Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004784.1 Kokia drynarioides strain JFW-HI SEQ_118398, 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: 10493
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Found at i:652 original size:26 final size:26
Alignment explanation
Indices: 623--755 Score: 133
Period size: 26 Copynumber: 5.1 Consensus size: 26
613 CGTAAACAAT
* *
623 TAAATAGCATGCCTTGACCCGGTGAA
1 TAAATAGCAAGCCTTGAGCCGGTGAA
* * * *
649 TAAATAACAAGCCTTGAGTCGATGGA
1 TAAATAGCAAGCCTTGAGCCGGTGAA
* *
675 TATATAGCAAGCCTTGAGCCAGTGAA
1 TAAATAGCAAGCCTTGAGCCGGTGAA
* * *
701 TATATAGCAGGCCTTGAGTCGGTGAA
1 TAAATAGCAAGCCTTGAGCCGGTGAA
* *
727 TAAATAGC-AGGCTTCGAGCCGGTGTA
1 TAAATAGCAAGCCTT-GAGCCGGTGAA
753 TAA
1 TAA
756 TTGACAATTA
Statistics
Matches: 86, Mismatches: 20, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
25 4 0.05
26 82 0.95
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (26 bp):
TAAATAGCAAGCCTTGAGCCGGTGAA
Found at i:4698 original size:35 final size:35
Alignment explanation
Indices: 4655--4765 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
4645 CTAAGATCCG
4655 ATGAGCGTTGGGAGCATATTACTTCAGACATACCA
1 ATGAGCGTTGGGAGCATATTACTTCAGACATACCA
* * * * *
4690 ATGAGCGTTGGGCA-CACAGTCCTTCTGTA-ATACATA
1 ATGAGCGTTGGG-AGCATATTACTTCAG-ACATAC-CA
4726 GATGA-CTGTTGGGAGCATATTACTTCAGACATACCA
1 -ATGAGC-GTTGGGAGCATATTACTTCAGACATACCA
4762 ATGA
1 ATGA
4766 ACATTAGGTG
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
35 29 0.49
36 7 0.12
37 23 0.39
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (35 bp):
ATGAGCGTTGGGAGCATATTACTTCAGACATACCA
Found at i:4985 original size:21 final size:21
Alignment explanation
Indices: 4935--4996 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
4925 GTTAATAGCG
4935 GTTATAATATGAGTATGACAT
1 GTTATAATATGAGTATGACAT
**
4956 GTTACATAATATAGAG-ATGATGT
1 GTT--ATAATAT-GAGTATGACAT
*
4979 GTTATAACTATGAATATG
1 GTTATAA-TATGAGTATG
4997 GTAAACATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 9 0.27
22 6 0.18
23 15 0.45
24 3 0.09
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (21 bp):
GTTATAATATGAGTATGACAT
Found at i:6645 original size:24 final size:24
Alignment explanation
Indices: 6618--6686 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
6608 AATATTTATA
*
6618 CATTTTGTGTATTTA-AAATTTAAT
1 CATTTT-TATATTTAGAAATTTAAT
*
6642 CATTTTTATTTTTAGAAATTTAAT
1 CATTTTTATATTTAGAAATTTAAT
* *
6666 C-TTTTAATATTT-TAAATTTAA
1 CATTTTTATATTTAGAAATTTAA
6687 AAATTTATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 8 0.21
23 15 0.38
24 16 0.41
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
CATTTTTATATTTAGAAATTTAAT
Found at i:7024 original size:14 final size:13
Alignment explanation
Indices: 7005--7044 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
6995 GTTAAAATTA
7005 AAATTAAAGTATAT
1 AAATTAAA-TATAT
7019 AAATTAAATAT-T
1 AAATTAAATATAT
7031 AAATTTAAATATAT
1 AAA-TTAAATATAT
7045 TAAGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.17
13 11 0.46
14 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
AAATTAAATATAT
Found at i:7040 original size:13 final size:12
Alignment explanation
Indices: 6996--7042 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
6986 TCAATTTATG
6996 TTAAA-ATTAAAA
1 TTAAATATT-AAA
7008 TTAAAGTATATAAA
1 TTAAA-TAT-TAAA
7022 TTAAATATTAAA
1 TTAAATATTAAA
7034 TTTAAATAT
1 -TTAAATAT
7043 ATTAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.29
13 11 0.35
14 10 0.32
15 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TTAAATATTAAA
Found at i:8815 original size:19 final size:20
Alignment explanation
Indices: 8779--8825 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
8769 AAAACTTACA
*
8779 AAAAATTTAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
8798 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
8818 AAAAATTC
1 AAAAATTC
8826 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Done.