Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008143.1 Kokia drynarioides strain JFW-HI SEQ_122801, 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: 35514
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:743 original size:6 final size:7
Alignment explanation
Indices: 728--752 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
718 ATGGGTATTC
728 TTTTCTT
1 TTTTCTT
735 TTTTCTT
1 TTTTCTT
742 TTTTCTT
1 TTTTCTT
749 TTTT
1 TTTT
753 TTGGCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:6438 original size:16 final size:15
Alignment explanation
Indices: 6422--6464 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
6412 CATTATTAAT
6422 TTAAAATTTTATAAA
1 TTAAAATTTTATAAA
** *
6437 TTATAAATGATCTAAA
1 TTA-AAATTTTATAAA
6453 TTAAAATTTTAT
1 TTAAAATTTTAT
6465 CATTTTAAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAAAATTTTATAAA
Found at i:17733 original size:30 final size:30
Alignment explanation
Indices: 17674--17733 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
17664 CGAATAAATT
* *
17674 TTTGTTCGTGTTCGTTTGTTTATTTTTAAG
1 TTTGTTCGTGTTCGTTTGTATATTATTAAG
17704 TTTGTTCGTGTTCAG-TT-TATATTCATTAAG
1 TTTGTTCGTGTTC-GTTTGTATATT-ATTAAG
17734 AATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
30 20 0.77
31 1 0.04
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.58
Consensus pattern (30 bp):
TTTGTTCGTGTTCGTTTGTATATTATTAAG
Found at i:30036 original size:16 final size:17
Alignment explanation
Indices: 30015--30049 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
30005 TTTAAAAATT
*
30015 ATAAAACATTCA-AAAA
1 ATAAAAAATTCATAAAA
30031 ATAAAAAATTCATAAAA
1 ATAAAAAATTCATAAAA
30048 AT
1 AT
30050 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAAAATTCATAAAA
Found at i:30045 original size:27 final size:26
Alignment explanation
Indices: 30008--30061 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
29998 TAATTAATTT
30008 AAAAATTATAAAACA-TTCAAAAAATA
1 AAAAATTATAAAA-ATTTCAAAAAATA
*
30034 AAAAATTCATAAAAATTTTAAAAAATA
1 AAAAATT-ATAAAAATTTCAAAAAATA
30061 A
1 A
30062 TCATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAATTATAAAAATTTCAAAAAATA
Found at i:30175 original size:30 final size:31
Alignment explanation
Indices: 30129--30191 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
30119 AAATTTTAAT
*
30129 AATCAATATATTTATAAATTTTAAAAAA-TTA
1 AATCAATATATTTAT-AATTTCAAAAAAGTTA
*
30160 AATCAA-ATTTTTATAATTTCAAAAAAGTTA
1 AATCAATATATTTATAATTTCAAAAAAGTTA
30190 AA
1 AA
30192 GTACAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (31 bp):
AATCAATATATTTATAATTTCAAAAAAGTTA
Found at i:33717 original size:12 final size:12
Alignment explanation
Indices: 33700--33726 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33690 CATACTATTA
33700 ATTGTTATGAAT
1 ATTGTTATGAAT
33712 ATTGTTATGAAT
1 ATTGTTATGAAT
33724 ATT
1 ATT
33727 ATTAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (12 bp):
ATTGTTATGAAT
Found at i:35016 original size:21 final size:20
Alignment explanation
Indices: 34978--35016 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34968 TTATTTGGTC
* *
34978 TTTATAATTTATTTTTATTT
1 TTTATAAATTATTATTATTT
34998 TTTATAAATTACTTATTAT
1 TTTATAAATTA-TTATTAT
35017 AAATTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATAAATTATTATTATTT
Done.