Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013243.1 Kokia drynarioides strain JFW-HI SEQ_128262, 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: 42852
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:1823 original size:19 final size:21
Alignment explanation
Indices: 1794--1837 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1784 ATTGTTCAAA
1794 AAAATTATTAAA-A-AAAATCT
1 AAAATTATTAAATATAAAAT-T
1814 AAAA-TATTAAATATAAAATT
1 AAAATTATTAAATATAAAATT
1834 AAAA
1 AAAA
1838 ATAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 5 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTATTAAATATAAAATT
Found at i:9412 original size:113 final size:113
Alignment explanation
Indices: 9213--9441 Score: 422
Period size: 113 Copynumber: 2.0 Consensus size: 113
9203 TTAATATATC
9213 AAGATGGTTATATAATAGAGGCGGGTGCTCTAGAAGAGACCTAAGATATAACTAATCATTAAAAC
1 AAGATGGTTATATAATAGAGGCGGGTGCTCTAGAAGAGACCTAAGATATAACTAATCATTAAAAC
*
9278 TCTAGAATAGATTTAGGTACATAATGATGAAAATAAAGAGATATCGAT
66 TCTAGAATAGATTTAGATACATAATGATGAAAATAAAGAGATATCGAT
***
9326 AAGATGGTTATATAATAGAGGCGGGTGCTCTAGAAGAGGTGTAAGATATAACTAATCATTAAAAC
1 AAGATGGTTATATAATAGAGGCGGGTGCTCTAGAAGAGACCTAAGATATAACTAATCATTAAAAC
9391 TCTAGAATAGATTTAGATACATAATGATGAAAATAAAGAGATATCGAT
66 TCTAGAATAGATTTAGATACATAATGATGAAAATAAAGAGATATCGAT
9439 AAG
1 AAG
9442 TTATGTCAAT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.27
Consensus pattern (113 bp):
AAGATGGTTATATAATAGAGGCGGGTGCTCTAGAAGAGACCTAAGATATAACTAATCATTAAAAC
TCTAGAATAGATTTAGATACATAATGATGAAAATAAAGAGATATCGAT
Found at i:13366 original size:20 final size:20
Alignment explanation
Indices: 13329--13366 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13319 TATTTTTTAG
*
13329 CTTTTTTTTTTGTCATCTAC
1 CTTTTTTTTTTGTAATCTAC
13349 CTTTATTTTTTT-TAATCT
1 CTTT-TTTTTTTGTAATCT
13367 GTTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (20 bp):
CTTTTTTTTTTGTAATCTAC
Found at i:13855 original size:2 final size:2
Alignment explanation
Indices: 13810--13835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13800 TAAGCCTATT
13810 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
13836 AAAGCATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15060 original size:41 final size:40
Alignment explanation
Indices: 15005--15121 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
14995 GCCATCTCCG
15005 GATCCATCCTTGCGAACTACCATGGTCCCATCCCACCCTCCA
1 GATCCATCC-TGCGAACTACCATGGTCCCATCCCACCC-CCA
* * **
15047 GGTCCATCCTGCGAACTGCCACCGTCCCATCCCACCCCCA
1 GATCCATCCTGCGAACTACCATGGTCCCATCCCACCCCCA
*
15087 GATCCATCCCTACGAACTACCATGGTCCCATCCCA
1 GATCCAT-CCTGCGAACTACCATGGTCCCATCCCA
15122 TTATATCACT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 9 0.14
41 48 0.74
42 8 0.12
ACGTcount: A:0.21, C:0.47, G:0.13, T:0.19
Consensus pattern (40 bp):
GATCCATCCTGCGAACTACCATGGTCCCATCCCACCCCCA
Found at i:18665 original size:27 final size:25
Alignment explanation
Indices: 18567--18665 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 25
18557 TATTTAATAA
*
18567 TATTA-TTATGTTTTATAATAAAATAT
1 TATTATTTATTTTTTA-AATAAAA-AT
*
18593 TATTATTTATTTTTTAAACTCTAAAA-
1 TATTATTTATTTTTTAAA-T-AAAAAT
*
18619 TATTTATTT-TTTACTTAAATAAAACAT
1 TA-TTATTTATTT-TTTAAATAAAA-AT
18646 TATTATTTATTTTTTGAAAT
1 TATTATTTATTTTTT-AAAT
18666 TCAAAATGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.05
26 22 0.37
27 31 0.53
28 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
TATTATTTATTTTTTAAATAAAAAT
Found at i:29865 original size:11 final size:11
Alignment explanation
Indices: 29842--29876 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
29832 AGGTGAATTA
29842 CCTTTCCTTTT
1 CCTTTCCTTTT
29853 CC-TTCCTTATT
1 CCTTTCCTT-TT
29864 CCTTTCCTTTT
1 CCTTTCCTTTT
29875 CC
1 CC
29877 ACGTATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (11 bp):
CCTTTCCTTTT
Done.