Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000924.1 Kokia drynarioides strain JFW-HI SEQ_112073, 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: 90430
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:697 original size:21 final size:22
Alignment explanation
Indices: 644--697 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
634 ATTAGCACTA
644 ACTCTCTGATTAGCACTTTGTGT
1 ACTCTCTG-TTAGCACTTTGTGT
* * *
667 GCTCTTTGTTAGTACTTTG-GT
1 ACTCTCTGTTAGCACTTTGTGT
688 ACTCTCTGTT
1 ACTCTCTGTT
698 CGTTCCGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (22 bp):
ACTCTCTGTTAGCACTTTGTGT
Found at i:2293 original size:13 final size:13
Alignment explanation
Indices: 2275--2299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2265 TAAGTTAAAA
2275 ATGCTAAAAATGC
1 ATGCTAAAAATGC
2288 ATGCTAAAAATG
1 ATGCTAAAAATG
2300 GTAAAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:17665 original size:15 final size:15
Alignment explanation
Indices: 17632--17666 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17622 CCAGAATTGC
*
17632 AAAAAAAAGAAAAAT
1 AAAAAAAAGAAAAAG
*
17647 AAAAAAAAGAAGAAG
1 AAAAAAAAGAAAAAG
17662 AAAAA
1 AAAAA
17667 GATGAGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:18888 original size:22 final size:22
Alignment explanation
Indices: 18844--18889 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18834 TCTTTGTAAT
*
18844 TTAGGTTTAATTATTTCTTTTC
1 TTAGGTTTAATTATTTCTGTTC
*
18866 TTAGGTTTTAGTTATTT-TGTTC
1 TTAGG-TTTAATTATTTCTGTTC
18888 TT
1 TT
18890 TTTTTATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (22 bp):
TTAGGTTTAATTATTTCTGTTC
Found at i:21013 original size:31 final size:31
Alignment explanation
Indices: 20962--21023 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20952 ATAAGTTATC
* **
20962 GTTGTCGGGCAATCTGAGGTAACGAGTCATT
1 GTTGTCGAGCAATCCAAGGTAACGAGTCATT
**
20993 GTTGTCGAGCAATCCAAGGTAGTGAGTCATT
1 GTTGTCGAGCAATCCAAGGTAACGAGTCATT
21024 ATTTTCAAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (31 bp):
GTTGTCGAGCAATCCAAGGTAACGAGTCATT
Found at i:24325 original size:10 final size:12
Alignment explanation
Indices: 24297--24328 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24287 TGAAAAACAT
24297 AAAATAAAAGAG
1 AAAATAAAAGAG
24309 AAAATAAAAG-G
1 AAAATAAAAGAG
24320 -AAATAAAAG
1 AAAATAAAAG
24329 TAAGATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:29384 original size:145 final size:145
Alignment explanation
Indices: 29168--29461 Score: 543
Period size: 145 Copynumber: 2.0 Consensus size: 145
29158 CTTGGTTCCT
29168 TGGGTAACCTGCAGGCTCAATCACTTCTTGGAATGCACTAGCAACATAGTTTGTTTTGCGCTTTA
1 TGGGTAACCTGCAGGCTCAATCACTTCTTGGAATGCACTAGCAACATAGTTTGTTTTGCGCTTTA
* *
29233 ACCCTCGGACAATGAATGTTTGTCTCCGAAATGATATTACATCTTATCATCAGTTGGATGATGAG
66 ACCCTCGGACAATGAATGTTTGTCTCCGAAATGATATTACATCTTATCATCAGGTAGATGATGAG
*
29298 AATCTTTACACCACA
131 AATCTTCACACCACA
*
29313 TGGGTAACCTGCAGGCTCAATTACTTCTTGGAATGCACTAGCAACATAGTTTGTTTTGCGCTTTA
1 TGGGTAACCTGCAGGCTCAATCACTTCTTGGAATGCACTAGCAACATAGTTTGTTTTGCGCTTTA
*
29378 ATCCTCGGACAATGAATGTTTGTCTCCGAAATGATATTACATCTTATCATCAGGTAGATGATGAG
66 ACCCTCGGACAATGAATGTTTGTCTCCGAAATGATATTACATCTTATCATCAGGTAGATGATGAG
29443 AATCTTCACACCACA
131 AATCTTCACACCACA
29458 TGGG
1 TGGG
29462 AACGTTATAA
Statistics
Matches: 144, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (145 bp):
TGGGTAACCTGCAGGCTCAATCACTTCTTGGAATGCACTAGCAACATAGTTTGTTTTGCGCTTTA
ACCCTCGGACAATGAATGTTTGTCTCCGAAATGATATTACATCTTATCATCAGGTAGATGATGAG
AATCTTCACACCACA
Found at i:39160 original size:20 final size:22
Alignment explanation
Indices: 39121--39164 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
39111 CAAACAACAA
39121 AAGAACAAAATAACTAAAACCT
1 AAGAACAAAATAACTAAAACCT
*
39143 AAGAA-AAAATAA-TTAAACCT
1 AAGAACAAAATAACTAAAACCT
39163 AA
1 AA
39165 ATTACAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.66, C:0.14, G:0.05, T:0.16
Consensus pattern (22 bp):
AAGAACAAAATAACTAAAACCT
Found at i:51079 original size:20 final size:21
Alignment explanation
Indices: 51056--51094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51046 CATGCATTTA
*
51056 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
51076 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
51095 TGCTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:65463 original size:34 final size:33
Alignment explanation
Indices: 65420--65483 Score: 119
Period size: 34 Copynumber: 1.9 Consensus size: 33
65410 AAAGCACTTA
65420 GATTCTTGGGTCACGTAGTATCTTCGAGAAGTTC
1 GATTCTTGGGTCACGTAGTATCTTC-AGAAGTTC
65454 GATTCTTGGGTCACGTAGTATCTTCAGAAG
1 GATTCTTGGGTCACGTAGTATCTTCAGAAG
65484 GAATAAGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (33 bp):
GATTCTTGGGTCACGTAGTATCTTCAGAAGTTC
Found at i:72446 original size:12 final size:12
Alignment explanation
Indices: 72416--72451 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
72406 ATGACCAGCT
72416 GAAGGAA-AAG-
1 GAAGGAAGAAGA
72426 GAA-GAAGAAGA
1 GAAGGAAGAAGA
72437 GAAGGAAGAAGA
1 GAAGGAAGAAGA
72449 GAA
1 GAA
72452 TAAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 3 0.13
12 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAGGAAGAAGA
Found at i:78155 original size:22 final size:23
Alignment explanation
Indices: 78125--78170 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
78115 ACTTTCATCA
*
78125 TTAAGCTTTGATT-AACC-ATTTT
1 TTAACCTTT-ATTAAACCTATTTT
78147 TTAACCTTTATTAAACCTATTTT
1 TTAACCTTTATTAAACCTATTTT
78170 T
1 T
78171 AATCAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.57
23 6 0.29
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAACCTTTATTAAACCTATTTT
Found at i:82758 original size:26 final size:26
Alignment explanation
Indices: 82657--82757 Score: 103
Period size: 26 Copynumber: 3.9 Consensus size: 26
82647 ATTCTGGGAG
* *
82657 CAATTCTGGACATGCTCATACAGCGA
1 CAATTCTGGACATGCTCATGCAGCAA
* * *
82683 CAACTCTGAACATGTTCATGCAGCAA
1 CAATTCTGGACATGCTCATGCAGCAA
* * * * *
82709 TAATTCTGGACAAGTTCCTGCAGTAA
1 CAATTCTGGACATGCTCATGCAGCAA
*
82735 CAATTCTAGACATGCTCATGCAG
1 CAATTCTGGACATGCTCATGCAG
82758 TGACATTAGT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAGCAA
Done.