Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020526.1 Corchorus olitorius cultivar O-4 contig20559, 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: 14881
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:2014 original size:13 final size:13
Alignment explanation
Indices: 1996--2020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1986 AAAGTAATAA
1996 TACTATTATTAAT
1 TACTATTATTAAT
2009 TACTATTATTAA
1 TACTATTATTAA
2021 CACTATTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TACTATTATTAAT
Found at i:8443 original size:5 final size:5
Alignment explanation
Indices: 8433--8466 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
8423 TAATAATCAA
8433 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
8467 ACATTGAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12972 original size:39 final size:40
Alignment explanation
Indices: 12916--12996 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
12906 TTTAATTCCT
12916 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * * *
12956 ATGTAATA-CTATAATAACTGAAATCCTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
12995 AT
1 AT
12997 TCTTAGATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:13022 original size:24 final size:23
Alignment explanation
Indices: 12987--13032 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
12977 AATCCTTATA
12987 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
*
13010 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
13033 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Found at i:13485 original size:200 final size:207
Alignment explanation
Indices: 13103--13515 Score: 705
Period size: 208 Copynumber: 2.0 Consensus size: 207
13093 TTCCTTAATA
13103 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
13168 AATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTTCTATATATATATATA
66 AATTTAATAAATCAACCACTAATATTCAACT-ATTTTTTTTGGTATAGTTCTATATATATATATA
*
13233 ATAGTAATGTGTTGTATCTTATACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACA
130 ATAGTAATGTATTGTATCTTATACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACA
* *
13298 ACGTTCATCATTG
195 ACATTCACCATTG
13311 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
13376 AATTTAATAAATCAAGCACTAATGTTCAACT-TTTTTTTTGGTATAGTT-T-TATATATA-AT-A
66 AATTTAATAAATCAACCACTAATATTCAACTATTTTTTTTGGTATAGTTCTATATATATATATAA
* *
13436 -A-TAATGTATTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA
131 TAGTAATGTATTGTATCTTATACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAA
13499 CATTCACCATTG
196 CATTCACCATTG
13511 ATAAA
1 ATAAA
13516 GTTATTAAGC
Statistics
Matches: 198, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
200 74 0.37
201 1 0.01
202 1 0.01
203 2 0.01
204 8 0.04
205 1 0.01
206 17 0.09
208 94 0.47
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (207 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATATTCAACTATTTTTTTTGGTATAGTTCTATATATATATATAA
TAGTAATGTATTGTATCTTATACACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAACAA
CATTCACCATTG
Found at i:14072 original size:36 final size:36
Alignment explanation
Indices: 14025--14094 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
14015 AAGATTTTGG
* *
14025 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
14061 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
14095 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.