Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013702.1 Kokia drynarioides strain JFW-HI SEQ_128730, 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: 51135
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2226 original size:20 final size:21
Alignment explanation
Indices: 2187--2226 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2177 TTGAAACAAT
*
2187 TTTTAAATCAAGTTAAAATGA
1 TTTTAAATCAAGTCAAAATGA
*
2208 TTTTAAA-CATGTCAAAATG
1 TTTTAAATCAAGTCAAAATG
2227 CTTACACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAATCAAGTCAAAATGA
Found at i:5303 original size:29 final size:29
Alignment explanation
Indices: 5259--5331 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
5249 AAATAGTTCA
*
5259 AAGACTAAATTACAAAAAAGCAAAAGTAC
1 AAGACTAAATTCCAAAAAAGCAAAAGTAC
* * *
5288 AAGACTAAATTCC-AAAAAGTAAATGTGC
1 AAGACTAAATTCCAAAAAAGCAAAAGTAC
5316 AAGGACTAAATTCCAA
1 AA-GACTAAATTCCAA
5332 GTTTGTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 14 0.37
29 23 0.61
30 1 0.03
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (29 bp):
AAGACTAAATTCCAAAAAAGCAAAAGTAC
Found at i:15871 original size:2 final size:2
Alignment explanation
Indices: 15864--15904 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
15854 CTATTAAATT
15864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15905 GTGTGTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16260 original size:28 final size:29
Alignment explanation
Indices: 16190--16253 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
16180 AATTTTAAAA
* *
16190 TTAATAATGATAAATTTTTATTTTGATATT
1 TTAA-AATGATAAATTTTTAATTTAATATT
16220 TTAAAATGATAAA-TTTTAATTTAAT-TT
1 TTAAAATGATAAATTTTTAATTTAATATT
16247 TTAAAAT
1 TTAAAAT
16254 TTATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 9 0.28
28 10 0.31
29 9 0.28
30 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAAAATGATAAATTTTTAATTTAATATT
Found at i:16262 original size:29 final size:29
Alignment explanation
Indices: 16190--16262 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
16180 AATTTTAAAA
* * *
16190 TTAATAATGATAAATTTTTATTTTGATATT
1 TTAA-AATGATAAAATTTTAATTTAATATT
16220 TTAAAATGAT-AAATTTTAATTTAAT-TT
1 TTAAAATGATAAAATTTTAATTTAATATT
*
16247 TTAAAATTTATAAAAT
1 TTAAAA-TGATAAAAT
16263 ATAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 8 0.22
28 15 0.41
29 10 0.27
30 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
TTAAAATGATAAAATTTTAATTTAATATT
Found at i:19503 original size:2 final size:2
Alignment explanation
Indices: 19496--19526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19486 TTTTCAGGCA
19496 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19527 TATATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27029 original size:21 final size:19
Alignment explanation
Indices: 27005--27056 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
26995 ATTATAGAAA
27005 TAAAATTTAAAGTTACTAAAT
1 TAAAATTTAAAG--ACTAAAT
* *
27026 TAAAATATAAAGATTAAAT
1 TAAAATTTAAAGACTAAAT
27045 TATAAATTTAAA
1 TA-AAATTTAAA
27057 ATTGTATAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 8 0.30
21 11 0.41
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (19 bp):
TAAAATTTAAAGACTAAAT
Found at i:29929 original size:17 final size:16
Alignment explanation
Indices: 29893--29934 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
29883 AATATAAAAA
29893 ATAAAAAATATAATTT
1 ATAAAAAATATAATTT
29909 -TAAAAAATAT-ATTT
1 ATAAAAAATATAATTT
29923 AGATAAAAAATA
1 --ATAAAAAATA
29935 AAATCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
17 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATAAAAAATATAATTT
Found at i:35573 original size:24 final size:26
Alignment explanation
Indices: 35546--35593 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
35536 AGAGAAATGT
35546 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
35570 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
35594 CGCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:35701 original size:23 final size:23
Alignment explanation
Indices: 35675--35732 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
35665 TCAGTACTGT
35675 GTGTGCTTACTGTTTCGCACCTC
1 GTGTGCTTACTGTTTCGCACCTC
35698 GTGTGCTTACTGTTTCGCACCTC
1 GTGTGCTTACTGTTTCGCACCTC
*
35721 GTGTGCCTACTG
1 GTGTGCTTACTG
35733 ATTTACGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.29, G:0.24, T:0.38
Consensus pattern (23 bp):
GTGTGCTTACTGTTTCGCACCTC
Found at i:37051 original size:13 final size:14
Alignment explanation
Indices: 37033--37072 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
37023 ATATAAAGAA
37033 TATTATTTAAAAT-
1 TATTATTTAAAATC
37046 TATTATTTTAAAATC
1 TATTA-TTTAAAATC
37061 TATTA-TTAAAAT
1 TATTATTTAAAAT
37073 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.48
14 8 0.32
15 5 0.20
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATTTAAAATC
Found at i:37066 original size:15 final size:14
Alignment explanation
Indices: 37033--37067 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
37023 ATATAAAGAA
37033 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
37046 TATTATTTTAAAAT
1 TATTATTTTAAAAT
37060 CTATTATT
1 -TATTATT
37068 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:48653 original size:20 final size:20
Alignment explanation
Indices: 48628--48674 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
48618 TTTAGAATTT
*
48628 TTTTTTATAAA-TGTTTTGAA
1 TTTTTTA-AAACTATTTTGAA
48648 TTTTTTAAAACTATTTTGAA
1 TTTTTTAAAACTATTTTGAA
48668 TTATTTT
1 TT-TTTT
48675 TGTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 17 0.71
21 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTTTAAAACTATTTTGAA
Done.