Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007307.1 Kokia drynarioides strain JFW-HI SEQ_121923, 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: 34189
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:871 original size:21 final size:20
Alignment explanation
Indices: 834--872 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
824 CTTGAGAAGT
*
834 ATATTTTACATCCAAAAATA
1 ATATTTTACATCAAAAAATA
*
854 ATATTTATACATTAAAAAA
1 ATATTT-TACATCAAAAAA
873 AATTACATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATTTTACATCAAAAAATA
Found at i:9848 original size:2 final size:2
Alignment explanation
Indices: 9841--9873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9831 CACTATACTT
9841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9874 CAACCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10742 original size:82 final size:82
Alignment explanation
Indices: 10615--10765 Score: 248
Period size: 82 Copynumber: 1.8 Consensus size: 82
10605 GTGAGTCCAA
* * *
10615 CTTTAGTTGAATTAACCAACAAATAATCCGTCAAATCTTGGCACCCAGTGCCTAGCGAATAAACC
1 CTTTAATTGAATTAACCAACAAATAATCCGTCAAATCCTGACACCCAGTGCCTAGCGAATAAACC
10680 GCAATTAGTGAGCTCAG
66 GCAATTAGTGAGCTCAG
* * *
10697 CTTTAATTGGATTAACCAACAAATAATCTGTCAAATCCTGACACCCAGTGCCTAGCGGATAAACC
1 CTTTAATTGAATTAACCAACAAATAATCCGTCAAATCCTGACACCCAGTGCCTAGCGAATAAACC
10762 GCAA
66 GCAA
10766 ATGTGTGTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (82 bp):
CTTTAATTGAATTAACCAACAAATAATCCGTCAAATCCTGACACCCAGTGCCTAGCGAATAAACC
GCAATTAGTGAGCTCAG
Found at i:13112 original size:42 final size:43
Alignment explanation
Indices: 13066--13155 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
13056 AACTTGTTAC
* * *
13066 TTTTTTTCTTCT-AAATTTAAATTTAA-AACTTATTAATTTCAT
1 TTTTTTTCTTATAAAATTTAAA-ATAACAACTTATTAATTTCAA
13108 TTTTTTTCTTATAAAATTTAAAATAACAACTTATTAATTTCAA
1 TTTTTTTCTTATAAAATTTAAAATAACAACTTATTAATTTCAA
13151 TTTTT
1 TTTTT
13156 CTTGTCTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 14 0.33
43 29 0.67
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (43 bp):
TTTTTTTCTTATAAAATTTAAAATAACAACTTATTAATTTCAA
Found at i:13569 original size:22 final size:22
Alignment explanation
Indices: 13543--13604 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
13533 TCATTAACAT
13543 TGTTCATGAACATGTTCAATTA
1 TGTTCATGAACATGTTCAATTA
* * *
13565 TGTTCGTGAACATATTCGATTA
1 TGTTCATGAACATGTTCAATTA
* *
13587 AGTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
13605 GTGAACATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (22 bp):
TGTTCATGAACATGTTCAATTA
Found at i:14191 original size:41 final size:41
Alignment explanation
Indices: 14124--14209 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
14114 TAGTGTAACC
* **
14124 GAATAAATTGTGATATTAATTGTACAATCATAGAT-TCAATT
1 GAATAAAATGTGATATTAATCATACAATCATAGATCT-AATT
* *
14165 GAATAAAATGT-ATAATTAATCATACAATTATTGATCTAATT
1 GAATAAAATGTGAT-ATTAATCATACAATCATAGATCTAATT
14206 GAAT
1 GAAT
14210 TGGTTCGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 2 0.05
41 35 0.92
42 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (41 bp):
GAATAAAATGTGATATTAATCATACAATCATAGATCTAATT
Found at i:22853 original size:9 final size:9
Alignment explanation
Indices: 22841--22882 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
22831 TTAAAATTTT
22841 AAAATTAAA
1 AAAATTAAA
*
22850 AAAATTATA
1 AAAATTAAA
22859 AAAATTCAAA
1 AAAATT-AAA
22869 AAAATTAAA
1 AAAATTAAA
22878 AAAAT
1 AAAAT
22883 GAATTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:22855 original size:17 final size:19
Alignment explanation
Indices: 22841--22882 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
22831 TTAAAATTTT
22841 AAAATT-AAAAAAATTATA
1 AAAATTCAAAAAAATTATA
*
22859 AAAATTCAAAAAAATTAAA
1 AAAATTCAAAAAAATTATA
22878 AAAAT
1 AAAAT
22883 GAATTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATTCAAAAAAATTATA
Found at i:25697 original size:42 final size:43
Alignment explanation
Indices: 25639--25740 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 43
25629 TAGTGGATGG
*
25639 TTTCCACGTAGCTTCCTTCTTTATCATTTCTTGGAA-GTGG-TT
1 TTTCCACGTAACTTCCTTCTTTATCATTTCTT-GAATGTGGCTT
* * *
25681 TTTCCACGTAATTTCCTTCTTTGTCGTTTCTTGAATGTGGCTT
1 TTTCCACGTAACTTCCTTCTTTATCATTTCTTGAATGTGGCTT
*
25724 TTTCCACATAACTTCCT
1 TTTCCACGTAACTTCCT
25741 CCTTCTTGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.06
42 32 0.62
43 17 0.33
ACGTcount: A:0.15, C:0.24, G:0.14, T:0.48
Consensus pattern (43 bp):
TTTCCACGTAACTTCCTTCTTTATCATTTCTTGAATGTGGCTT
Done.