Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006515.1 Kokia drynarioides strain JFW-HI SEQ_121099, 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: 45791
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:1049 original size:26 final size:25
Alignment explanation
Indices: 1004--1068 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
994 AGACTCCTCT
* * *
1004 AAATGCTCCGTTTAACTTAAGACCCA
1 AAATGCACCGTTTTACTTAA-ACACA
*
1030 AAATGCACCGTTTTATTTAAACACA
1 AAATGCACCGTTTTACTTAAACACA
*
1055 AAACGCACCGTTTT
1 AAATGCACCGTTTT
1069 CTACTTCTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (25 bp):
AAATGCACCGTTTTACTTAAACACA
Found at i:30467 original size:18 final size:18
Alignment explanation
Indices: 30435--30486 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
30425 TTGGAATGAG
30435 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
30451 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
30469 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
30487 CAATTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:31479 original size:24 final size:26
Alignment explanation
Indices: 31451--31500 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
31441 TGTCTATGAA
31451 TTATTTTAT-GA-TCTGAATTT-AATT
1 TTATTTTATAGACT-TGAATTTGAATT
31475 TTATTTTATAGACTTGAATTTGAATT
1 TTATTTTATAGACTTGAATTTGAATT
31501 GAACTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.39
25 9 0.39
26 5 0.22
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.56
Consensus pattern (26 bp):
TTATTTTATAGACTTGAATTTGAATT
Found at i:32095 original size:129 final size:129
Alignment explanation
Indices: 31860--32097 Score: 422
Period size: 129 Copynumber: 1.8 Consensus size: 129
31850 TTAGTTTTTT
* *
31860 ATGTCAGGGATCAGATTATATAGCAAGTTGTGTTAACGATTGTGATTACATGTCAAACCATAACT
1 ATGTCAAGGATCAGATTATATAGCAAGTTGTGTTAACGATTGTGATTACATGTCAAACCACAACT
* *
31925 TTTGCCACAATTTAATCATAAGTTAGCAGTTTTTAATTTTGTATAAGTTGTGGGTTTAATCTTC
66 TTTGCCACAATTTAATCATAAGTTAGCAATTTTTAACTTTGTATAAGTTGTGGGTTTAATCTTC
31989 ATGTCAAGGATCAGATTATATAGCAAGTTGTGTTAACGATTGTGATTACATGTCAAACCACAACT
1 ATGTCAAGGATCAGATTATATAGCAAGTTGTGTTAACGATTGTGATTACATGTCAAACCACAACT
* *
32054 TTTGTCACAATTTAATCATAAGTTAGCAATTTTTGACTTTGTAT
66 TTTGCCACAATTTAATCATAAGTTAGCAATTTTTAACTTTGTAT
32098 TATCATTATA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 103 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.39
Consensus pattern (129 bp):
ATGTCAAGGATCAGATTATATAGCAAGTTGTGTTAACGATTGTGATTACATGTCAAACCACAACT
TTTGCCACAATTTAATCATAAGTTAGCAATTTTTAACTTTGTATAAGTTGTGGGTTTAATCTTC
Found at i:40798 original size:9 final size:9
Alignment explanation
Indices: 40784--40810 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40774 TGAATCGATC
40784 AATTAAATA
1 AATTAAATA
40793 AATTAAATA
1 AATTAAATA
40802 AATTAAATA
1 AATTAAATA
40811 GATTTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTAAATA
Done.