Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018902.1 Corchorus olitorius cultivar O-4 contig18935, 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: 15667
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:10345 original size:13 final size:12
Alignment explanation
Indices: 10303--10347 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
10293 TCATGCACCC
10303 AAAACAATTTATTT
1 AAAACAATTTA--T
*
10317 AAAACCATTTAT
1 AAAACAATTTAT
10329 AAAACAATTTGAT
1 AAAACAATTT-AT
10342 AAAACA
1 AAAACA
10348 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAACAATTTAT
Found at i:12874 original size:22 final size:22
Alignment explanation
Indices: 12849--12973 Score: 87
Period size: 22 Copynumber: 5.7 Consensus size: 22
12839 ATAGGAAAGT
*
12849 TTATTAAAATTTCATAGTTAGA
1 TTATCAAAATTTCATAGTTAGA
* * *
12871 TTATCAAAGTTTCATA-TGGAGT
1 TTATCAAAATTTCATAGT-TAGA
* * *
12893 TTATCACAATTTTATAGGTA-A
1 TTATCAAAATTTCATAGTTAGA
* *
12914 TTATCAAAATTTCATATGGT-GG
1 TTATCAAAATTTCATA-GTTAGA
* * *
12936 TTTTCAAAATTTAATAGGGTA-A
1 TTATCAAAATTTCATA-GTTAGA
12958 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
12974 AAAATATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
21 15 0.19
22 64 0.81
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:12895 original size:44 final size:44
Alignment explanation
Indices: 12846--12973 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
12836 TTCATAGGAA
* * * *
12846 AGTTTATTAAAATTTCATAGTTAGATTATCAAAGTTTCATATGG-
1 AGTTTATCAAAATTTAATAGGTA-ATTATCAAAATTTCATATGGT
* *
12890 AGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGT
1 AGTTTATCAAAATTTAATAGGTAATTATCAAAATTTCATATGGT
*
12934 GGTTT-TCAAAATTTAATAGGGTAATTATCAAAATTTCATA
1 AGTTTATCAAAATTTAATA-GGTAATTATCAAAATTTCATA
12974 AAAATATTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 30 0.41
44 44 0.59
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (44 bp):
AGTTTATCAAAATTTAATAGGTAATTATCAAAATTTCATATGGT
Found at i:15150 original size:26 final size:28
Alignment explanation
Indices: 15106--15157 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
15096 TTAATTGAGT
15106 TTTTTTGGACATTATTAAACTTTTTTCC
1 TTTTTTGGACATTATTAAACTTTTTTCC
* *
15134 TTTTTTGG-CCTTA-TAAAGTTTTTT
1 TTTTTTGGACATTATTAAACTTTTTT
15158 AGTCATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 8 0.36
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTTTTGGACATTATTAAACTTTTTTCC
Found at i:15173 original size:21 final size:21
Alignment explanation
Indices: 15143--15213 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
15133 CTTTTTTGGC
*
15143 CTTATAAAGTTTTTTAGTCAT
1 CTTATTAAGTTTTTTAGTCAT
* *
15164 CTTATTAAGTGTTTTTA-CCTAA
1 CTTATTAAGT-TTTTTAGTC-AT
* *
15186 CTTTATTAAGATTTTTAGTAAT
1 C-TTATTAAGTTTTTTAGTCAT
15208 CTTATT
1 CTTATT
15214 GTGGATTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 15 0.38
22 16 0.41
23 8 0.21
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (21 bp):
CTTATTAAGTTTTTTAGTCAT
Done.