Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008713.1 Kokia drynarioides strain JFW-HI SEQ_123395, 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: 30293
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:266 original size:19 final size:21
Alignment explanation
Indices: 226--266 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
216 GCAAGTTCTT
226 TAATTTTATTAAAATAATTAA
1 TAATTTTATTAAAATAATTAA
247 TAATTTT-TTAAAAT-ATTAA
1 TAATTTTATTAAAATAATTAA
266 T
1 T
267 CTCATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTTATTAAAATAATTAA
Found at i:4174 original size:16 final size:16
Alignment explanation
Indices: 4153--4183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4143 CTATGCATGC
*
4153 AAAATATAAAAGACAA
1 AAAATAAAAAAGACAA
4169 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
4184 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAA
Found at i:4674 original size:21 final size:19
Alignment explanation
Indices: 4648--4702 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
4638 AAAAAATTTT
4648 TATTTTTAATATTTTAAATA
1 TATTTTTAATATTTTAAA-A
* *
4668 CTATTTTGAATTTTTTAAAA
1 -TATTTTTAATATTTTAAAA
* *
4688 TTTTTTTAATGTTTT
1 TATTTTTAATATTTT
4703 TGAATTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 1 0.03
21 16 0.55
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TATTTTTAATATTTTAAAA
Found at i:6627 original size:15 final size:15
Alignment explanation
Indices: 6590--6633 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
6580 ACTCTCAAAT
6590 TTTCTTTTTCCTTTTCA
1 TTTC-TTTTCC-TTTCA
**
6607 AATCTTTTCCTTTCA
1 TTTCTTTTCCTTTCA
6622 TTTCTTTTCCTT
1 TTTCTTTTCCTT
6634 GCATATACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 15 0.65
16 6 0.26
17 2 0.09
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTCTTTTCCTTTCA
Found at i:14003 original size:15 final size:16
Alignment explanation
Indices: 13971--14008 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13961 AACCTGAAAC
*
13971 TGAAAAAGCTTGAGCT
1 TGAAAAAGCTTGAACT
*
13987 TGAAAAATC-TGAACT
1 TGAAAAAGCTTGAACT
14002 TGAAAAA
1 TGAAAAA
14009 AACCCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (16 bp):
TGAAAAAGCTTGAACT
Found at i:21746 original size:21 final size:21
Alignment explanation
Indices: 21720--21760 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
21710 CCCCTTCTCT
21720 ACCACCACCTCTTCCTCCTCC
1 ACCACCACCTCTTCCTCCTCC
21741 ACCACCACCTCTTCCTCCTC
1 ACCACCACCTCTTCCTCCTC
21761 AACTCTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.61, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCACCACCTCTTCCTCCTCC
Found at i:28053 original size:35 final size:35
Alignment explanation
Indices: 28007--28087 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
27997 TAGATTGAAG
28007 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
28042 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
28077 TGGTTGGTGAG
1 TGGTTGGTGAG
28088 ATGGTGGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.36, C:0.00, G:0.42, T:0.22
Consensus pattern (35 bp):
TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
Done.