Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003839.1 Kokia drynarioides strain JFW-HI SEQ_116858, 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: 24531
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:958 original size:13 final size:13
Alignment explanation
Indices: 940--964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
930 GGATGCAATG
940 TATGATATCAGTA
1 TATGATATCAGTA
953 TATGATATCAGT
1 TATGATATCAGT
965 GTTGGCGTAC
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TATGATATCAGTA
Found at i:3266 original size:21 final size:21
Alignment explanation
Indices: 3242--3292 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3232 TAGAAGTAAA
* *
3242 ACTTGTTTCGGTAAAAGAGTC
1 ACTTGTATCGGTAAAACAGTC
* *
3263 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAAAACAGTC
3284 ACTTGTATC
1 ACTTGTATC
3293 AGTAGAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAAAACAGTC
Found at i:3297 original size:21 final size:21
Alignment explanation
Indices: 3260--3299 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3250 CGGTAAAAGA
*
3260 GTCACTTGTATCGGTAGAACT
1 GTCACTTGTATCAGTAGAACT
3281 GTCACTTGTATCAGTAGAA
1 GTCACTTGTATCAGTAGAA
3300 GTCTACACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GTCACTTGTATCAGTAGAACT
Found at i:11144 original size:7 final size:7
Alignment explanation
Indices: 11132--11160 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
11122 ATGTAGAATG
11132 CTCTAGC
1 CTCTAGC
11139 CTCTAGC
1 CTCTAGC
11146 CTCTAGC
1 CTCTAGC
11153 CTCTAGC
1 CTCTAGC
11160 C
1 C
11161 ATGTTCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.28
Consensus pattern (7 bp):
CTCTAGC
Found at i:11681 original size:16 final size:17
Alignment explanation
Indices: 11660--11694 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11650 AATGGATGAT
11660 AATAAATTT-TTAATTA
1 AATAAATTTATTAATTA
11676 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
11694 A
1 A
11695 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:12252 original size:39 final size:39
Alignment explanation
Indices: 12203--12281 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
12193 AACAGAATTT
* *
12203 AACGGCACAGTGATCACTTCGTAACAAAATATTAACATA
1 AACGGCACAGTGATCACTTCATAACAAAATACTAACATA
*
12242 AACGGTACAGTGATCACTTCATAACAAAATACTAACATA
1 AACGGCACAGTGATCACTTCATAACAAAATACTAACATA
12281 A
1 A
12282 GTGATTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (39 bp):
AACGGCACAGTGATCACTTCATAACAAAATACTAACATA
Found at i:17327 original size:12 final size:14
Alignment explanation
Indices: 17310--17341 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
17300 GCTCCCATTG
17310 CTCTTTCTC-T-TT
1 CTCTTTCTCGTGTT
17322 CTCTTTCTCGTGTT
1 CTCTTTCTCGTGTT
17336 CTCTTT
1 CTCTTT
17342 TGTCCTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.06, T:0.62
Consensus pattern (14 bp):
CTCTTTCTCGTGTT
Done.