Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005189.1 Kokia drynarioides strain JFW-HI SEQ_119047, 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: 8113
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:3259 original size:21 final size:21
Alignment explanation
Indices: 3208--3250 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3198 TAATACTTAG
*
3208 AATA-ATTTTTATAGAATTTT
1 AATACATTTTTATAAAATTTT
3228 AATACATTTTTATAAAATTTT
1 AATACATTTTTATAAAATTTT
3249 AA
1 AA
3251 ATATGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATACATTTTTATAAAATTTT
Found at i:3311 original size:26 final size:28
Alignment explanation
Indices: 3275--3333 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
3265 AGTTTATATT
3275 TTTTTACAATTTATTAGAA-TT-TTATA
1 TTTTTACAATTTATTAGAACTTCTTATA
* * *
3301 TTTTTATAATTTTTTATAACTTCTTATA
1 TTTTTACAATTTATTAGAACTTCTTATA
3329 TTTTT
1 TTTTT
3334 TATGGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.57
27 2 0.07
28 10 0.36
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTTACAATTTATTAGAACTTCTTATA
Found at i:3606 original size:26 final size:30
Alignment explanation
Indices: 3575--3635 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 30
3565 TTAAACATGC
*
3575 TTTATTA-ATTTT-ATATATT-TTTTGA-A
1 TTTATTAGATTTTAATATATTCTTTTAATA
3601 TTTATTAGATTTTAATATATTCTTTTAATA
1 TTTATTAGATTTTAATATATTCTTTTAATA
3631 TTTAT
1 TTTAT
3636 AAGTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.23
27 5 0.17
28 7 0.23
29 5 0.17
30 6 0.20
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTATTAGATTTTAATATATTCTTTTAATA
Found at i:3682 original size:7 final size:7
Alignment explanation
Indices: 3670--3719 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
3660 TTTATATAAA
3670 TTTTAAT
1 TTTTAAT
3677 TTTTAAT
1 TTTTAAT
*
3684 TTAATAATT
1 TT-TTAA-T
*
3693 TTTTTAT
1 TTTTAAT
3700 TTTATAAT
1 TTT-TAAT
3708 TTTTAAT
1 TTTTAAT
3715 TTTTA
1 TTTTA
3720 TGAGAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 22 0.61
8 11 0.31
9 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:3693 original size:15 final size:15
Alignment explanation
Indices: 3673--3716 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
3663 ATATAAATTT
3673 TAATTTTTAATTTAA
1 TAATTTTTAATTTAA
* *
3688 TAATTTTTTTATTTTA
1 TAA-TTTTTAATTTAA
3704 TAATTTTTAATTT
1 TAATTTTTAATTT
3717 TTATGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTAATTTAA
Found at i:3701 original size:68 final size:76
Alignment explanation
Indices: 3575--3711 Score: 166
Period size: 76 Copynumber: 1.9 Consensus size: 76
3565 TTAAACATGC
* **
3575 TTTATTAATTTTATATATTTTTTGAATTTATTAGATTTTAATATATTCTTTTA-ATATTTATAAG
1 TTTATTAAGTTTATATAAATTTTGAATTTATTAGATTTTAATATATTCTTTTATAT-TTTATAA-
3639 TTTTTTTATTGTT
64 TTTTTTTATTGTT
3652 TTTA-TAAGTTTATATAAATTTT-AATTT-TTA-A-TTTAATA-ATT-TTTT-TATTTTATAATT
1 TTTATTAAGTTTATATAAATTTTGAATTTATTAGATTTTAATATATTCTTTTATATTTTATAATT
3709 TTT
66 TTT
3712 AATTTTTATG
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
68 5 0.09
69 7 0.12
70 6 0.11
71 3 0.05
72 7 0.12
73 1 0.02
74 3 0.05
75 5 0.09
76 15 0.27
77 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.65
Consensus pattern (76 bp):
TTTATTAAGTTTATATAAATTTTGAATTTATTAGATTTTAATATATTCTTTTATATTTTATAATT
TTTTTATTGTT
Found at i:3707 original size:24 final size:24
Alignment explanation
Indices: 3651--3718 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
3641 TTTTTATTGT
*
3651 TTTTATAAGTTTATATAA-ATTTTAA
1 TTTTATAA-TTTA-ATAATTTTTTAA
*
3676 TTTT-TAATTTAATAATTTTTTTA
1 TTTTATAATTTAATAATTTTTTAA
*
3699 TTTTATAATTT-TTAATTTTT
1 TTTTATAATTTAATAATTTTT
3719 ATGAGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.11
23 21 0.55
24 9 0.24
25 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (24 bp):
TTTTATAATTTAATAATTTTTTAA
Found at i:4290 original size:33 final size:33
Alignment explanation
Indices: 4253--4354 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
4243 ATGTTACAAT
4253 TTTAATAGTTTATATTTTTATAATTTATAAAA-A
1 TTTAATA-TTTATATTTTTATAATTTATAAAACA
* * *
4286 TTTAA-ATTAAT-TTTTTATTATTTTTAAAACA
1 TTTAATATTTATATTTTTATAATTTATAAAACA
* * * *
4317 -TTACTAATTTAAATTTTTATAAATTATAAAAGA
1 TTTAAT-ATTTATATTTTTATAATTTATAAAACA
4350 TTTAA
1 TTTAA
4355 ATGATAAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
30 19 0.36
31 5 0.09
32 5 0.09
33 21 0.40
34 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (33 bp):
TTTAATATTTATATTTTTATAATTTATAAAACA
Found at i:4363 original size:33 final size:30
Alignment explanation
Indices: 4266--4365 Score: 101
Period size: 33 Copynumber: 3.1 Consensus size: 30
4256 AATAGTTTAT
4266 ATTTTTATAATTTATAAAAATTTAAATTAA
1 ATTTTTATAATTTATAAAAATTTAAATTAA
* * * *
4296 TTTTTTATTATTTTTAAAACATTACTAATTTAA
1 ATTTTTATAATTTATAAAA-ATT--TAAATTAA
*
4329 ATTTTTATAAATTATAAAAGATTTAAATGATAA
1 ATTTTTATAATTTATAAAA-ATTTAAAT--TAA
4362 ATTT
1 ATTT
4366 CGTATTAGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
30 16 0.29
31 7 0.13
33 32 0.58
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTTTATAATTTATAAAAATTTAAATTAA
Done.