Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012166.1 Kokia drynarioides strain JFW-HI SEQ_127167, 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: 19889
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:6446 original size:30 final size:30
Alignment explanation
Indices: 6411--6479 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
6401 ATTTTTGAAG
6411 ACAGTGTGGGAGTGAAGTGAAAAATTAGTA
1 ACAGTGTGGGAGTGAAGTGAAAAATTAGTA
6441 ACAGTGTGGGAGTGAAGTGAAAAATTAGTA
1 ACAGTGTGGGAGTGAAGTGAAAAATTAGTA
*
6471 GCAGTGTGG
1 ACAGTGTGG
6480 AAGAAGAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.23
Consensus pattern (30 bp):
ACAGTGTGGGAGTGAAGTGAAAAATTAGTA
Found at i:7609 original size:19 final size:19
Alignment explanation
Indices: 7565--7610 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
7555 ATTTATTTTT
*
7565 AAAATT-AAAAATTATTAA
1 AAAATTAAAAAAATATTAA
*
7583 AATTATTAAAAAAATATTAA
1 AA-AATTAAAAAAATATTAA
7603 AAAATTAA
1 AAAATTAA
7611 TTACTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 8 0.35
20 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAAAAAATATTAA
Found at i:7613 original size:12 final size:11
Alignment explanation
Indices: 7571--7609 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
7561 TTTTAAAATT
7571 AAAAATTATT-
1 AAAAATTATTA
7581 -AAAATTATTA
1 AAAAATTATTA
*
7591 AAAAAATATTA
1 AAAAATTATTA
7602 AAAAATTA
1 AAAAATTA
7610 ATTACTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:10024 original size:11 final size:11
Alignment explanation
Indices: 10008--10037 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9998 GTTCGTGAAC
10008 ATGTTCGTTTA
1 ATGTTCGTTTA
10019 ATGTTCGTTTA
1 ATGTTCGTTTA
*
10030 ACGTTCGT
1 ATGTTCGT
10038 GAACATCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:10103 original size:24 final size:24
Alignment explanation
Indices: 10019--10103 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 24
10009 TGTTCGTTTA
** *
10019 ATGTTCGTTTA-ACGTTCGTGAAC
1 ATGTTCGTTTATGTGTTCGCGAAC
* **
10042 ATCTTCGTTTATGCATTCGCGAAC
1 ATGTTCGTTTATGTGTTCGCGAAC
10066 ATGTTCGTTTATGTGTTCGCGAAC
1 ATGTTCGTTTATGTGTTCGCGAAC
*
10090 ATGTTTGTTTATGT
1 ATGTTCGTTTATGT
10104 TAACTAACCA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 10 0.19
24 43 0.81
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (24 bp):
ATGTTCGTTTATGTGTTCGCGAAC
Found at i:11371 original size:20 final size:17
Alignment explanation
Indices: 11346--11384 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
11336 ATCATGTATG
11346 AAATTAAATAACATAAATGA
1 AAATTAAA-AA-AT-AATGA
11366 AAATTAAAAAATAATGA
1 AAATTAAAAAATAATGA
11383 AA
1 AA
11385 TAAAACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 2 0.11
20 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAATAATGA
Found at i:14661 original size:12 final size:12
Alignment explanation
Indices: 14617--14671 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
14607 TAAATAGGCT
14617 TTAAACGAGCT-
1 TTAAACGAGCTA
* *
14628 TATAAATGAG-TT
1 T-TAAACGAGCTA
*
14640 TTATACGAGCTA
1 TTAAACGAGCTA
14652 TTAAACGAGCTA
1 TTAAACGAGCTA
*
14664 ATAAACGA
1 TTAAACGA
14672 ATCATAAACG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (12 bp):
TTAAACGAGCTA
Found at i:14683 original size:35 final size:35
Alignment explanation
Indices: 14617--14685 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
14607 TAAATAGGCT
* * * ** *
14617 TTAAACGAGCTTATAAATGAGTTTTATACGAGCTA
1 TTAAACGAGCTAATAAACGAATCATAAACGAGCTA
14652 TTAAACGAGCTAATAAACGAATCATAAACGAGCT
1 TTAAACGAGCTAATAAACGAATCATAAACGAGCT
14686 TGTTTGTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (35 bp):
TTAAACGAGCTAATAAACGAATCATAAACGAGCTA
Found at i:15722 original size:16 final size:16
Alignment explanation
Indices: 15712--15771 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
15702 AATTTGAATA
15712 ATTTTGGATTTAAATT
1 ATTTTGGATTTAAATT
* * *
15728 ATTTTGGGTTTGAATC
1 ATTTTGGATTTAAATT
* **
15744 GTTTTAAATTTAAATT
1 ATTTTGGATTTAAATT
15760 ATTTTGGATTTA
1 ATTTTGGATTTA
15772 GGTTAAATGA
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (16 bp):
ATTTTGGATTTAAATT
Found at i:15740 original size:32 final size:32
Alignment explanation
Indices: 15704--15766 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
15694 TGATTTCGAA
**
15704 TTTGAATAATTTTGGATTTAAATTATTTTGGG
1 TTTGAATAATTTTAAATTTAAATTATTTTGGG
**
15736 TTTGAATCGTTTTAAATTTAAATTATTTTGG
1 TTTGAATAATTTTAAATTTAAATTATTTTGG
15767 ATTTAGGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.54
Consensus pattern (32 bp):
TTTGAATAATTTTAAATTTAAATTATTTTGGG
Found at i:17662 original size:59 final size:59
Alignment explanation
Indices: 17507--17663 Score: 185
Period size: 59 Copynumber: 2.7 Consensus size: 59
17497 TAAGTATCTG
* *
17507 AACTTGAC-ATATTTTCCTAATTTGGTACCTAAAT-TTTTTTGGGTCAAATTTGGTACCTA
1 AACTTGACTAT-TTTTCTTAATTTGGTACCT-AATCTTTTTGGGGTCAAATTTGGTACCTA
* ** * * *
17566 AACTTGA-TAGTTTTTCTTAAGTTAATACTTAAACTTTTTGGGGTCCAATTTGGTACCTA
1 AACTTGACTA-TTTTTCTTAATTTGGTACCTAATCTTTTTGGGGTCAAATTTGGTACCTA
*
17625 AACTTGACTATTTTTCTTAATTTGGTGCCTAATCTTTTT
1 AACTTGACTATTTTTCTTAATTTGGTACCTAATCTTTTT
17664 TTTTTTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.03
59 75 0.94
60 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (59 bp):
AACTTGACTATTTTTCTTAATTTGGTACCTAATCTTTTTGGGGTCAAATTTGGTACCTA
Found at i:18137 original size:30 final size:29
Alignment explanation
Indices: 18042--18141 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
18032 ATAAATTTAG
* * *
18042 ATACCAAATTAGTAAAAAGTGTCAAATTTAA
1 ATACCAAATTA--AAAAAATATCAAATTCAA
* * *
18073 ATATCAAATTGAAACAAAA-A-AAAATTTCAG
1 ATACCAAATT-AAA-AAAATATCAAA-TTCAA
18103 ATACCAAATTAAAAAAATTATCAAATTCAA
1 ATACCAAATTAAAAAAA-TATCAAATTCAA
18133 ATACCAAAT
1 ATACCAAAT
18142 ATTATATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
28 4 0.07
29 6 0.11
30 28 0.52
31 15 0.28
32 1 0.02
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (29 bp):
ATACCAAATTAAAAAAATATCAAATTCAA
Found at i:19279 original size:68 final size:68
Alignment explanation
Indices: 19170--19304 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 68
19160 GGATGGTGTG
**
19170 TGTCAGCTGATGGCACTCCTGAAGTTGGCCTGAAGAGGTTAGACAATGGGTCTGCAAAATGTGAT
1 TGTCAGCTGATGGCACTCCTGAAGTTGGCCTGAAGAGGTTAGACAATAAGTCTGCAAAATGTGAT
19235 GGA
66 GGA
* * *
19238 TGTCAGCTTATGGCACTCTTGAAGTTGGCCTTAAGAGGTTAGACAATAAGTCTGCAAAATGTGAT
1 TGTCAGCTGATGGCACTCCTGAAGTTGGCCTGAAGAGGTTAGACAATAAGTCTGCAAAATGTGAT
19303 GG
66 GG
19305 GTTGATTAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (68 bp):
TGTCAGCTGATGGCACTCCTGAAGTTGGCCTGAAGAGGTTAGACAATAAGTCTGCAAAATGTGAT
GGA
Done.