Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009140.1 Kokia drynarioides strain JFW-HI SEQ_123844, 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: 28168
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:86 original size:2 final size:2
Alignment explanation
Indices: 79--108 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69 ACAATCTATT
79 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109 ATGAATTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3316 original size:2 final size:2
Alignment explanation
Indices: 3309--3333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3299 TTGTTTGATT
3309 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3334 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8596 original size:12 final size:13
Alignment explanation
Indices: 8568--8602 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
8558 TCAAAAGTAC
8568 TTTTTAAAATCAT
1 TTTTTAAAATCAT
8581 TTTTCTAAAA-CAT
1 TTTT-TAAAATCAT
8594 TTTTTAAAA
1 TTTTTAAAA
8603 GCACTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTTAAAATCAT
Found at i:9417 original size:15 final size:17
Alignment explanation
Indices: 9383--9417 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
9373 ATATCAATTG
9383 TATAGGGAATTTTGAAT
1 TATAGGGAATTTTGAAT
9400 TATA-GGAATTTT-AAT
1 TATAGGGAATTTTGAAT
9415 TAT
1 TAT
9418 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
TATAGGGAATTTTGAAT
Found at i:10980 original size:23 final size:24
Alignment explanation
Indices: 10949--11013 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 24
10939 GTATACTAGT
*
10949 TAACCATTCTGGGCTCGTAAGAGC
1 TAACAATTCTGGGCTCGTAAGAGC
*
10973 TAA-AATTCTAGGCTCGTAAGAGC
1 TAACAATTCTGGGCTCGTAAGAGC
* *
10996 TAACCATTATGGGCTCGT
1 TAACAATTCTGGGCTCGT
11014 GTGAGTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (24 bp):
TAACAATTCTGGGCTCGTAAGAGC
Found at i:15733 original size:2 final size:2
Alignment explanation
Indices: 15726--15755 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15716 TATGGTGATA
15726 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
15756 AAGTGATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:15983 original size:21 final size:22
Alignment explanation
Indices: 15942--15983 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
15932 TAAATATTAG
*
15942 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
15964 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
15984 ACCCACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:16918 original size:24 final size:24
Alignment explanation
Indices: 16886--16942 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
16876 AGATAATGAA
16886 TTTAGGGGTAAT-AGACATTCATTC
1 TTTAGGGGTAATGA-ACATTCATTC
*
16910 TTTAAGGGTAATGAACATTCATTC
1 TTTAGGGGTAATGAACATTCATTC
16934 TTTAGGGGT
1 TTTAGGGGT
16943 TATAATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (24 bp):
TTTAGGGGTAATGAACATTCATTC
Found at i:17665 original size:14 final size:13
Alignment explanation
Indices: 17637--17679 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
17627 AAGTGAAACA
17637 GAAAAAAAAAGTT
1 GAAAAAAAAAGTT
*
17650 GAAAATAAATAGTT
1 GAAAA-AAAAAGTT
*
17664 GAAACAAAAAAATT
1 GAAA-AAAAAAGTT
17678 GA
1 GA
17680 GGGGAAAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 5 0.20
14 19 0.76
15 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.14, T:0.19
Consensus pattern (13 bp):
GAAAAAAAAAGTT
Found at i:17838 original size:21 final size:20
Alignment explanation
Indices: 17786--17838 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
17776 AATTTTAGAT
*
17786 GAGATGAGAGTGAAAAATAAA
1 GAGA-GAGAGAGAAAAATAAA
*
17807 GAGATATGAGAGAAAAATAAA
1 GAGAGA-GAGAGAAAAATAAA
17828 GAGACGAGAGA
1 GAGA-GAGAGA
17839 ATAAAAGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.30, T:0.11
Consensus pattern (20 bp):
GAGAGAGAGAGAAAAATAAA
Found at i:17844 original size:21 final size:21
Alignment explanation
Indices: 17786--17831 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
17776 AATTTTAGAT
17786 GAGATGAGAGTGAAAAATAAAGA
1 GAGATGAGA--GAAAAATAAAGA
*
17809 GATATGAGAGAAAAATAAAGA
1 GAGATGAGAGAAAAATAAAGA
17830 GA
1 GA
17832 CGAGAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (21 bp):
GAGATGAGAGAAAAATAAAGA
Found at i:17977 original size:84 final size:83
Alignment explanation
Indices: 17846--18053 Score: 276
Period size: 84 Copynumber: 2.5 Consensus size: 83
17836 AGAATAAAAG
* * *
17846 TCAAATATGGGAAAGGAAATA-ATAACA-ACAATGTAAAATAGAGATATGAAAGAGAATTGAATA
1 TCAAATATGAGAAAGGAAATAGATAACATA-TATGGAAAATAGAGATATGAAAGAGAATTGAATA
** **
17909 TTTTATTTAAAATAGATTA
65 TTTTATGAAAAATAGAGAA
*
17928 TCAAATATGAGAAAGGAAATAGTATAACATATATGGAAAATAGAGATATGAAAGAGAATTTAATA
1 TCAAATATGAGAAAGGAAATAG-ATAACATATATGGAAAATAGAGATATGAAAGAGAATTGAATA
17993 TTTTATGAAAAATAGAGAA
65 TTTTATGAAAAATAGAGAA
** *
18012 TCAAATACAAGAAAGGAAAGAGAATAACATATATGGAAAATA
1 TCAAATATGAGAAAGGAAATAG-ATAACATATATGGAAAATA
18054 AAAAAAACAA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
82 20 0.18
84 90 0.81
85 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.25
Consensus pattern (83 bp):
TCAAATATGAGAAAGGAAATAGATAACATATATGGAAAATAGAGATATGAAAGAGAATTGAATAT
TTTATGAAAAATAGAGAA
Found at i:22551 original size:19 final size:19
Alignment explanation
Indices: 22524--22570 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
22514 ATAAATTGAT
22524 TTTTAAAAA-ATAAAAATTA
1 TTTTAAAAATATAAAAA-TA
22543 TTCTTAAAAATATAAAAATA
1 TT-TTAAAAATATAAAAATA
22563 TTTTAAAA
1 TTTTAAAA
22571 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.31
20 11 0.42
21 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAAATATAAAAATA
Found at i:22551 original size:20 final size:20
Alignment explanation
Indices: 22505--22570 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
22495 TTAAAATTCA
*
22505 AAAAATTATATAAATTGATTTTT
1 AAAAA-TATAAAAATT-A-TTTT
22528 AAAAA-ATAAAAATTATTCTT
1 AAAAATATAAAAATTATT-TT
22548 AAAAATATAAAAA-TATTTT
1 AAAAATATAAAAATTATTTT
22567 AAAA
1 AAAA
22571 TTTTTAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 8 0.20
20 12 0.30
21 15 0.38
23 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATATAAAAATTATTTT
Found at i:26841 original size:13 final size:13
Alignment explanation
Indices: 26823--26847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26813 ATTTTAATTT
26823 AAAAAAAAAAACA
1 AAAAAAAAAAACA
26836 AAAAAAAAAAAC
1 AAAAAAAAAAAC
26848 CAATGTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Done.