Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007233.1 Kokia drynarioides strain JFW-HI SEQ_121848, 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: 29699
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:3447 original size:21 final size:22
Alignment explanation
Indices: 3423--3469 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3413 AGAGATAATA
*
3423 TCTCTA-TTTCATACCATCATT
1 TCTCTATTTTCATACAATCATT
*
3444 TCTCTATTTTCATACAATTATT
1 TCTCTATTTTCATACAATCATT
3466 TCTC
1 TCTC
3470 CATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (22 bp):
TCTCTATTTTCATACAATCATT
Found at i:13493 original size:25 final size:25
Alignment explanation
Indices: 13464--13520 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
13454 AAAAGTATTG
*
13464 ACAATTTAAAATTCAGTTATCTTTA
1 ACAATATAAAATTCAGTTATCTTTA
13489 ACAATATAAAATTCAGTTATCTTTA
1 ACAATATAAAATTCAGTTATCTTTA
13514 ACAATAT
1 ACAATAT
13521 TAGTTGGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (25 bp):
ACAATATAAAATTCAGTTATCTTTA
Found at i:17491 original size:25 final size:24
Alignment explanation
Indices: 17441--17493 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
17431 GTCCATATTA
17441 TTTTTAATTTTTAATATTTAATAAT
1 TTTTTAATTTTT-ATATTTAATAAT
*
17466 TTTTTACATTTTT-TATTTATTGAAT
1 TTTTTA-ATTTTTATATTTAAT-AAT
17491 TTT
1 TTT
17494 GTATATAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTAATTTTTATATTTAATAAT
Found at i:19564 original size:22 final size:22
Alignment explanation
Indices: 19481--19564 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 22
19471 TTTTTTAACA
* *
19481 TATTACTAAATTAAAATTTA-AAA
1 TATTA-TAAATT-TAATTTAGAAT
*
19504 TAATATAATATTTAATTTAGAATT
1 TATTATAA-ATTTAATTTAGAA-T
*
19528 ATATTTTGATGAATTTAATTTAGAAT
1 -TA--TT-ATAAATTTAATTTAGAAT
19554 TATTATAAATT
1 TATTATAAATT
19565 AAAAAAGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
22 15 0.31
23 11 0.23
25 4 0.08
26 1 0.02
27 14 0.29
28 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (22 bp):
TATTATAAATTTAATTTAGAAT
Found at i:20979 original size:39 final size:39
Alignment explanation
Indices: 20925--21002 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
20915 TATAAGCTCA
20925 AAACCAATGGAGGGTAAGGAAGAAAAGAAGGAGATTGTG
1 AAACCAATGGAGGGTAAGGAAGAAAAGAAGGAGATTGTG
20964 AAACCAATGGAGGGTAAGGAAGAAAAGAAGGAGATTGTG
1 AAACCAATGGAGGGTAAGGAAGAAAAGAAGGAGATTGTG
21003 GAAGTTGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.05, G:0.36, T:0.13
Consensus pattern (39 bp):
AAACCAATGGAGGGTAAGGAAGAAAAGAAGGAGATTGTG
Found at i:23932 original size:25 final size:26
Alignment explanation
Indices: 23898--23953 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
23888 AATACAAACA
* * * *
23898 AATTGAATCTGATTTGAATTTTAA-T
1 AATTTAATCTGAATCGAATTTAAATT
23923 AATTTAATCTGAATCGAATTTAAATT
1 AATTTAATCTGAATCGAATTTAAATT
23949 AATTT
1 AATTT
23954 TAAACTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (26 bp):
AATTTAATCTGAATCGAATTTAAATT
Found at i:26370 original size:31 final size:31
Alignment explanation
Indices: 26335--26393 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
26325 AGTAATAAAA
26335 TTTAATAGTTT-ATTTGATAAATAAATTTAAT
1 TTTAATA-TTTAATTTGATAAATAAATTTAAT
**
26366 TTTAATATTTAATTTGATATTTAAATTT
1 TTTAATATTTAATTTGATAAATAAATTT
26394 TTTTTATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTAATATTTAATTTGATAAATAAATTTAAT
Found at i:26834 original size:22 final size:21
Alignment explanation
Indices: 26804--26844 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
26794 TTTCTAATAA
* *
26804 TTTTTATAATTTTTTTTATCG
1 TTTTTATAAATTTTATTATCG
26825 TTTTTAATAAATTTTATTAT
1 TTTTT-ATAAATTTTATTAT
26845 TTTAAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTATAAATTTTATTATCG
Found at i:28738 original size:13 final size:13
Alignment explanation
Indices: 28720--28762 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
28710 TTTAAACTTG
*
28720 AACTCAAATCCTA
1 AACTCAAACCCTA
28733 AACTCAAACCCTA
1 AACTCAAACCCTA
*
28746 AACCTCAAACTCTA
1 AA-CTCAAACCCTA
28760 AAC
1 AAC
28763 ATTAAACTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (13 bp):
AACTCAAACCCTA
Found at i:28754 original size:14 final size:14
Alignment explanation
Indices: 28722--28762 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
28712 TAAACTTGAA
*
28722 CTCAAATCCTAAA-
1 CTCAAACCCTAAAC
28735 CTCAAACCCTAAAC
1 CTCAAACCCTAAAC
*
28749 CTCAAACTCTAAAC
1 CTCAAACCCTAAAC
28763 ATTAAACTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.20
Consensus pattern (14 bp):
CTCAAACCCTAAAC
Found at i:28769 original size:14 final size:14
Alignment explanation
Indices: 28730--28771 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
28720 AACTCAAATC
*
28730 CTAAAC-TCAAACC
1 CTAAACATCAAACT
*
28743 CTAAACCTCAAACT
1 CTAAACATCAAACT
*
28757 CTAAACATTAAACT
1 CTAAACATCAAACT
28771 C
1 C
28772 GAATTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACATCAAACT
Done.