Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012958.1 Kokia drynarioides strain JFW-HI SEQ_127976, 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: 48838
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 360 characters in sequence are not A, C, G, or T
Found at i:9551 original size:29 final size:29
Alignment explanation
Indices: 9518--9575 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9508 TATTTTTTGC
9518 ATCAGCTATTAAGAAGCCTTAGAGATGAA
1 ATCAGCTATTAAGAAGCCTTAGAGATGAA
9547 ATCAGCTATTAAGAAGCCTTAGAGATGAA
1 ATCAGCTATTAAGAAGCCTTAGAGATGAA
9576 CATATTCGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (29 bp):
ATCAGCTATTAAGAAGCCTTAGAGATGAA
Found at i:12917 original size:50 final size:50
Alignment explanation
Indices: 12858--12957 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
12848 TTTTAATCCG
12858 AAAACAAAATGATATTATACTACTATGGATGTTACTTTTTCAGAAAACAT
1 AAAACAAAATGATATTATACTACTATGGATGTTACTTTTTCAGAAAACAT
12908 AAAACAAAATGATATTATACTACTATGGATGTTACTTTTTCAGAAAACAT
1 AAAACAAAATGATATTATACTACTATGGATGTTACTTTTTCAGAAAACAT
12958 TCCCTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (50 bp):
AAAACAAAATGATATTATACTACTATGGATGTTACTTTTTCAGAAAACAT
Found at i:13391 original size:15 final size:15
Alignment explanation
Indices: 13371--13401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13361 TTGTCTCTTC
13371 CTACTCTATCTGAAT
1 CTACTCTATCTGAAT
*
13386 CTACTCTTTCTGAAT
1 CTACTCTATCTGAAT
13401 C
1 C
13402 CAACAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (15 bp):
CTACTCTATCTGAAT
Found at i:18383 original size:24 final size:24
Alignment explanation
Indices: 18303--18371 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
18293 AATCTTTCTG
*
18303 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
18327 TTAAACTTTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
18351 TTAAACTCTATTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
18372 GAGTCAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:34069 original size:26 final size:26
Alignment explanation
Indices: 34040--34122 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
34030 TAAAAGAGAT
34040 GTAAGTTCATGTAGTATTATCAGAAA
1 GTAAGTTCATGTAGTATTATCAGAAA
* ** * ** *
34066 GTAAACTTCAT-TCTTGTTAAAAGAGAT
1 GT-AAGTTCATGTAGTATTATCAGA-AA
34093 GTAAGTTCATGTAGTATTATCAGAAA
1 GTAAGTTCATGTAGTATTATCAGAAA
34119 GTAA
1 GTAA
34123 ACTTCATTCT
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
26 22 0.55
27 18 0.45
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (26 bp):
GTAAGTTCATGTAGTATTATCAGAAA
Found at i:34075 original size:27 final size:27
Alignment explanation
Indices: 34045--34129 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
34035 GAGATGTAAG
34045 TTCATGTAGTATTATCAGAAAGTAAAC
1 TTCATGTAGTATTATCAGAAAGTAAAC
** * ** * *
34072 TTCAT-TCTTGTTAAAAGAGATGT-AAG
1 TTCATGTAGTATTATCAGA-AAGTAAAC
34098 TTCATGTAGTATTATCAGAAAGTAAAC
1 TTCATGTAGTATTATCAGAAAGTAAAC
34125 TTCAT
1 TTCAT
34130 TCTTGTTACT
Statistics
Matches: 41, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
26 18 0.44
27 23 0.56
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (27 bp):
TTCATGTAGTATTATCAGAAAGTAAAC
Found at i:34110 original size:53 final size:53
Alignment explanation
Indices: 34030--34137 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
34020 AAGAGAAAAG
34030 TAAAAGAGATGTAAGTTCATGTAGTATTATCAGAAAGTAAACTTCATTCTTGT
1 TAAAAGAGATGTAAGTTCATGTAGTATTATCAGAAAGTAAACTTCATTCTTGT
34083 TAAAAGAGATGTAAGTTCATGTAGTATTATCAGAAAGTAAACTTCATTCTTGT
1 TAAAAGAGATGTAAGTTCATGTAGTATTATCAGAAAGTAAACTTCATTCTTGT
34136 TA
1 TA
34138 CTTATTTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (53 bp):
TAAAAGAGATGTAAGTTCATGTAGTATTATCAGAAAGTAAACTTCATTCTTGT
Found at i:38684 original size:34 final size:31
Alignment explanation
Indices: 38629--38704 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 31
38619 AGACTCGTTC
*
38629 ATATTATTTTTTTAATTTTTAAAAAAATATTT
1 ATATTATTTTTTTAATATTTAAAAAAAT-TTT
*
38661 ATATTATATTATTTTAATATTTAATAAAATTTT
1 ATATTAT-TT-TTTTAATATTTAAAAAAATTTT
38694 ATA-TATTTTTT
1 ATATTATTTTTT
38705 ATTTATTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 3 0.08
31 2 0.05
32 10 0.25
33 8 0.20
34 17 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATTATTTTTTTAATATTTAAAAAAATTTT
Found at i:43870 original size:20 final size:20
Alignment explanation
Indices: 43840--43889 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43830 ATTAGCATGA
43840 TTTATATTAAGATTAAACAG-G
1 TTTA-ATTAAGATTAAA-AGTG
43861 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAGATTAAAAGTG
*
43881 ATTAATTAA
1 TTTAATTAA
43890 AGCTTAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTAATTAAGATTAAAAGTG
Found at i:45774 original size:21 final size:21
Alignment explanation
Indices: 45725--45782 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
45715 TTGAAATAAG
* *
45725 ACTTGTAGCAGTAGAATAGTC
1 ACTTGTATCGGTAGAATAGTC
45746 ACTTGTATCGGTAGAACTA-TC
1 ACTTGTATCGGTAGAA-TAGTC
*
45767 ACTTGTATCGATAGAA
1 ACTTGTATCGGTAGAA
45783 GTCTGTACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTTGTATCGGTAGAATAGTC
Done.