Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004411.1 Kokia drynarioides strain JFW-HI SEQ_117791, 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: 62378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:15930 original size:31 final size:31
Alignment explanation
Indices: 15873--15933 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
15863 AAACGACCCA
* *
15873 TTATTTATTCTTTACTTATTTCGGGTTCTTT
1 TTATTTATTATTTACTTATTTAGGGTTCTTT
*
15904 TTATTTATTATTTA-TTCTTTTAGGGTTCTT
1 TTATTTATTATTTACTT-ATTTAGGGTTCTT
15934 CCTGTATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (31 bp):
TTATTTATTATTTACTTATTTAGGGTTCTTT
Found at i:18368 original size:16 final size:16
Alignment explanation
Indices: 18349--18379 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18339 ATATTAATTT
*
18349 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
18365 TATTTAATATTAAAA
1 TATTTAATATTAAAA
18380 CAATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:18465 original size:16 final size:16
Alignment explanation
Indices: 18444--18476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18434 TTCATTTTTT
18444 TATAATTTTATATTTA
1 TATAATTTTATATTTA
18460 TATAATTTTATATTTA
1 TATAATTTTATATTTA
18476 T
1 T
18477 CTTTACTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATAATTTTATATTTA
Found at i:18792 original size:2 final size:2
Alignment explanation
Indices: 18785--18818 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18775 ATAAAAATTA
18785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18819 CAAATTGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42756 original size:73 final size:71
Alignment explanation
Indices: 42563--42775 Score: 363
Period size: 72 Copynumber: 3.0 Consensus size: 71
42553 TAATATATAT
*
42563 AAAAGTATTTTTTAAAATAAGGGTTTTTTTAATTAGGGAAATAGGTTAAATTTAAAGATAAAGTG
1 AAAAGTATTTTTTAAAATAAGGGTTTTTTTAATTAGGGAAATAGGTTAAATTTGAAGATAAAGTG
42628 TGATAA
66 TGATAA
* *
42634 AAAAGTATTTTTTAAAATAAGGGTTTTTTTTAATTAGGGAAATATGTTAAATTTGAAGATAGAGT
1 AAAAGTATTTTTTAAAATAAGGG-TTTTTTTAATTAGGGAAATAGGTTAAATTTGAAGATAAAGT
42699 GTGATAA
65 GTGATAA
*
42706 AAAAGTATTTTTTTTTAAATAAGGGTTTTTTTAATTAGGGAAATAGGTTAAATTTGAAGATAAAG
1 AAAAGTA--TTTTTTAAAATAAGGGTTTTTTTAATTAGGGAAATAGGTTAAATTTGAAGATAAAG
42771 TGTGA
64 TGTGA
42776 AAACGTATTC
Statistics
Matches: 133, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
71 23 0.17
72 52 0.39
73 43 0.32
74 15 0.11
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.40
Consensus pattern (71 bp):
AAAAGTATTTTTTAAAATAAGGGTTTTTTTAATTAGGGAAATAGGTTAAATTTGAAGATAAAGTG
TGATAA
Found at i:52674 original size:9 final size:9
Alignment explanation
Indices: 52660--52854 Score: 76
Period size: 9 Copynumber: 20.9 Consensus size: 9
52650 TTCCAATTCA
52660 AATTTTTAT
1 AATTTTTAT
52669 AATTTTTAT
1 AATTTTTAT
*
52678 AAATTTATAT
1 -AATTTTTAT
52688 CAA-TTTTAT
1 -AATTTTTAT
*
52697 TATTTTTAT
1 AATTTTTAT
* *
52706 TATTTTTAAG
1 AATTTTT-AT
** *
52716 AAGTCTAATAC
1 AA-T-TTTTAT
*
52727 AATTTTTTTT
1 AA-TTTTTAT
*
52737 AATTTTAAAT
1 AATTTT-TAT
**
52747 AAGATTTATT
1 AATTTTTA-T
52757 AA-TTTTAT
1 AATTTTTAT
*
52765 AAATTTTTAC
1 -AATTTTTAT
*
52775 AA-TTTAAT
1 AATTTTTAT
*
52783 -TTTTTTAT
1 AATTTTTAT
52791 -ATTTTTAT
1 AATTTTTAT
**
52799 AATACTTAT
1 AATTTTTAT
*
52808 AAATTTCTAT
1 -AATTTTTAT
52818 AATTTTTTAT
1 AA-TTTTTAT
52828 AATTTTTAT
1 AATTTTTAT
*
52837 AAGTTTATAT
1 AA-TTTTTAT
*
52847 CATTTTTA
1 AATTTTTA
52855 ATATTTTTTT
Statistics
Matches: 137, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
8 18 0.13
9 62 0.45
10 50 0.36
11 5 0.04
12 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:52824 original size:29 final size:29
Alignment explanation
Indices: 52792--52853 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
52782 TTTTTTTATA
*
52792 TTTTTATAATACTTATAAATTTCTATAAT
1 TTTTTATAATACTTATAAATTTATATAAT
** * *
52821 TTTTTATAATTTTTATAAGTTTATATCAT
1 TTTTTATAATACTTATAAATTTATATAAT
52850 TTTT
1 TTTT
52854 AATATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTATAATACTTATAAATTTATATAAT
Found at i:52862 original size:29 final size:29
Alignment explanation
Indices: 52791--52863 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 29
52781 ATTTTTTTAT
** *
52791 ATTTTT-ATAATACTTATAAATTTCTATA
1 ATTTTTAATAATTTTTATAAATTTATATA
* * *
52819 ATTTTTTATAATTTTTATAAGTTTATATC
1 ATTTTTAATAATTTTTATAAATTTATATA
*
52848 ATTTTTAATATTTTTT
1 ATTTTTAATAATTTTT
52864 TCTTTTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 6 0.16
29 31 0.84
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTTTAATAATTTTTATAAATTTATATA
Found at i:57321 original size:18 final size:18
Alignment explanation
Indices: 57298--57358 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
57288 GATGATGACA
57298 AGGAGAATCCAAGAGAAG
1 AGGAGAATCCAAGAGAAG
**
57316 AGGAGAATCCAAGAGTTG
1 AGGAGAATCCAAGAGAAG
57334 AGGAGAATCCAAGAGAAG
1 AGGAGAATCCAAGAGAAG
57352 AGGAGAA
1 AGGAGAA
57359 ATTGAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.48, C:0.10, G:0.34, T:0.08
Consensus pattern (18 bp):
AGGAGAATCCAAGAGAAG
Found at i:58555 original size:29 final size:30
Alignment explanation
Indices: 58522--58580 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
58512 TATAGTTTAA
58522 TGTGTAATTATATAT-ATG-AACTTTGATTT
1 TGTGTAATTATAT-TCATGAAACTTTGATTT
*
58551 TGTGTAATTATATTCATGAAATTTTGATTT
1 TGTGTAATTATATTCATGAAACTTTGATTT
58581 GATCCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.59
30 10 0.37
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGTAATTATATTCATGAAACTTTGATTT
Found at i:58869 original size:6 final size:6
Alignment explanation
Indices: 58858--58888 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
58848 CCTAATTCAT
*
58858 TTAAAA TTAAAA TCAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
58889 CTATTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:59004 original size:29 final size:29
Alignment explanation
Indices: 58940--59005 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
58930 TCGTATTTGG
58940 TACTTGTACTTTCATGAAATGTCTAATATA
1 TACTTGTACTTTCA-GAAATGTCTAATATA
* * *
58970 TCACTTGTACTTTGA-AAATGTTTAATGTGA
1 T-ACTTGTACTTTCAGAAATGTCTAATAT-A
59000 TACTTG
1 TACTTG
59006 GAATATCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 16 0.52
30 3 0.10
31 12 0.39
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (29 bp):
TACTTGTACTTTCAGAAATGTCTAATATA
Done.