Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008779.1 Kokia drynarioides strain JFW-HI SEQ_123462, 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: 17823
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:2730 original size:6 final size:6
Alignment explanation
Indices: 2709--2743 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2699 TTATTTAATT
*
2709 ATCTCA AT-TAA ATCTCA ATCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
2744 TAATATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCTCA
Found at i:13942 original size:99 final size:99
Alignment explanation
Indices: 13716--13993 Score: 495
Period size: 99 Copynumber: 2.8 Consensus size: 99
13706 TCAGAGACCT
* * *
13716 ACACATATAATTGCTCATGGTGAGTCTCGAACCCAGGTACTTAGGACCAGGGCCTCTGCCTTTG-
1 ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTCTGCCTTCGC
13780 CAACATGGCATAGCTTATGGTGGCACTAAGACGC
66 CAACATGGCATAGCTTATGGTGGCACTAAGACGC
13814 ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTCTGCCTTCGC
1 ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTCTGCCTTCGC
* *
13879 CAACATGGCATAGCTTATGGTGGCTCTGAGACGC
66 CAACATGGCATAGCTTATGGTGGCACTAAGACGC
*
13913 ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTGTGCCTTCGC
1 ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTCTGCCTTCGC
13978 CAACATGGCATAGCTT
66 CAACATGGCATAGCTT
13994 TGTTGAATGA
Statistics
Matches: 173, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 61 0.35
99 112 0.65
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (99 bp):
ACACATATAATTGCTCATGGTGAGTCTCGAACCCCGGTACTTAAGACCAGGGCCTCTGCCTTCGC
CAACATGGCATAGCTTATGGTGGCACTAAGACGC
Found at i:16865 original size:13 final size:13
Alignment explanation
Indices: 16849--16887 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
16839 ATATTATTAT
*
16849 TATATAATAATAA
1 TATATAAAAATAA
16862 TATATAAAAATAA
1 TATATAAAAATAA
*
16875 TATATAAATATAA
1 TATATAAAAATAA
16888 AAATATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATAAAAATAA
Found at i:16875 original size:16 final size:16
Alignment explanation
Indices: 16852--16952 Score: 53
Period size: 18 Copynumber: 5.9 Consensus size: 16
16842 TTATTATTAT
*
16852 ATAATAATAATATATAA
1 ATAATAAT-ATATAAAA
*
16869 A-AATAATATATAAAT
1 ATAATAATATATAAAA
*
16884 ATAAAAATATATCAAATA
1 ATAATAATATAT-AAA-A
* * *
16902 TTTAGAATATATATAAA
1 ATAATAATATATA-AAA
*
16919 ATAA-AATAGATATAATAT
1 ATAATAAT--ATATAA-AA
16937 ATAAATAATATATAAA
1 AT-AATAATATATAAA
16953 TAAATTGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 7 0.11
16 18 0.28
17 10 0.15
18 25 0.38
19 2 0.03
20 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAATAATATATAAAA
Found at i:16876 original size:19 final size:19
Alignment explanation
Indices: 16852--16954 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 19
16842 TTATTATTAT
16852 ATAATA-ATAATATATAAAA
1 ATAATATATAA-ATATAAAA
16871 ATAATATATAAATATAAAA
1 ATAATATATAAATATAAAA
* * *
16890 AT-ATAT-CAAATATTTAGA
1 ATAATATATAAATA-TAAAA
16908 AT-ATATATAAA-AT-AAA
1 ATAATATATAAATATAAAA
* *
16924 AT-AGATAT-AATATATAA
1 ATAATATATAAATATAAAA
16941 ATAATATATAAATA
1 ATAATATATAAATA
16955 AATTGAATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.03
16 11 0.16
17 10 0.14
18 19 0.28
19 23 0.33
20 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATATATAAATATAAAA
Found at i:16921 original size:11 final size:11
Alignment explanation
Indices: 16849--16952 Score: 53
Period size: 10 Copynumber: 9.7 Consensus size: 11
16839 ATATTATTAT
16849 TATATAATAATAA
1 TATATAA-AAT-A
16862 TATATAAAA-A
1 TATATAAAATA
*
16872 TA-AT-ATATA
1 TATATAAAATA
*
16881 AATATAAAA-A
1 TATATAAAATA
*
16891 TATATCAAATA
1 TATATAAAATA
*
16902 T-T-TAGAATA
1 TATATAAAATA
16911 TATATAAAATA
1 TATATAAAATA
* *
16922 -AAAT-AGATA
1 TATATAAAATA
16931 TAATATATAAATAA
1 T-ATATA-AAAT-A
16945 TATATAAA
1 TATATAAA
16953 TAAATTGAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 23
0.66 0.12 0.22
Matches are distributed among these distances:
8 2 0.03
9 14 0.21
10 18 0.26
11 13 0.19
12 4 0.06
13 15 0.22
14 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (11 bp):
TATATAAAATA
Found at i:16925 original size:34 final size:33
Alignment explanation
Indices: 16858--16990 Score: 101
Period size: 34 Copynumber: 3.8 Consensus size: 33
16848 TTATATAATA
*
16858 ATAATATATAAAAATAATATATAAATATAAAA-ATAT
1 ATAATATAT--AAAT-ATATATAAA-ATAAAATAGAT
*
16894 ATCAAATATTTAGAATATATATAAAATAAAATAGAT
1 AT--AATATATA-AATATATATAAAATAAAATAGAT
*
16930 ATAATATATAAATA-ATATATAAAT-AAATTGAAT
1 ATAATATATAAATATATATA-AAATAAAATAG-AT
* * *
16963 ATAATATTATACATATAAATAAATTAAA
1 ATAATA-TATAAATATATATAAAATAAA
16991 CCAAAAGAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 19
0.76 0.07 0.18
Matches are distributed among these distances:
32 10 0.12
33 16 0.20
34 17 0.21
35 12 0.15
36 17 0.21
37 3 0.04
38 6 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (33 bp):
ATAATATATAAATATATATAAAATAAAATAGAT
Found at i:16947 original size:36 final size:35
Alignment explanation
Indices: 16858--16954 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 35
16848 TTATATAATA
*
16858 ATAATATATAAAAATAATATATAAATATAAAAATAT
1 ATAATATATAAAAAT-ATATATAAATATAAAAAGAT
* *
16894 ATCAA-ATATTTAGAATATATATAAA-ATAAAATAGAT
1 AT-AATATA-TAAAAATATATATAAATATAAAA-AGAT
*
16930 ATAATATATAAATA-ATATATAAATA
1 ATAATATATAAAAATATATATAAATA
16955 AATTGAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
34 9 0.18
35 12 0.24
36 22 0.44
37 7 0.14
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (35 bp):
ATAATATATAAAAATATATATAAATATAAAAAGAT
Found at i:16953 original size:11 final size:11
Alignment explanation
Indices: 16857--16955 Score: 79
Period size: 11 Copynumber: 9.5 Consensus size: 11
16847 ATTATATAAT
16857 AATAATATATA
1 AATAATATATA
16868 AA-AATA-ATA
1 AATAATATATA
*
16877 TATAA-ATATA
1 AATAATATATA
16887 AA-AATATATCA
1 AATAATATAT-A
16898 AAT-AT-T-TA
1 AATAATATATA
16906 GAAT-ATATATAA
1 -AATAATATAT-A
* *
16918 AATAAAATAGA
1 AATAATATATA
*
16929 TATAATATATA
1 AATAATATATA
16940 AATAATATATA
1 AATAATATATA
16951 AATAA
1 AATAA
16956 ATTGAATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
8 1 0.01
9 13 0.19
10 16 0.23
11 35 0.50
12 5 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAATATATA
Done.