Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000662.1 Kokia drynarioides strain JFW-HI SEQ_111644, 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: 45552
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:94 original size:24 final size:24
Alignment explanation
Indices: 63--133 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
53 GAAAACTGTT
*
63 TATTATTATTAATGTCATTAATAA
1 TATTATTATTAATGTTATTAATAA
* *
87 TATTATTATTATTGTTATTATTAA
1 TATTATTATTAATGTTATTAATAA
* ** *
111 AACAATTATTAATATTATTAATA
1 TATTATTATTAATGTTATTAATA
134 GTTATTGAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (24 bp):
TATTATTATTAATGTTATTAATAA
Found at i:822 original size:23 final size:22
Alignment explanation
Indices: 785--847 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 22
775 ATTGGACTTG
* *
785 ATTTAAATAGATTTAAACTTAA
1 ATTTAAGTAAATTTAAACTTAA
807 ATTTATAGTAAATTTAAA--T--
1 ATTTA-AGTAAATTTAAACTTAA
826 -TTTAAGTAAATTTAAACTTAA
1 ATTTAAGTAAATTTAAACTTAA
847 A
1 A
848 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 12 0.36
18 4 0.12
19 1 0.03
21 1 0.03
22 5 0.15
23 10 0.30
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (22 bp):
ATTTAAGTAAATTTAAACTTAA
Found at i:823 original size:17 final size:17
Alignment explanation
Indices: 798--862 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
788 TAAATAGATT
*
798 TAAACTTAAATTTATAG
1 TAAATTTAAATTTATAG
815 TAAATTTAAATTT-TAAG
1 TAAATTTAAATTTAT-AG
* * *
832 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTATAG
*
849 TAAATTTAATTTTA
1 TAAATTTAAATTTA
863 AAAAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAG
Found at i:3685 original size:30 final size:29
Alignment explanation
Indices: 3645--3718 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
3635 TTTAATTATA
* *
3645 TTTATTATTTTAAAAGAATTAAATTA-AATT
1 TTTA-TATTTTAAAAGAATCAAAATATAA-T
* *
3675 TTTATCATTTTAAATGAGTCAAAATATAAT
1 TTTAT-ATTTTAAAAGAATCAAAATATAAT
3705 TTTATATTTTAAAA
1 TTTATATTTTAAAA
3719 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 9 0.24
30 26 0.70
31 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTATATTTTAAAAGAATCAAAATATAAT
Found at i:6390 original size:17 final size:18
Alignment explanation
Indices: 6365--6411 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
6355 TAAATAGATT
*
6365 TAAACTTAAATTTAT-AG
1 TAAATTTAAATTTATAAG
6382 TAAATTTAAATTT-TAAG
1 TAAATTTAAATTTATAAG
6399 TAAATTT-AATTTA
1 TAAATTTAAATTTA
6412 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
TAAATTTAAATTTATAAG
Found at i:9409 original size:26 final size:26
Alignment explanation
Indices: 9374--9427 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
9364 TAACTCAAAC
* *
9374 AATTTCACTCGATTCGACTCAACTTG
1 AATTTCACTCCACTCGACTCAACTTG
* * *
9400 AATTTTACTCCACTCGATTCAATTTG
1 AATTTCACTCCACTCGACTCAACTTG
9426 AA
1 AA
9428 AAAAATTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (26 bp):
AATTTCACTCCACTCGACTCAACTTG
Found at i:15195 original size:19 final size:19
Alignment explanation
Indices: 15171--15216 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
15161 AGTTTAATTA
*
15171 AAATTTTTCA-AAAATTTT
1 AAATTTTTAATAAAATTTT
*
15189 AAGATTTTAAATAAAATTTT
1 AA-ATTTTTAATAAAATTTT
15209 AAATTTTT
1 AAATTTTT
15217 TGAAGGGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTTTTAATAAAATTTT
Found at i:17566 original size:22 final size:23
Alignment explanation
Indices: 17522--17566 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
17512 TATTTTTATA
**
17522 ATTTTAAACATAAAAATTTAATT
1 ATTTTAAACATAAAAATAAAATT
*
17545 ATTTTAAATA-AAAAATAAAATT
1 ATTTTAAACATAAAAATAAAATT
17567 TCGGATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTTAAACATAAAAATAAAATT
Found at i:32562 original size:21 final size:20
Alignment explanation
Indices: 32533--32573 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
32523 TTTATTTTTT
32533 TTTTCCTCTTTCTCGCTCGC
1 TTTTCCTCTTTCTCGCTCGC
32553 TTTTCTCTCTTTCTCGCTCGC
1 TTTTC-CTCTTTCTCGCTCGC
32574 GGGGATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.00, C:0.39, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTCCTCTTTCTCGCTCGC
Found at i:35049 original size:32 final size:32
Alignment explanation
Indices: 35008--35070 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
34998 TCATAATGAC
* *
35008 GAATGGACACTACAGATGGTACTCTAGGTGAA
1 GAATGGACACTACAAATAGTACTCTAGGTGAA
*
35040 GAATGGACACTATAAATAGTACTCTAGGTGA
1 GAATGGACACTACAAATAGTACTCTAGGTGA
35071 GTTCAATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (32 bp):
GAATGGACACTACAAATAGTACTCTAGGTGAA
Done.