Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008068.1 Kokia drynarioides strain JFW-HI SEQ_122724, 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: 64299
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2014 original size:28 final size:28
Alignment explanation
Indices: 1974--2042 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
1964 CAAACTACAG
1974 TAAGTGGCGAGCTTCCATAAATGAACAA
1 TAAGTGGCGAGCTTCCATAAATGAACAA
* *
2002 TAAGTGGCGAGCTTTCATAAATGAACAG
1 TAAGTGGCGAGCTTCCATAAATGAACAA
*
2030 TAAGTGGTGAGCT
1 TAAGTGGCGAGCT
2043 CATTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (28 bp):
TAAGTGGCGAGCTTCCATAAATGAACAA
Found at i:14046 original size:85 final size:85
Alignment explanation
Indices: 13922--14103 Score: 244
Period size: 85 Copynumber: 2.1 Consensus size: 85
13912 TTTTTCAAAC
* *
13922 TGTCTCTTCTAACTCAATACTTACGTTATTATCCTATGATTTCTCCATCTTTTGAGA-TGTTGCT
1 TGTC-CTTCTAACTCAATACTTACGTTATCATCCTATGATTCCTCCATCTTTTGAGACT-TTG-T
*
13986 -TCACTTCACCTTTCCATTAGCA
63 ATCACTGCACCTTTCCATTAGCA
* **
14008 TTTCCTTCTAACTCAATACTCTTTG-TATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTAT
1 TGTCCTTCTAACTCAATACT-TACGTTATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTAT
14072 CACTGCACCTTTCCATTAGCA
65 CACTGCACCTTTCCATTAGCA
*
14093 TGTCCTACTAA
1 TGTCCTTCTAA
14104 TACATCACAA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
84 1 0.01
85 78 0.92
86 6 0.07
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.43
Consensus pattern (85 bp):
TGTCCTTCTAACTCAATACTTACGTTATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTATC
ACTGCACCTTTCCATTAGCA
Found at i:19374 original size:2 final size:2
Alignment explanation
Indices: 19367--19397 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19357 TTTGGGAAGC
*
19367 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19398 TGATATTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35119 original size:21 final size:21
Alignment explanation
Indices: 35095--35144 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35085 CCATTTGCAA
35095 CTGAGTTGTGCTACTCACTTG
1 CTGAGTTGTGCTACTCACTTG
* *
35116 CTGAGATGTGCTGCTCACTTG
1 CTGAGTTGTGCTACTCACTTG
35137 CTGAGTTG
1 CTGAGTTG
35145 GGGCCCTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (21 bp):
CTGAGTTGTGCTACTCACTTG
Found at i:35958 original size:24 final size:24
Alignment explanation
Indices: 35893--35960 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
35883 AAGTTTAAGG
35893 TATTAAAAAAAAGCATACAAAACAA
1 TATT-AAAAAAAGCATACAAAACAA
* * *
35918 -AATAAAGAACAA-TATACAAAATAA
1 TATTAAA-AA-AAGCATACAAAACAA
35942 TATTAAAAAAAGCATACAA
1 TATTAAAAAAAGCATACAA
35961 GTCAGAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 5 0.15
24 22 0.65
25 7 0.21
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (24 bp):
TATTAAAAAAAGCATACAAAACAA
Found at i:41586 original size:17 final size:19
Alignment explanation
Indices: 41564--41606 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41554 CCGGTTCTAT
*
41564 ATAAAA-AT-TATTTAAAA
1 ATAAAATATCTATATAAAA
*
41581 ATAAAATTTCTATATAAAA
1 ATAAAATATCTATATAAAA
41600 ATAAAAT
1 ATAAAAT
41607 CTCGAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATATCTATATAAAA
Found at i:42958 original size:7 final size:7
Alignment explanation
Indices: 42942--42983 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
42932 CTCCTACTTG
*
42942 ATTTTGT
1 ATTTTTT
42949 ATTTTTT
1 ATTTTTT
42956 ATTTTATT
1 ATTTT-TT
42964 -TTATTTT
1 ATT-TTTT
42971 ATTTTTT
1 ATTTTTT
42978 ATTTTT
1 ATTTTT
42984 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:42970 original size:17 final size:17
Alignment explanation
Indices: 42948--42982 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42938 CTTGATTTTG
42948 TATTTT-TTATTTTATTT
1 TATTTTATT-TTTTATTT
42965 TATTTTATTTTTTATTT
1 TATTTTATTTTTTATTT
42982 T
1 T
42983 TAATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TATTTTATTTTTTATTT
Found at i:43166 original size:69 final size:72
Alignment explanation
Indices: 43084--43222 Score: 212
Period size: 69 Copynumber: 2.0 Consensus size: 72
43074 AATATGCATT
** *
43084 TGTTTCAAACTTTTTTAATTTTTAATTAATGTTTATAATTAATAAATATA-T-TT-TCAGGTTTT
1 TGTTTCAAACTTTTTTAATTTTTAATTAATACTTATAATTAATAAATATATTGTTGTCAAGTTTT
43146 AAACATG
66 AAACATG
* *
43153 TGTTTCAAGCTTTTTTTATTTTTAATTAATACTTATAATTAATAAATATATTGTTGTCAAGTTTT
1 TGTTTCAAACTTTTTTAATTTTTAATTAATACTTATAATTAATAAATATATTGTTGTCAAGTTTT
43218 AAACA
66 AAACA
43223 ATATAAAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
69 46 0.74
70 1 0.02
71 2 0.03
72 13 0.21
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (72 bp):
TGTTTCAAACTTTTTTAATTTTTAATTAATACTTATAATTAATAAATATATTGTTGTCAAGTTTT
AAACATG
Found at i:51315 original size:31 final size:31
Alignment explanation
Indices: 51280--51342 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
51270 AAAGCTCCGC
* *
51280 AATTTAT-AAGCTTGATTAAACCCCAATAACA
1 AATTTATGAA-CTTCATGAAACCCCAATAACA
*
51311 AATTTATGAACTTCATGAAGCCCCAATAACA
1 AATTTATGAACTTCATGAAACCCCAATAACA
51342 A
1 A
51343 TTCAAAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (31 bp):
AATTTATGAACTTCATGAAACCCCAATAACA
Found at i:61426 original size:17 final size:16
Alignment explanation
Indices: 61404--61439 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
61394 TAATTATATT
61404 TATTTTTATGATAATTA
1 TATTTTTAT-ATAATTA
*
61421 TATTTTTATTTAATTA
1 TATTTTTATATAATTA
61437 TAT
1 TAT
61440 GTGTTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTTTATATAATTA
Done.