Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014673.1 Kokia drynarioides strain JFW-HI SEQ_129712, 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: 43492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:5030 original size:6 final size:6
Alignment explanation
Indices: 5019--5047 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5009 GTATGGGGCA
5019 TGTGGC TGTGGC TGTGGC TGTGGC TGTGG
1 TGTGGC TGTGGC TGTGGC TGTGGC TGTGG
5048 GGGCTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.34
Consensus pattern (6 bp):
TGTGGC
Found at i:13049 original size:24 final size:26
Alignment explanation
Indices: 12995--13049 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 26
12985 GATATTTAAT
*
12995 TTTTTTAATTAAAACATTAATTTTAAA
1 TTTTTTAA-TAAAACATTAATTATAAA
13022 TTTTTTAA-AAAA-ATTAA-TATAAA
1 TTTTTTAATAAAACATTAATTATAAA
*
13045 GTTTT
1 TTTTT
13050 CGTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 9 0.35
24 5 0.19
25 4 0.15
27 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTTTAATAAAACATTAATTATAAA
Found at i:20978 original size:6 final size:6
Alignment explanation
Indices: 20967--21003 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
20957 TTTTGATGAT
*
20967 GGATGG GGATGG GGAGGG GGATGG GGATGG GGATGG G
1 GGATGG GGATGG GGATGG GGATGG GGATGG GGATGG G
21004 CTGGGTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.70, T:0.14
Consensus pattern (6 bp):
GGATGG
Found at i:27887 original size:4 final size:4
Alignment explanation
Indices: 27878--27916 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
27868 ACCTTCAGTA
*
27878 TATG TATG TATG TAGG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
27917 ACATATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:28393 original size:2 final size:2
Alignment explanation
Indices: 28386--28425 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28376 TGCCATCTTA
28386 AT AT AT 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 AT AT AT
28426 GGCATGTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35689 original size:5 final size:6
Alignment explanation
Indices: 35667--35698 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
35657 ATGAACCCAA
35667 AAAATAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT A
35699 TATAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:35695 original size:26 final size:25
Alignment explanation
Indices: 35666--35727 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
35656 GATGAACCCA
35666 AAAAATATAAAAATAAAAATAAAAAT
1 AAAAATATAAAAA-AAAAATAAAAAT
* ** *
35692 AAAAATATATAAAACAAAATTCAACT
1 AAAAATATA-AAAAAAAAATAAAAAT
35718 AAAAATATAA
1 AAAAATATAA
35728 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 1 0.03
26 26 0.84
27 4 0.13
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (25 bp):
AAAAATATAAAAAAAAAATAAAAAT
Done.