Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001596.1 Kokia drynarioides strain JFW-HI SEQ_113217, 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: 6310
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Found at i:4483 original size:10 final size:10
Alignment explanation
Indices: 4463--4537 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
4453 TTGCTTTATA
*
4463 TTTTGCTTTG
1 TTTTACTTTG
*
4473 TATTACTTTG
1 TTTTACTTTG
* *
4483 TTTTGCTTTT
1 TTTTACTTTG
4493 TTTTA-TATTG
1 TTTTACT-TTG
*
4503 TTTTACTTTA
1 TTTTACTTTG
*
4513 TATTACTTTG
1 TTTTACTTTG
*
4523 TTTTGCTTTG
1 TTTTACTTTG
*
4533 CTTTA
1 TTTTA
4538 TATTATTTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
9 1 0.02
10 47 0.96
11 1 0.02
ACGTcount: A:0.12, C:0.09, G:0.11, T:0.68
Consensus pattern (10 bp):
TTTTACTTTG
Found at i:4488 original size:20 final size:20
Alignment explanation
Indices: 4463--4841 Score: 197
Period size: 20 Copynumber: 19.2 Consensus size: 20
4453 TTGCTTTATA
*
4463 TTTTGCTTTGTATTACTTTG
1 TTTTGCTTTATATTACTTTG
* *
4483 TTTTGCTTTTTTTTA-TATTG
1 TTTTGCTTTATATTACT-TTG
*
4503 TTTTACTTTATATTACTTTG
1 TTTTGCTTTATATTACTTTG
*
4523 TTTTGCTTTGCTTTATATTATTTTG
1 ---T--TTTGCTTTATATTACTTTG
* * *
4548 TTTTGTTTTACATTGCTTTG
1 TTTTGCTTTATATTACTTTG
* * *
4568 TATTACTTTACGTCGCTTTA-TATT-
1 TTTTGCTTTA--T---ATTACT-TTG
4592 TCTTTGCTTTATA-TAGCTTTG
1 T-TTTGCTTTATATTA-CTTTG
* *
4613 TTTTGTTTTATATTGCTTTG
1 TTTTGCTTTATATTACTTTG
*
4633 CTTTG-TTT-TA-TA-TTT-
1 TTTTGCTTTATATTACTTTG
*
4648 TTTTGTTTTATATTACTTTG
1 TTTTGCTTTATATTACTTTG
*
4668 CTTTGC-TT-TA-TA--TTG
1 TTTTGCTTTATATTACTTTG
* *
4683 TTTTGTTTTATATTGCTTTG
1 TTTTGCTTTATATTACTTTG
* *
4703 CTTTG-TTT-T-GTA--TTG
1 TTTTGCTTTATATTACTTTG
*
4718 CTTTGCTTTATATTACTTTG
1 TTTTGCTTTATATTACTTTG
* *
4738 CTTTGTTTTATATTGA-TTTG
1 TTTTGCTTTATATT-ACTTTG
* * *
4758 TTTTGTTTTGTATTGCTTTG
1 TTTTGCTTTATATTACTTTG
* *
4778 CTTTGTTTTATATTACTTTG
1 TTTTGCTTTATATTACTTTG
*
4798 CTTTGCTTTATATTACTTTG
1 TTTTGCTTTATATTACTTTG
*
4818 TTTTGCTTTA-CTTAGCTTTG
1 TTTTGCTTTATATTA-CTTTG
4838 TTTT
1 TTTT
4842 ATATACATTT
Statistics
Matches: 279, Mismatches: 44, Indels: 72
0.71 0.11 0.18
Matches are distributed among these distances:
15 19 0.07
16 11 0.04
17 9 0.03
18 10 0.04
19 17 0.06
20 175 0.63
21 5 0.02
22 1 0.00
23 2 0.01
24 2 0.01
25 28 0.10
ACGTcount: A:0.13, C:0.09, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTTGCTTTATATTACTTTG
Found at i:4574 original size:65 final size:65
Alignment explanation
Indices: 4500--4632 Score: 162
Period size: 65 Copynumber: 2.0 Consensus size: 65
4490 TTTTTTTATA
* * * * *
4500 TTGTTTTACTTTATATTACTTTGT-TTTGCTTTGCTTTATATTA-TTTTGTTTTGTTTTACATTG
1 TTGTATTACTTTACATCACTTTATATTT-CTTTGCTTTATA-TAGCTTTGTTTTGTTTTACATTG
4563 CT
64 CT
* * *
4565 TTGTATTACTTTACGTCGCTTTATATTTCTTTGCTTTATATAGCTTTGTTTTGTTTTATATTGCT
1 TTGTATTACTTTACATCACTTTATATTTCTTTGCTTTATATAGCTTTGTTTTGTTTTACATTGCT
4630 TTG
1 TTG
4633 CTTTGTTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.03
65 53 0.91
66 3 0.05
ACGTcount: A:0.14, C:0.11, G:0.12, T:0.63
Consensus pattern (65 bp):
TTGTATTACTTTACATCACTTTATATTTCTTTGCTTTATATAGCTTTGTTTTGTTTTACATTGCT
Found at i:4623 original size:35 final size:34
Alignment explanation
Indices: 4525--4781 Score: 168
Period size: 35 Copynumber: 7.4 Consensus size: 34
4515 TTACTTTGTT
* *
4525 TTGCTTTGCTTTATATTATTTTGTTTTGTTTTACA
1 TTGCTTTGCTTTAT-TTAGTTTGTTTTGTTTTATA
* *** * *
4560 TTGCTTTG---TA-TTACTTTACGTCGCTTTATA
1 TTGCTTTGCTTTATTTAGTTTGTTTTGTTTTATA
* *
4590 TTTCTTTGCTTTATATAGCTTTGTTTTGTTTTATA
1 TTGCTTTGCTTTATTTAG-TTTGTTTTGTTTTATA
* *
4625 TTGCTTTGCTTTGTTTTA-TATTTTTTTGTTTTATA
1 TTGCTTTGCTTT-ATTTAGT-TTGTTTTGTTTTATA
* *
4660 TTACTTTGCTTTGCTTTA-TATTGTTTTGTTTTATA
1 TTGCTTTGCTTT-ATTTAGT-TTGTTTTGTTTTATA
* * *
4695 TTGCTTTGCTTTGTTTTGTATTGCTTTGCTTTATATTA
1 TTGCTTTGCTTTATTTAGT-TTGTTTTG-TTT-TA-TA
* *
4733 CTTTGCTTTGTTTTATATT-GATTTGTTTTGTTTTGTA
1 --TTGCTTTGCTTTAT-TTAG-TTTGTTTTGTTTTATA
4770 TTGCTTTGCTTT
1 TTGCTTTGCTTT
4782 GTTTTATATT
Statistics
Matches: 176, Mismatches: 31, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
30 20 0.11
32 2 0.01
33 2 0.01
34 6 0.03
35 107 0.61
36 6 0.03
37 4 0.02
38 3 0.02
39 3 0.02
40 20 0.11
41 3 0.02
ACGTcount: A:0.12, C:0.09, G:0.13, T:0.65
Consensus pattern (34 bp):
TTGCTTTGCTTTATTTAGTTTGTTTTGTTTTATA
Found at i:4634 original size:70 final size:68
Alignment explanation
Indices: 4528--4801 Score: 236
Period size: 70 Copynumber: 3.9 Consensus size: 68
4518 CTTTGTTTTG
* * * * *
4528 CTTTGCTTTATATTATTTTGTTTTGTTTTACATTGCTTTG---T-ATTACT-TTACGTCGCTTTA
1 CTTTGCTTTATA-TAGTTTGTTTTGTTTTATATTGCTTTGCTTTGTTTA-TATTACTTTGCTTTA
4588 TATTT
64 TATTT
** *
4593 CTTTGCTTTATATAGCTTTGTTTTGTTTTATATTGCTTTGCTTTGTTTTATATTTTTTTGTTTTA
1 CTTTGCTTTATATAG-TTTGTTTTGTTTTATATTGCTTTGCTTTG-TTTATATTACTTTGCTTTA
*
4658 TATTA
64 TATTT
* * * *
4663 CTTTGCTTTGCTTTA-TATTGTTTTGTTTTATATTGCTTTGCTTTGTTTTGTATTGCTTTGCTTT
1 CTTTGCTTT-ATATAGT-TTGTTTTGTTTTATATTGCTTTGCTTTG-TTTATATTACTTTGC-TT
4727 ATATTACTTT
62 -TA-TA-TTT
* * *
4737 GCTTTGTTTTATATTGATTTGTTTTGTTTTGTATTGCTTTGCTTTGTTTTATATTACTTTGCTTT
1 -CTTTGCTTTATATAG-TTTGTTTTGTTTTATATTGCTTTGCTTTG-TTTATATTACTTTGCTTT
4802 GCTTTATATT
Statistics
Matches: 170, Mismatches: 23, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
64 2 0.01
65 35 0.21
68 1 0.01
69 2 0.01
70 64 0.38
71 5 0.03
72 2 0.01
73 3 0.02
74 6 0.04
75 49 0.29
76 1 0.01
ACGTcount: A:0.13, C:0.09, G:0.13, T:0.65
Consensus pattern (68 bp):
CTTTGCTTTATATAGTTTGTTTTGTTTTATATTGCTTTGCTTTGTTTATATTACTTTGCTTTATA
TTT
Found at i:4822 original size:55 final size:55
Alignment explanation
Indices: 4524--4845 Score: 238
Period size: 55 Copynumber: 5.9 Consensus size: 55
4514 ATTACTTTGT
* * *
4524 TTTGCTTTGCTTTATATTATTTTGTTTTGTTTTACATTGCTTTG-----TATTAC
1 TTTGCTTTGCTTTATATTACTTTGTTTTGTATTACTTTGCTTTGTTTTATATTAC
* * * * * * * *
4574 TTTACGTCGCTTTATATTTCTTTGCTTTATA-TAGCTTTGTTTTGTTTTATATTGC
1 TTTGCTTTGCTTTATATTACTTTGTTTTGTATTA-CTTTGCTTTGTTTTATATTAC
* ** * *
4629 TTTGCTTTGTTTTATATTTTTTTGTTTTATATTACTTTGCTTTG-CTT-TA-TA-
1 TTTGCTTTGCTTTATATTACTTTGTTTTGTATTACTTTGCTTTGTTTTATATTAC
* * * * ** *
4680 -TTGTTTTGTTTTATATTGCTTTGCTTTGT-TTTGTATTGCTTTGCTTTATATTAC
1 TTTGCTTTGCTTTATATTACTTTGTTTTGTATTACT-TTGCTTTGTTTTATATTAC
* * *
4734 TTTGCTTTGTTTTATATTGATTTGTTTTGTTTTGTATTGCTTTGCTTTGTTTTATATTAC
1 TTTGCTTTGCTTTATATT-A----CTTTGTTTTGTATTACTTTGCTTTGTTTTATATTAC
*
4794 TTTGCTTTGCTTTATATTACTTTGTTTTGCT-TTACTTAGCTTTGTTTTATAT
1 TTTGCTTTGCTTTATATTACTTTGTTTTG-TATTACTTTGCTTTGTTTTATAT
4846 ACATTTAAAC
Statistics
Matches: 213, Mismatches: 39, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
49 5 0.02
50 63 0.30
51 2 0.01
52 3 0.01
53 4 0.02
54 2 0.01
55 83 0.39
56 3 0.01
59 1 0.00
60 44 0.21
61 3 0.01
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (55 bp):
TTTGCTTTGCTTTATATTACTTTGTTTTGTATTACTTTGCTTTGTTTTATATTAC
Found at i:4837 original size:40 final size:39
Alignment explanation
Indices: 4593--4837 Score: 183
Period size: 35 Copynumber: 6.5 Consensus size: 39
4583 CTTTATATTT
* * * *
4593 CTTTGCTTTATATAGCTTTGTTTTGTTTTATATTGCTTTG
1 CTTTGTTTTAT-TAGCTTTGCTTTGCTTTATATTACTTTG
* *
4633 CTTTGTTTTA-TA--TTT-TTTTGTTTTATATTACTTTG
1 CTTTGTTTTATTAGCTTTGCTTTGCTTTATATTACTTTG
* * * *
4668 CTTTGCTTTA-TA---TTGTTTTGTTTTATATTGCTTTG
1 CTTTGTTTTATTAGCTTTGCTTTGCTTTATATTACTTTG
*
4703 CTTTGTTTT-GTA---TTGCTTTGCTTTATATTACTTTG
1 CTTTGTTTTATTAGCTTTGCTTTGCTTTATATTACTTTG
* * * * * *
4738 CTTTGTTTTATATTGATTTGTTTTGTTTTGTATTGCTTTG
1 CTTTGTTTTAT-TAGCTTTGCTTTGCTTTATATTACTTTG
4778 CTTTGTTTTATATTA-CTTTGCTTTGCTTTATATTACTTTG
1 CTTTG-TTT-TATTAGCTTTGCTTTGCTTTATATTACTTTG
* *
4818 TTTTGCTTTACTTAGCTTTG
1 CTTTGTTTTA-TTAGCTTTG
4838 TTTTATATAC
Statistics
Matches: 172, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.01
35 88 0.51
36 3 0.02
37 1 0.01
38 4 0.02
39 5 0.03
40 62 0.36
41 4 0.02
42 3 0.02
ACGTcount: A:0.12, C:0.09, G:0.13, T:0.65
Consensus pattern (39 bp):
CTTTGTTTTATTAGCTTTGCTTTGCTTTATATTACTTTG
Found at i:5120 original size:28 final size:29
Alignment explanation
Indices: 5089--5144 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
5079 TTTTTCAACA
5089 TATAATATTATATAT-AAATTTTGATTTG
1 TATAATATTATATATGAAATTTTGATTTG
* *
5117 TATAATTTTATATATGATATTTTGATTT
1 TATAATATTATATATGAAATTTTGATTT
5145 TATTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (29 bp):
TATAATATTATATATGAAATTTTGATTTG
Found at i:5153 original size:30 final size:28
Alignment explanation
Indices: 5089--5165 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
5079 TTTTTCAACA
*
5089 TATAATATTATATATAAATTTTGATTTG
1 TATAATTTTATATATAAATTTTGATTTG
*
5117 TATAATTTTATATATGATATTTTGATTT-
1 TATAATTTTATATAT-AAATTTTGATTTG
*
5145 TATTTAATTTT-TTTATAAATT
1 TA--TAATTTTATATATAAATT
5166 ATCAACACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
28 20 0.48
29 15 0.36
30 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TATAATTTTATATATAAATTTTGATTTG
Done.