Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008246.1 Kokia drynarioides strain JFW-HI SEQ_122911, 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: 5628
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:484 original size:25 final size:24
Alignment explanation
Indices: 427--484 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 24
417 AAACTTGATG
*
427 AAAATTAATAAAATAAACGAATAAT
1 AAAATTAA-AAAATAAACGAATAAA
*
452 AAAA-TAAATAATAAA-GAACTAACA
1 AAAATTAAAAAATAAACGAA-TAA-A
476 AAAATTAAA
1 AAAATTAAA
485 CTAGGGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 7 0.25
25 8 0.29
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (24 bp):
AAAATTAAAAAATAAACGAATAAA
Found at i:3186 original size:40 final size:39
Alignment explanation
Indices: 3081--3169 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 39
3071 TGTCATGACG
* *
3081 TAGACATGCTATGTCTCATGACGAAAGGGGTTTGTTGTAACA
1 TAGACATTCTATG-C-CA-GACGAAGGGGGTTTGTTGTAACA
*
3123 TAGATATTCTATGCCATGACGAAGGGGGTTTGTTGTAACA
1 TAGACATTCTATGCCA-GACGAAGGGGGTTTGTTGTAACA
3163 TAGACAT
1 TAGACAT
3170 GTTATGTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 31 0.72
41 1 0.02
42 11 0.26
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (39 bp):
TAGACATTCTATGCCAGACGAAGGGGGTTTGTTGTAACA
Found at i:4409 original size:273 final size:275
Alignment explanation
Indices: 3921--4462 Score: 926
Period size: 273 Copynumber: 2.0 Consensus size: 275
3911 CTTTACAAAG
* * *
3921 CTCTTTATGGGCTGAAACAAGCTCCTAGAGCCTGGTATAATATAATTGACTCCTATTTACTACAA
1 CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
* *
3986 GAAAGGTTTATAAGAAGTGAAAGTGAAGCTACATTGTATGTTAAGAAGCTTGAGGATGAGAAGAA
66 GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
* * *
4051 ACTTATTGTTTCATTGTATGTTGATGATCTGCTTGTTATGGGAGATAATGAAGTGTCTATAGAGC
131 ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
* *
4116 AGTTCAAACAAAGAATGAAAAATATGTTTGAAATGTCTGATTT-GATAATATGAAGTGTTTTCTT
196 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
4180 GGGATGGAAATTCAC
261 GGGATGGAAATTCAC
* * *
4195 CTCTTTATGAGTTGAAACAAGCTCCTAAAGCCTGTTATATTAGAATTGACTCCTATTTACTACAA
1 CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
4260 G-AAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
66 GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
*
4324 ACTCATTGTTTGATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
131 ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
* *
4389 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGGTGATATGAAGTGTTTTCTT
196 AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
4454 GGGATGGAA
261 GGGATGGAA
4463 CCAATATGAT
Statistics
Matches: 251, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
273 163 0.65
274 88 0.35
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (275 bp):
CTCTTTATGAGCTGAAACAAGCTCCTAAAGCCTGGTATAATAGAATTGACTCCTATTTACTACAA
GAAAGGGTTATAAGAAGTGAAAGTGAAGCTACATTGCATGTTAAGAAGCTTGAGGATGAGAAGAA
ACTCATTGTTTCATTGTATGTTGATGATCTACTTGTAATGGGAGATAATGAAGTGTCTATAGAGC
AATTCAAACAAAGAATGAAAAATATGTTTGAAATGCCTGATTTGGATAATATGAAGTGTTTTCTT
GGGATGGAAATTCAC
Done.