Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014004.1 Kokia drynarioides strain JFW-HI SEQ_129035, 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: 196764
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 39 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:167485 original size:21 final size:20
Alignment explanation
Indices: 167461--167500 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
167451 ACGCATGTTA
*
167461 ACATATAAGGTTTCACATATC
1 ACATA-AAGGGTTCACATATC
*
167482 ACATACAGGGTTCACATAT
1 ACATAAAGGGTTCACATAT
167501 TATACTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (20 bp):
ACATAAAGGGTTCACATATC
Found at i:170813 original size:2 final size:2
Alignment explanation
Indices: 170806--170837 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
170796 TAAGTGAAAC
170806 TA 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 TA
170838 ACTCAACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:173925 original size:17 final size:17
Alignment explanation
Indices: 173903--173936 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
173893 GTCTTTATGT
173903 TAAATTAAAAATTAAAA
1 TAAATTAAAAATTAAAA
**
173920 TAAATTTCAAATTAAAA
1 TAAATTAAAAATTAAAA
173937 ACATTAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTAAAAATTAAAA
Found at i:174986 original size:21 final size:21
Alignment explanation
Indices: 174952--175007 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
174942 GATCTAAGAA
174952 AAAATAAAAG-AAACA-AATTT
1 AAAATAAAAGAAAACACAA-TT
174972 AAAATAAAAGAAAACACAATT
1 AAAATAAAAGAAAACACAATT
*
174993 AAAAGAAATAGAAAA
1 AAAATAAA-AGAAAA
175008 TAGGGAAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.31
21 14 0.44
22 8 0.25
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.14
Consensus pattern (21 bp):
AAAATAAAAGAAAACACAATT
Found at i:176622 original size:104 final size:105
Alignment explanation
Indices: 176448--176641 Score: 232
Period size: 104 Copynumber: 1.9 Consensus size: 105
176438 ATACATTGGA
* ** * **
176448 CCTTTTGACGCGAAATGAAATGACACCCAAGGACTCCATCCCAGTTACTCAGCCCAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCAGTTACTCAGCCCAACACACTCT
176513 CAATTT-TTTTCTTCTCTTTTTTTTGTAGAATGTGTTAGC
66 CAATTTATTTTCTTCTCTTTTTTTTGTAGAATGTGTTAGC
* * * * *
176552 CCTTTTGACGTGAAGTGAAATGACAACCAAACACTCCACCCC-GATTACTCAGTCTAACACATTC
1 CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCAG-TTACTCAGCCCAACACACTC
* *
176616 -CGAATTTATTTTTTTTTCTTTTTTTT
65 TC-AATTTATTTTCTTCTCTTTTTTTT
176642 ATTTGGGTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
103 2 0.03
104 56 0.76
105 16 0.22
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.37
Consensus pattern (105 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAACACTCCACCCCAGTTACTCAGCCCAACACACTCT
CAATTTATTTTCTTCTCTTTTTTTTGTAGAATGTGTTAGC
Found at i:182855 original size:21 final size:21
Alignment explanation
Indices: 182831--182886 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
182821 CAATCTAAGG
182831 AAAAATAAAAGAAATAGAATT
1 AAAAATAAAAGAAATAGAATT
*
182852 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAA-GAAATAGAATT
*
182874 AAAAA-AATAGAAA
1 AAAAATAAAAGAAA
182887 ATAGGGAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 13 0.42
22 15 0.48
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAGAAATAGAATT
Found at i:182887 original size:21 final size:22
Alignment explanation
Indices: 182831--182890 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
182821 CAATCTAAGG
182831 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
182852 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
182874 AAAAA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
182891 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:187181 original size:15 final size:14
Alignment explanation
Indices: 187144--187177 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
187134 AACAAATTAA
187144 TTTTTTCTTTTTAT
1 TTTTTTCTTTTTAT
*
187158 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTAT
187172 TTTTTT
1 TTTTTT
187178 TCTTCCCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTCTTTTTAT
Found at i:188315 original size:15 final size:17
Alignment explanation
Indices: 188295--188328 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
188285 GTAACATTTC
188295 AAATATAA-ATGA-TTA
1 AAATATAATATGAGTTA
188310 AAATATAATATGAGTTA
1 AAATATAATATGAGTTA
188327 AA
1 AA
188329 CAAAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (17 bp):
AAATATAATATGAGTTA
Done.