Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012997.1 Kokia drynarioides strain JFW-HI SEQ_128015, 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: 47182
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2099 original size:21 final size:20
Alignment explanation
Indices: 2038--2100 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
2028 CTAGTTATGT
*
2038 TTTCGAGTTTTGAATTTCAAA
1 TTTCG-GTTTTGAATTTCAAG
*
2059 TTTTGGTTTCTGAA-TTCAAG
1 TTTCGGTTT-TGAATTTCAAG
2079 TTTCGGATTTTGAATTTCAAG
1 TTTCGG-TTTTGAATTTCAAG
2100 T
1 T
2101 AGCAATGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (20 bp):
TTTCGGTTTTGAATTTCAAG
Found at i:3607 original size:16 final size:16
Alignment explanation
Indices: 3588--3619 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3578 TAAAATTTTA
*
3588 TAAATTATAAAAAAAT
1 TAAATTAAAAAAAAAT
3604 TAAATTAAAAAAAAAT
1 TAAATTAAAAAAAAAT
3620 CATTTTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAATTAAAAAAAAAT
Found at i:9120 original size:26 final size:26
Alignment explanation
Indices: 9091--9142 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9081 TCACTAATGA
9091 TAAAAATTAAAATATGATATAAGTCT
1 TAAAAATTAAAATATGATATAAGTCT
9117 TAAAAATTAAAATATGATATAAGTCT
1 TAAAAATTAAAATATGATATAAGTCT
9143 CTGTACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (26 bp):
TAAAAATTAAAATATGATATAAGTCT
Found at i:9744 original size:78 final size:78
Alignment explanation
Indices: 9642--9799 Score: 264
Period size: 78 Copynumber: 2.0 Consensus size: 78
9632 GGACATAAGG
* *
9642 TCTTAAACAAAAAAAAACATATGATTTGAATTAAATATGAGCAAACATAAAAATTAAAAAATTAA
1 TCTTAAACAAAAAAAAACATATGATTTGAACTAAATACGAGCAAACATAAAAATTAAAAAATT-A
*
9707 AAAATCAATTGAAA
65 AAAACCAATTGAAA
*
9721 TCTTAAAC-AAAAAAAACATATGATTTGAACTAAATACGAGCAAACATAAAAATTTAAAAATTAA
1 TCTTAAACAAAAAAAAACATATGATTTGAACTAAATACGAGCAAACATAAAAATTAAAAAATTAA
9785 AAACCAATTGAAA
66 AAACCAATTGAAA
9798 TC
1 TC
9800 GTTCTGTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
77 16 0.21
78 51 0.68
79 8 0.11
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (78 bp):
TCTTAAACAAAAAAAAACATATGATTTGAACTAAATACGAGCAAACATAAAAATTAAAAAATTAA
AAACCAATTGAAA
Found at i:10155 original size:31 final size:31
Alignment explanation
Indices: 10117--10197 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
10107 ACAGAAAAAA
*
10117 AAATTTGGGTACCAAATTGAACGTTGAAGTC
1 AAATTTGGGTACCAAATTGAACGTTGAAGCC
*
10148 AAATTTGGGTACCAAATTGAATGTTGAAGCC
1 AAATTTGGGTACCAAATTGAACGTTGAAGCC
** *
10179 AAATCCGAGTACCAAATTG
1 AAATTTGGGTACCAAATTG
10198 GGACAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (31 bp):
AAATTTGGGTACCAAATTGAACGTTGAAGCC
Found at i:14968 original size:13 final size:14
Alignment explanation
Indices: 14951--14983 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
14941 ATTTTAATTT
*
14951 TATTTTAATAATAA
1 TATTTTAAAAATAA
14965 -ATTTTAAAAATAA
1 TATTTTAAAAATAA
14978 TATTTT
1 TATTTT
14984 TCACATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTTTAAAAATAA
Found at i:15032 original size:15 final size:15
Alignment explanation
Indices: 15012--15063 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
15002 ATTCAATATT
15012 AATATTTTAATAATA
1 AATATTTTAATAATA
*
15027 AATATTTATAACAATTATA
1 AATATTT-T---AATAATA
*
15046 AATATATTAATAATA
1 AATATTTTAATAATA
15061 AAT
1 AAT
15064 GTTTGTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 16 0.53
16 1 0.03
18 1 0.03
19 12 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17865 original size:31 final size:29
Alignment explanation
Indices: 17808--17878 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
17798 AATTTTGGCC
* *
17808 CTTGAACTTAGCAACTATGTCTACTTTAAT
1 CTTGAACTTGGCAACTAGGTCTACTTT-AT
*
17838 ACTTGAACTTGGCAATTAGGT-TCACTTTAT
1 -CTTGAACTTGGCAACTAGGTCT-ACTTTAT
17868 CTTTGAACTTG
1 C-TTGAACTTG
17879 AAAAATTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 12 0.34
31 22 0.63
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (29 bp):
CTTGAACTTGGCAACTAGGTCTACTTTAT
Found at i:38992 original size:4 final size:4
Alignment explanation
Indices: 38983--39033 Score: 88
Period size: 4 Copynumber: 13.2 Consensus size: 4
38973 ACATTAAAAA
38983 ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACA- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
39029 ACAT A
1 ACAT A
39034 TGCATACCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 6 0.13
4 39 0.87
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:41292 original size:4 final size:4
Alignment explanation
Indices: 41278--41342 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
41268 AAATAAACGG
* * * *
41278 GAAA AAAA GAAA GAAAA GAAG GAAA GAAA G-AA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
41327 G-AA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
41343 GTACTGTGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
3 6 0.12
4 37 0.73
5 8 0.16
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:41320 original size:20 final size:18
Alignment explanation
Indices: 41283--41342 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 18
41273 AACGGGAAAA
41283 AAAGAAAGAA-AAGAAGG
1 AAAGAAAGAAGAAGAAGG
41300 AAAGAAAGAAGAAGGAGAGG
1 AAAGAAAGAAGAA-GA-AGG
*
41320 AAAGAAAGAAGAAAGAAAG
1 AAAGAAAGAAG-AAGAAGG
41339 AAAG
1 AAAG
41343 GTACTGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
17 10 0.26
18 2 0.05
19 8 0.21
20 16 0.42
21 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGAAGAAGG
Found at i:41416 original size:19 final size:20
Alignment explanation
Indices: 41394--41436 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
41384 TTTAAAATCG
*
41394 TATTTTATTTATTAA-AT-TT
1 TATTTAATTT-TTAACATATT
41413 TATTTAATTTTTAACATATT
1 TATTTAATTTTTAACATATT
41433 TATT
1 TATT
41437 GAAGATGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTAATTTTTAACATATT
Found at i:44783 original size:21 final size:21
Alignment explanation
Indices: 44761--44799 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44751 GTCCATTTGC
*
44761 CCCG-GAGGAGTAGAGTATTG
1 CCCGAGAGGAATAGAGTATTG
44781 CCCGAGAGGAATAGAGTAT
1 CCCGAGAGGAATAGAGTAT
44800 CGCGATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.36, T:0.18
Consensus pattern (21 bp):
CCCGAGAGGAATAGAGTATTG
Found at i:44924 original size:45 final size:45
Alignment explanation
Indices: 44794--44930 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
44784 GAGAGGAATA
* * * * * **
44794 GAGTATCGCGATGGTTCGTCAAACTCAGCCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAAGACTGATATCCTTGGCTT
* * *
44839 GAGTATTGTGGTGGCTCGTCAAATTGAGACTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAAGACTGATATCCTTGGCTT
**
44884 GAGTATTGCGGTGGCTCGTCAAACTAAGGTTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAAGACTGATATCCTTGGCTT
44929 GA
1 GA
44931 TGAGCTATGC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTAAGACTGATATCCTTGGCTT
Found at i:46888 original size:16 final size:16
Alignment explanation
Indices: 46867--46916 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
46857 TGATGGGGAT
46867 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
46883 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
46898 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
46913 ATTA
1 ATTA
46917 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Done.