Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000460.1 Kokia drynarioides strain JFW-HI SEQ_111327, 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: 19899
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:46 original size:34 final size:32
Alignment explanation
Indices: 7--75 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1 TATTAA
*
7 ATAATAAATAGAT-AGTTAATGAACATATTAATAT
1 ATAATAAATA-ATAAGTAAAT--ACATATTAATAT
*
41 ATAATAAATAATAAGTAAATATATATTAATAT
1 ATAATAAATAATAAGTAAATACATATTAATAT
73 ATA
1 ATA
76 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.44
33 2 0.06
34 16 0.50
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (32 bp):
ATAATAAATAATAAGTAAATACATATTAATAT
Found at i:815 original size:17 final size:17
Alignment explanation
Indices: 773--819 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
763 TTTGAACTTT
** *
773 ATTTAAATGAATTTTAA
1 ATTTAAATTTATTATAA
790 ATTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
807 ATTTAAATTTATT
1 ATTTAAATTTATT
820 GGGCCCAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:1763 original size:22 final size:22
Alignment explanation
Indices: 1723--1783 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
1713 TGATCTAAGG
*
1723 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
1744 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
1766 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
1784 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:1774 original size:15 final size:16
Alignment explanation
Indices: 1749--1778 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1739 GAATTAAAAA
1749 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
1765 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
1779 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:7021 original size:21 final size:22
Alignment explanation
Indices: 6975--7035 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
6965 CGATCTAAGG
6975 AAAAATAAAAGAAACAT--AATT
1 AAAAATAAAAGAAA-ATAGAATT
6996 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
7018 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
7036 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 2 0.06
21 14 0.39
22 19 0.53
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:7028 original size:15 final size:16
Alignment explanation
Indices: 7001--7030 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6991 TAATTAAAAA
7001 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
7017 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
7031 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:13354 original size:20 final size:20
Alignment explanation
Indices: 13329--13368 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13319 TTTCCAGTAC
13329 AACAAGTTAAAAATTCTATG
1 AACAAGTTAAAAATTCTATG
13349 AACAAGTTAAAAATTCTATG
1 AACAAGTTAAAAATTCTATG
13369 TCTTGTGGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AACAAGTTAAAAATTCTATG
Found at i:17753 original size:18 final size:18
Alignment explanation
Indices: 17732--17798 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
17722 ATGCTCTTAT
*
17732 GAGCTAGTATGCTCAGAC
1 GAGCCAGTATGCTCAGAC
*
17750 GAGCCAATATGCTCAAGA-
1 GAGCCAGTATGCTC-AGAC
* * *
17768 AAGCCAGTTTGCTCAAAC
1 GAGCCAGTATGCTCAGAC
17786 GAGCCAGTATGCT
1 GAGCCAGTATGCT
17799 ATTCCCTTCG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 2 0.05
18 34 0.87
19 3 0.08
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (18 bp):
GAGCCAGTATGCTCAGAC
Done.