGATGACAAATAGTCATTAGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
* *
18872 ATACTCACGATGACACATAATCATTAGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
18924 ATACTCACGATGACACATAGT
1 ATACTCACGATGACACATAGT
18945 TATCGGACTT
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
Found at i:20626 original size:18 final size:19
Alignment explanation
Indices: 20585--20626 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
20575 TTCTTCTCCC
20585 TTTTTGTTTACGAAAGAAA
1 TTTTTGTTTACGAAAGAAA
20604 TTTTTGTTTACGAAAGAAA
1 TTTTTGTTTACGAAAGAAA
20623 TTTT
1 TTTT
20627 GAAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (19 bp):
TTTTTGTTTACGAAAGAAA
Found at i:21199 original size:59 final size:59
Alignment explanation
Indices: 21123--21259 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
21113 AACCTTAGGA
* *
21123 ACCAAATTAGGGAAAAAATGCCAAGTT-TAGGTACCAAATTGGGTCCAAAAAAAGTTTATGT
1 ACCAAAGTA-GGAAAAAATGCCAAGTTCT-GCTACCAAATTGGGT-CAAAAAAAGTTTATGT
* *
21184 ACCAAAGTATGAAAAAATGTCAAGTTCTGCTACCAAATTGGGTCAAAAAAAGTTTATGT
1 ACCAAAGTAGGAAAAAATGCCAAGTTCTGCTACCAAATTGGGTCAAAAAAAGTTTATGT
*
21243 ACCAAATTAGGAAAAAA
1 ACCAAAGTAGGAAAAAA
21260 AATGTTAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 31 0.45
60 29 0.42
61 9 0.13
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (59 bp):
ACCAAAGTAGGAAAAAATGCCAAGTTCTGCTACCAAATTGGGTCAAAAAAAGTTTATGT
Found at i:21271 original size:61 final size:61
Alignment explanation
Indices: 21123--21282 Score: 211
Period size: 61 Copynumber: 2.6 Consensus size: 61
21113 AACCTTAGGA
* *
21123 ACCAAATTAGGGAAAAAATGCCAAGTT-TAGGTACCAAATTGGGTCCAAAAAAAGTTTATGT
1 ACCAAATTA-GGAAAAAATGTCAAGTTCTAGCTACCAAATTGGGTCCAAAAAAAGTTTATGT
* *
21184 ACCAAAGTATGAAAAAATGTCAAGTTCT-GCTACCAAATTGGGT-CAAAAAAAGTTTATGT
1 ACCAAATTAGGAAAAAATGTCAAGTTCTAGCTACCAAATTGGGTCCAAAAAAAGTTTATGT
* *
21243 ACCAAATTAGGAAAAAAAATGTTAAGTTCAAG-TACCAAAT
1 ACCAAATTAGG--AAAAAATGTCAAGTTCTAGCTACCAAAT
21283 GTTATATTAA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 25 0.29
60 29 0.33
61 32 0.37
62 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (61 bp):
ACCAAATTAGGAAAAAATGTCAAGTTCTAGCTACCAAATTGGGTCCAAAAAAAGTTTATGT
Done.