Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007684.1 Kokia drynarioides strain JFW-HI SEQ_122315, 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: 48452
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 147 characters in sequence are not A, C, G, or T
Found at i:3875 original size:23 final size:22
Alignment explanation
Indices: 3846--3901 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
3836 AAATTCAAAT
3846 AATAAGGTTTACATTGTGAAAAA
1 AATAAGGTTTACATTGT-AAAAA
***
3869 AATAAGGAGAACATTGTAAAAA
1 AATAAGGTTTACATTGTAAAAA
* *
3891 AAAAAAGTTTA
1 AATAAGGTTTA
3902 GTGCGATGAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (22 bp):
AATAAGGTTTACATTGTAAAAA
Found at i:12085 original size:14 final size:14
Alignment explanation
Indices: 12068--12101 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12058 TATATGTCAT
*
12068 TTTTTATGTTTACA
1 TTTTAATGTTTACA
*
12082 TTTTAATGTTTATA
1 TTTTAATGTTTACA
12096 TTTTAA
1 TTTTAA
12102 GTAGGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTAATGTTTACA
Found at i:15188 original size:6 final size:6
Alignment explanation
Indices: 15177--15201 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15167 AATTAGTATA
15177 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
15202 TGTATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:30716 original size:16 final size:18
Alignment explanation
Indices: 30677--30710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30667 TAAATTTATA
30677 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
30694 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
30711 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:31012 original size:21 final size:22
Alignment explanation
Indices: 30974--31027 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
30964 CAAATCAGTA
*
30974 TATTAAATA-TATATATAAAAT
1 TATTAAATATTATAAATAAAAT
*
30995 TATTAAATATTA-AAATAATAT
1 TATTAAATATTATAAATAAAAT
*
31016 AATATAAATATT
1 TAT-TAAATATT
31028 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAATATTATAAATAAAAT
Found at i:45651 original size:66 final size:66
Alignment explanation
Indices: 45545--45681 Score: 274
Period size: 66 Copynumber: 2.1 Consensus size: 66
45535 GCAAATCAAT
45545 TATTAAATTCATCAAGCAGTGAACTTCCTTCTCCATAGAGGACCCCAAACATTCAATCCTTTTCT
1 TATTAAATTCATCAAGCAGTGAACTTCCTTCTCCATAGAGGACCCCAAACATTCAATCCTTTTCT
45610 A
66 A
45611 TATTAAATTCATCAAGCAGTGAACTTCCTTCTCCATAGAGGACCCCAAACATTCAATCCTTTTCT
1 TATTAAATTCATCAAGCAGTGAACTTCCTTCTCCATAGAGGACCCCAAACATTCAATCCTTTTCT
45676 A
66 A
45677 TATTA
1 TATTA
45682 CTTGCTCAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (66 bp):
TATTAAATTCATCAAGCAGTGAACTTCCTTCTCCATAGAGGACCCCAAACATTCAATCCTTTTCT
A
Found at i:48347 original size:35 final size:35
Alignment explanation
Indices: 48296--48369 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
48286 TGAAGTAAGG
*
48296 AAGGTTAGAATTTTTTTTTTTAAGGATTAAATAGTA
1 AAGGTTAGAA-ATTTTTTTTTAAGGATTAAATAGTA
48332 AAGG-TAGAAATTTTTTTTTAAGGATTAAATAGTA
1 AAGGTTAGAAATTTTTTTTTAAGGATTAAATAGTA
48366 AAGG
1 AAGG
48370 AGAGAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
34 28 0.76
35 5 0.14
36 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (35 bp):
AAGGTTAGAAATTTTTTTTTAAGGATTAAATAGTA
Found at i:48376 original size:35 final size:34
Alignment explanation
Indices: 48308--48376 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
48298 GGTTAGAATT
*
48308 TTTTTTTTTAAGGATTAAATAGTAAAGGTAGAAA
1 TTTTTTTTTAAGGATTAAATAGTAAAGGGAGAAA
48342 TTTTTTTTTAAGGATTAAATAGTAAAGGAGAGAAA
1 TTTTTTTTTAAGGATTAAATAGTAAAGG-GAGAAA
48377 ATATGAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 28 0.85
35 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (34 bp):
TTTTTTTTTAAGGATTAAATAGTAAAGGGAGAAA
Done.