Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009921.1 Kokia drynarioides strain JFW-HI SEQ_124661, 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: 30640
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:29 original size:4 final size:4
Alignment explanation
Indices: 22--60 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
12 TTCTTCCTTC
*
22 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
61 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:49 original size:21 final size:20
Alignment explanation
Indices: 20--64 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
10 CCTTCTTCCT
20 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
41 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
61 -CTTC
1 TCTTC
65 AATTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:5555 original size:28 final size:28
Alignment explanation
Indices: 5492--5560 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
5482 GAAAAATATT
* *
5492 AAATTAAATTAATTTTTTAATTATTTTTA
1 AAATTAAATT-ATTTTCTAATTATTTTAA
*
5521 AAA-TAAATTATTTTCTCATT-TTATTAA
1 AAATTAAATTATTTTCTAATTATT-TTAA
*
5548 AAATTAAAATATT
1 AAATTAAATTATT
5561 CAAATTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.06
27 15 0.44
28 14 0.41
29 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATTAAATTATTTTCTAATTATTTTAA
Found at i:9879 original size:73 final size:73
Alignment explanation
Indices: 9760--9906 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
9750 TACTTTAAAC
*
9760 ACAAATTACACTAGTAACCAAACGAGGCATAAGTACTTTAAACAAGACCAACTGCTTCCCCCAAT
1 ACAAATTACACTAGTAACCAAACGAGGCATAAGCACTTTAAACAAGACCAACTGCTTCCCCCAAT
9825 AACCTGCA
66 AACCTGCA
9833 ACAAATTACACTAGTAACCAAACGAGGCATAAGCACTTTAAACAAGACCAACTGCTTCCCCCAAT
1 ACAAATTACACTAGTAACCAAACGAGGCATAAGCACTTTAAACAAGACCAACTGCTTCCCCCAAT
9898 AACCTGCA
66 AACCTGCA
9906 A
1 A
9907 TGATCTTAGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.18
Consensus pattern (73 bp):
ACAAATTACACTAGTAACCAAACGAGGCATAAGCACTTTAAACAAGACCAACTGCTTCCCCCAAT
AACCTGCA
Found at i:13859 original size:26 final size:28
Alignment explanation
Indices: 13806--13859 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
13796 AATTTATTAT
*
13806 TAAAATATTAATATAAAATACTTTTCAA
1 TAAAATATTAATATAAAATACTATTCAA
*
13834 TAAAATATTAA-A-AATATACTATTCAA
1 TAAAATATTAATATAAAATACTATTCAA
13860 GCATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 1 0.04
28 11 0.46
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAAATATTAATATAAAATACTATTCAA
Found at i:21853 original size:18 final size:19
Alignment explanation
Indices: 21812--21854 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21802 AAAAAAAAAA
*
21812 ACAAAATTCAAAATAATTT
1 ACAAAAATCAAAATAATTT
*
21831 TCAAAAATCAAAAT-ATTT
1 ACAAAAATCAAAATAATTT
21849 ACAAAA
1 ACAAAA
21855 TATTTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (19 bp):
ACAAAAATCAAAATAATTT
Done.