Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006265.1 Kokia drynarioides strain JFW-HI SEQ_120836, 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: 10636
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3542 original size:23 final size:25
Alignment explanation
Indices: 3518--3565 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3508 TAAATAAATA
3518 AAAAT-ATCTCT-AAA-AATTTTCT
1 AAAATAATCTCTAAAAGAATTTTCT
3540 AAAATAATCTCTCAAAAGAATTTTCT
1 AAAATAATCTCT-AAAAGAATTTTCT
3566 CTCTGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
25 3 0.14
26 8 0.36
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATAATCTCTAAAAGAATTTTCT
Found at i:3699 original size:15 final size:16
Alignment explanation
Indices: 3681--3710 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3671 TTAATATTAA
3681 ATTAATAT-AATATTT
1 ATTAATATAAATATTT
3696 ATTAATATAAATATT
1 ATTAATATAAATATT
3711 AGATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATATAAATATTT
Found at i:3818 original size:11 final size:11
Alignment explanation
Indices: 3802--3877 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
3792 GATACTCATT
3802 TTAATATTAAA
1 TTAATATTAAA
3813 TTAATA--AAA
1 TTAATATTAAA
*
3822 -TACTATTAAAA
1 TTAATATT-AAA
*
3833 TAAATATTAAA
1 TTAATATTAAA
*
3844 TTAATTTTAATA
1 TTAATATTAA-A
3856 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
3869 ATAATATTA
1 TTAATATTA
3878 TTTTTGAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
11 25 0.49
12 10 0.20
13 4 0.08
14 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:4044 original size:19 final size:19
Alignment explanation
Indices: 4002--4044 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3992 TACTTGATCA
4002 AAATTAAATTTTCAAAAAT
1 AAATTAAATTTTCAAAAAT
* * * *
4021 CAATTAGATTTTCCAAATT
1 AAATTAAATTTTCAAAAAT
4040 AAATT
1 AAATT
4045 TTCAAGAAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATTAAATTTTCAAAAAT
Found at i:4348 original size:52 final size:52
Alignment explanation
Indices: 4286--4387 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
4276 TCGCAATTAG
4286 TTAATCATGGAGTCAATCCACAAGAAGTATCATGATTGAAAGCTCCTTATAC
1 TTAATCATGGAGTCAATCCACAAGAAGTATCATGATTGAAAGCTCCTTATAC
* * *
4338 TTAATCATGGAGTCAGTTCACGAGAAGTATCATGATTGAAAGCTCCTTAT
1 TTAATCATGGAGTCAATCCACAAGAAGTATCATGATTGAAAGCTCCTTAT
4388 TGTATACTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TTAATCATGGAGTCAATCCACAAGAAGTATCATGATTGAAAGCTCCTTATAC
Found at i:8532 original size:2 final size:2
Alignment explanation
Indices: 8525--8555 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8515 ACCAATTTGA
8525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8556 GGTACTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.