Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000613.1 Kokia drynarioides strain JFW-HI SEQ_111565, 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: 62958
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:4476 original size:29 final size:30
Alignment explanation
Indices: 4434--4513 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
4424 GAGTTAGATC
*
4434 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
* *
4464 AAATCAAAGTTCATGTTTACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
* *
4495 AAACCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
4514 GTTTAGGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.50
30 5 0.12
31 16 0.38
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:10622 original size:18 final size:17
Alignment explanation
Indices: 10600--10642 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
10590 TTTAATTCGG
10600 GTAATTTGGTTAATTCAA
1 GTAATTTGG-TAATTCAA
* *
10618 TTAATTCAGGTAATTCAA
1 GTAATT-TGGTAATTCAA
10636 GTAATTT
1 GTAATTT
10643 TTTATACTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (17 bp):
GTAATTTGGTAATTCAA
Found at i:11129 original size:2 final size:2
Alignment explanation
Indices: 11122--11147 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11112 TTCAGCAATC
11122 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11148 ATTAGAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16378 original size:18 final size:18
Alignment explanation
Indices: 16355--16389 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16345 AAACCCCTTT
16355 TTTTTTTTTCTTTTTTTC
1 TTTTTTTTTCTTTTTTTC
16373 TTTTTTTTTCTTTTTTT
1 TTTTTTTTTCTTTTTTT
16390 GTTGGTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTTTC
Found at i:19961 original size:22 final size:22
Alignment explanation
Indices: 19936--19978 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19926 TAAGAGTCAT
*
19936 ATAATATTGAAACAATAACAAC
1 ATAATAGTGAAACAATAACAAC
**
19958 ATAATAGTGAAATGATAACAA
1 ATAATAGTGAAACAATAACAA
19979 AACAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAATAGTGAAACAATAACAAC
Found at i:20555 original size:23 final size:25
Alignment explanation
Indices: 20529--20589 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 25
20519 AAATAAATTT
*
20529 AATATACTTTATTGATTA-A-TATA
1 AATATAATTTATTGATTATACTATA
* *
20552 AATACAATTTATTTATTATTACTATA
1 AATATAATTTATTGATTA-TACTATA
20578 AATATAAATTTA
1 AATAT-AATTTA
20590 ATGAGTTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 15 0.50
25 1 0.03
26 8 0.27
27 6 0.20
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (25 bp):
AATATAATTTATTGATTATACTATA
Found at i:26171 original size:45 final size:45
Alignment explanation
Indices: 26107--26197 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
26097 AAGCACCCGT
26107 GTCCGGCACATATGCAAACAAAGGTACCGGGATATGATCCTCCAA
1 GTCCGGCACATATGCAAACAAAGGTACCGGGATATGATCCTCCAA
26152 GTCCGGCACATATGCAAACAAAGGTACCGGGATATGATCCTCCAA
1 GTCCGGCACATATGCAAACAAAGGTACCGGGATATGATCCTCCAA
26197 G
1 G
26198 GACATATCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (45 bp):
GTCCGGCACATATGCAAACAAAGGTACCGGGATATGATCCTCCAA
Found at i:41213 original size:10 final size:10
Alignment explanation
Indices: 41182--41235 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
41172 GAAATTTTAG
41182 AAAAATTATT
1 AAAAATTATT
*
41192 AATAATTA-T
1 AAAAATTATT
*
41201 AAAAAATATT
1 AAAAATTATT
*
41211 AAAAAGTTAAT
1 AAAAA-TTATT
*
41222 CAAAATTATT
1 AAAAATTATT
41232 AAAA
1 AAAA
41236 TATACAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 7 0.21
10 20 0.59
11 7 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:56646 original size:6 final size:6
Alignment explanation
Indices: 56635--56666 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
56625 CTAATTTTTG
*
56635 TTCGTC TTCGTC TTCGTC TTCGTC TTTGTC TT
1 TTCGTC TTCGTC TTCGTC TTCGTC TTCGTC TT
56667 GAGGTCTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.28, G:0.16, T:0.56
Consensus pattern (6 bp):
TTCGTC
Found at i:56919 original size:24 final size:24
Alignment explanation
Indices: 56887--56969 Score: 166
Period size: 24 Copynumber: 3.5 Consensus size: 24
56877 TTATAGAGCT
56887 TGGATGGAACTCGGAAGTGCTCTA
1 TGGATGGAACTCGGAAGTGCTCTA
56911 TGGATGGAACTCGGAAGTGCTCTA
1 TGGATGGAACTCGGAAGTGCTCTA
56935 TGGATGGAACTCGGAAGTGCTCTA
1 TGGATGGAACTCGGAAGTGCTCTA
56959 TGGATGGAACT
1 TGGATGGAACT
56970 TGATGATAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (24 bp):
TGGATGGAACTCGGAAGTGCTCTA
Done.