Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007249.1 Kokia drynarioides strain JFW-HI SEQ_121865, 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: 29205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1525 original size:29 final size:28
Alignment explanation
Indices: 1467--1527 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
1457 ATGGAAAGTG
*
1467 AATTTTTAAATAAAAAAAATAGGGATTA
1 AATTTTTAAATAAAAAAAATAGGGACTA
*
1495 AATTTTTAAA-AATAAAAATAAGAGGACTA
1 AATTTTTAAATAAAAAAAAT-AG-GGACTA
1524 AATT
1 AATT
1528 CAAAATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.28
28 12 0.41
29 9 0.31
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (28 bp):
AATTTTTAAATAAAAAAAATAGGGACTA
Found at i:5059 original size:6 final size:6
Alignment explanation
Indices: 5050--5074 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5040 TTTTTATAAA
5050 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
5075 TCCTCTTAAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:9651 original size:12 final size:12
Alignment explanation
Indices: 9634--9659 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9624 CCCCCTCTCC
9634 TCTTCCTCTTCT
1 TCTTCCTCTTCT
9646 TCTTCCTCTTCT
1 TCTTCCTCTTCT
9658 TC
1 TC
9660 ACTCTGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTCCTCTTCT
Found at i:9997 original size:25 final size:26
Alignment explanation
Indices: 9968--10024 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
9958 TTGGTCACTA
9968 ATTTTATCATTT-TAAAATTAATTTT
1 ATTTTATCATTTCTAAAATTAATTTT
* * * *
9993 ATTTTTTCTTTTCTAGAATTATTTTT
1 ATTTTATCATTTCTAAAATTAATTTT
10019 AGTTTT
1 A-TTTT
10025 TTTTTTTCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 10 0.38
26 12 0.46
27 4 0.15
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (26 bp):
ATTTTATCATTTCTAAAATTAATTTT
Found at i:16929 original size:30 final size:28
Alignment explanation
Indices: 16895--16963 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
16885 AATTAAATTT
*
16895 AAATTTTAAAATCTAAAAAATAAAAAGACA
1 AAATTTTAAAA-AT-AAAAATAAAAAGACA
* * *
16925 AAATTTATAAAAATAAAAATACATAGACT
1 AAATTT-TAAAAATAAAAATAAAAAGACA
16954 AAATTTTAAA
1 AAATTTTAAA
16964 TTTACGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.12
29 18 0.53
30 7 0.21
31 5 0.15
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (28 bp):
AAATTTTAAAAATAAAAATAAAAAGACA
Found at i:24181 original size:9 final size:10
Alignment explanation
Indices: 24169--24219 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
24159 TAAAAAATTC
24169 AAAAT-TAAA
1 AAAATATAAA
24178 AAAATATAAA
1 AAAATATAAA
**
24188 AATTTATAATA
1 AAAATATAA-A
*
24199 AAAAAATAAA
1 AAAATATAAA
24209 ATAAATATAAA
1 A-AAATATAAA
24220 TTGTCATGCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 5 0.15
10 13 0.39
11 15 0.45
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAATATAAA
Found at i:24183 original size:23 final size:22
Alignment explanation
Indices: 24157--24209 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
24147 ATTGCGTGAC
24157 AATAAAAAATTCAAAATTAAAAA
1 AATAAAAAATTCAAAA-TAAAAA
* *
24180 AATATAAAAATTTATAATAAAAA
1 AATA-AAAAATTCAAAATAAAAA
24203 AATAAAA
1 AATAAAA
24210 TAAATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 14 0.52
24 10 0.37
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AATAAAAAATTCAAAATAAAAA
Found at i:27695 original size:19 final size:18
Alignment explanation
Indices: 27671--27709 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
27661 ACTCAATTTT
27671 ATTTTAATATAATATT-TAC
1 ATTTTAAT-T-ATATTATAC
27690 ATTTTAATTATATTATAC
1 ATTTTAATTATATTATAC
27708 AT
1 AT
27710 ACTTCATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATTATATTATAC
Found at i:29192 original size:24 final size:24
Alignment explanation
Indices: 29117--29193 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
29107 AATTAATTAT
*
29117 AAATAATTATTATAAAAATTAAATAAA
1 AAATAATTA-TATTAAAA-TAAA-AAA
* * *
29144 AAGT--TTATATTAATACT-AAACA
1 AAATAATTATATTAA-AATAAAAAA
29166 AAATAATTATATTAAAATAAAAAA
1 AAATAATTATATTAAAATAAAAAA
29190 AAAT
1 AAAT
29194 CCTCCCCACC
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
22 5 0.13
23 4 0.10
24 23 0.59
25 4 0.10
27 3 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (24 bp):
AAATAATTATATTAAAATAAAAAA
Done.