Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013469.1 Kokia drynarioides strain JFW-HI SEQ_128495, 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: 6046
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:401 original size:11 final size:11
Alignment explanation
Indices: 385--447 Score: 81
Period size: 11 Copynumber: 5.7 Consensus size: 11
375 AAAAGGCAGC
385 AATATAAATAT
1 AATATAAATAT
*
396 AATATAAATCT
1 AATATAAATAT
*
407 AAAATAAATAT
1 AATATAAATAT
*
418 AATATAAGTAT
1 AATATAAATAT
* *
429 AATACAAATCT
1 AATATAAATAT
440 AATATAAA
1 AATATAAA
448 ACTAATAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (11 bp):
AATATAAATAT
Found at i:454 original size:33 final size:33
Alignment explanation
Indices: 385--447 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
375 AAAAGGCAGC
*
385 AATATAAATATAATATAAATCTAAAATAAATAT
1 AATATAAATATAATACAAATCTAAAATAAATAT
* *
418 AATATAAGTATAATACAAATCTAATATAAA
1 AATATAAATATAATACAAATCTAAAATAAA
448 ACTAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (33 bp):
AATATAAATATAATACAAATCTAAAATAAATAT
Found at i:3102 original size:30 final size:30
Alignment explanation
Indices: 3068--3200 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
3058 TAGAAATCAT
* *
3068 ATTTTGACCCTCGAACTTTCAAAAAATATC
1 ATTTTGACCCTCAAACTTTCAAAAATTATC
* * *
3098 ATTTTTTA-CCTTAAACTTTCCAAAAATTACC
1 A-TTTTGACCCTCAAACTTT-CAAAAATTATC
** * *
3129 ATTTT-ACCC-CGGA-TGTCCAAAATTA-C
1 ATTTTGACCCTCAAACTTTCAAAAATTATC
*
3155 AATTTTGACCCTAAAACTTTCAAAAATTATC
1 -ATTTTGACCCTCAAACTTTCAAAAATTATC
* *
3186 ATTTTTACCCCCAAA
1 ATTTTGACCCTCAAA
3201 TATCCAGAAT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
26 1 0.01
27 13 0.17
28 6 0.08
29 3 0.04
30 38 0.49
31 16 0.21
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTTCAAAAATTATC
Found at i:3172 original size:58 final size:57
Alignment explanation
Indices: 3110--3386 Score: 299
Period size: 58 Copynumber: 4.8 Consensus size: 57
3100 TTTTTACCTT
* *
3110 AAACTTTCCAAAAATTACCATTTTA-CCCCGGATGTCCAAAATTACAATTTTGACCCTA
1 AAAC-TTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTACATTTTTGACCC-A
* * * * * *
3168 AAACTTTCAAAAATTATCATTTTTACCCCCAAATATCCAGAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCCCGAATGTCCAAAATTACATTTTTGA-CCCA
* * * * *
3227 AAACTTCTAAAAATTACTATTTTACCCCCTAATGTCCAAAAATTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCC-AAAATTACATTTTTGACCCA
* *
3285 AAACTTCCAAAAATTACCATTTTACCCCTCGAATGTCTAAAA--ACTATTTTTGACCACG
1 AAACTTCCAAAAATTACCATTTTACCCC-CGAATGTCCAAAATTAC-ATTTTTGACC-CA
* * *
3343 AACCTTCCAAAAATTACCATTTTACCCTCGAGTGTCCAAAATTA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTA
3387 TCGTTTTACC
Statistics
Matches: 185, Mismatches: 25, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 34 0.18
58 86 0.46
59 61 0.33
60 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTACATTTTTGACCCA
Found at i:3253 original size:29 final size:30
Alignment explanation
Indices: 3110--3312 Score: 142
Period size: 29 Copynumber: 7.0 Consensus size: 30
3100 TTTTTACCTT
3110 AAACTTTCCAAAAATTACCATTTT-ACCCC-
1 AAAC-TTCCAAAAATTACCATTTTGACCCCA
** * *
3139 GGA-TGTCC-AAAATTACAATTTTGACCCTA
1 AAACT-TCCAAAAATTACCATTTTGACCCCA
* * * *
3168 AAACTTTCAAAAATTATCATTTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTGACCCCA
*
3198 AAA-TATCC-AGAATT-CCATTTTTGACCCCA
1 AAACT-TCCAAAAATTACCA-TTTTGACCCCA
* * *
3227 AAACTTCTAAAAATTACTATTTT-ACCCCC
1 AAACTTCCAAAAATTACCATTTTGACCCCA
* *
3256 TAA-TGTCCAAAAATT-CCATTTTTGA-CCCG
1 AAACT-TCCAAAAATTACCA-TTTTGACCCCA
3285 AAACTTCCAAAAATTACCATTTT-ACCCC
1 AAACTTCCAAAAATTACCATTTTGACCCC
3313 TCGAATGTCT
Statistics
Matches: 132, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
27 14 0.11
28 13 0.10
29 66 0.50
30 37 0.28
31 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTTGACCCCA
Found at i:3380 original size:29 final size:29
Alignment explanation
Indices: 3116--3413 Score: 117
Period size: 29 Copynumber: 10.3 Consensus size: 29
3106 CCTTAAACTT
*
3116 TCCAAAAATTACCATTTTACCC-CGGATG
1 TCCAAAAATTACCATTTTACCCTCGAATG
* **
3144 TCC-AAAATTACAATTTTGACCCTAAAACT-
1 TCCAAAAATTACCATTTT-ACCCTCGAA-TG
* * * * *
3173 TTCAAAAATTATCATTTTTACCCCCAAATA
1 TCCAAAAATTACCA-TTTTACCCTCGAATG
* *
3203 TCC-AGAATT-CCATTTTTGACCC-CAAAACT-
1 TCCAAAAATTACCA-TTTT-ACCCTC-GAA-TG
* * * *
3232 TCTAAAAATTACTATTTTACCCCCTAATG
1 TCCAAAAATTACCATTTTACCCTCGAATG
3261 TCCAAAAATT-CCATTTTTGA-CC-CGAAACT-
1 TCCAAAAATTACCA-TTTT-ACCCTCG-AA-TG
3290 TCCAAAAATTACCATTTTACCCCTCGAATG
1 TCCAAAAATTACCATTTTA-CCCTCGAATG
* * * *
3320 TCTAAAAACTA--TTTTTGA-CCACGAACCT-
1 TCCAAAAATTACCATTTT-ACCCTCGAA--TG
*
3348 TCCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTACCATTTTACCCTCGAATG
* * **
3377 TCC-AAAATTATCGTTTTA-CCTCCGAACA
1 TCCAAAAATTACCATTTTACCCT-CGAATG
3405 TCCAAAAAT
1 TCCAAAAAT
3414 CACTTTTTTA
Statistics
Matches: 206, Mismatches: 33, Indels: 61
0.69 0.11 0.20
Matches are distributed among these distances:
27 22 0.11
28 53 0.26
29 67 0.33
30 56 0.27
31 8 0.04
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAATG
Done.