Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006304.1 Kokia drynarioides strain JFW-HI SEQ_120878, 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: 49077
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:6668 original size:68 final size:69
Alignment explanation
Indices: 6536--6670 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 69
6526 TGCACTGATA
6536 ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAACATAGACTC
1 ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAACATAGACTC
6601 GATT
66 GATT
* *
6605 ATTTGTTTTCAAAGATGATGAAACATTTACA-TCCCAGAGTTCATCAATGAAGAAACATTGACTC
1 ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAACATAGACTC
6669 GA
66 GA
6671 AACAATCTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 33 0.52
69 31 0.48
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (69 bp):
ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAACATAGACTC
GATT
Found at i:9716 original size:21 final size:21
Alignment explanation
Indices: 9692--9736 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9682 CTCCTCTGTA
*
9692 TCCTCTGTCTCCTCAGCGGCC
1 TCCTCTGTCTCCTCAGCAGCC
*
9713 TCCTCTGTCTCCTCTGCAGCC
1 TCCTCTGTCTCCTCAGCAGCC
9734 TCC
1 TCC
9737 ATTTCCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.49, G:0.16, T:0.31
Consensus pattern (21 bp):
TCCTCTGTCTCCTCAGCAGCC
Found at i:22094 original size:19 final size:20
Alignment explanation
Indices: 22067--22106 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
22057 TATATAAATG
22067 TTTATAATATATTATTAAAA
1 TTTATAATATATTATTAAAA
*
22087 TTTA-AATATATTTTTAAAA
1 TTTATAATATATTATTAAAA
22106 T
1 T
22107 GTTCCATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATAATATATTATTAAAA
Found at i:22676 original size:18 final size:18
Alignment explanation
Indices: 22636--22678 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
22626 TTTTCAGTTG
22636 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
22654 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
22672 TAATTAA
1 TAATTAA
22679 AAATATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:28064 original size:256 final size:256
Alignment explanation
Indices: 27604--28121 Score: 865
Period size: 256 Copynumber: 2.0 Consensus size: 256
27594 TTGTCACTTT
27604 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAA-TTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
* * * * *
27669 GTGTTGAATTTTTCTCAATGACACTACTATGTGAATAACTATTTACTATATTCTTTAGGGATAAT
65 GCGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAAT
* * * **
27734 TATTCATATCCAGTTGGATTTGAAGTAATCATTACCACAATAATGTCTTCAAGTAGTGAATATTG
130 TATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTG
*
27799 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCTACTATATTTGCTCAACCCA
195 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
* *
27861 TCAATTTAAATTGAAACAAAGACTATGGGGCGTAGTTTTATGATAGTTTGCTTAATTAGATTCAG
1 TCAATTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCAG
* *
27926 CGTTGAATCTTTCTCATTAACACTAATATTTGAATAACTATTTAATATATTCTTTAGGGATAATT
66 CGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAATT
* *
27991 ATTCATATCCAGTTGGATTTGTAGTAATAAATACCACAATAATGTGTTAAAGTACAGAATATTGA
131 ATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTGA
*
28056 TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACTCA
196 TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
28117 TCAAT
1 TCAAT
28122 GTTTTGCTAT
Statistics
Matches: 243, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
256 239 0.98
257 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (256 bp):
TCAATTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCAG
CGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAATT
ATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTGA
TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
Found at i:34496 original size:31 final size:31
Alignment explanation
Indices: 34459--34517 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
34449 CATCAGCTAT
34459 TATTTACTAAATTTCTTATTGGCTTTATAAC
1 TATTTACTAAATTTCTTATTGGCTTTATAAC
34490 TATTTACTAAATTTCTTATTGGCTTTAT
1 TATTTACTAAATTTCTTATTGGCTTTAT
34518 TATTGCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (31 bp):
TATTTACTAAATTTCTTATTGGCTTTATAAC
Done.