Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023537.1 Corchorus olitorius cultivar O-4 contig23570, 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: 14370
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Found at i:12748 original size:2 final size:2
Alignment explanation
Indices: 12736--12781 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
12726 CTTTTGTCAC
*
12736 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12778 AT AT
1 AT AT
12782 GAGATTGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12947 original size:43 final size:42
Alignment explanation
Indices: 12888--13178 Score: 374
Period size: 43 Copynumber: 6.8 Consensus size: 42
12878 CATAAGGAAA
* *
12888 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
*
12930 AATTGCCCCTGTTTTATATATGTGTTTGGGGACTTTG-ATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTA-ATAG
* * *
12973 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG
*
13015 AAATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
1 -AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
* *
13058 AATTGCCCCTGTGTTATATATGTTTTTGGGGACTTGGGT-ATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGGGGACTT-TGTAATAG
* * *
13101 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG
13143 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 -AATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
13179 TTGGTTATTG
Statistics
Matches: 217, Mismatches: 20, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
41 55 0.25
42 21 0.10
43 82 0.38
44 59 0.27
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (42 bp):
AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
Found at i:13028 original size:128 final size:128
Alignment explanation
Indices: 12887--13178 Score: 514
Period size: 128 Copynumber: 2.3 Consensus size: 128
12877 CCATAAGGAA
* *
12887 AAATG-CCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTTTTATATAT
1 AAATGCCCT-TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATAT
*
12951 GTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
65 GTGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
13015 AAATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
* *
13080 TTTTTGGGGACTTGGGTATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
*
13143 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 AAATGCCCTTGTGTTATATATGTGTTTGGGGACTTT
13179 TTGGTTATTG
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
128 154 0.98
129 3 0.02
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (128 bp):
AAATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
TGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
Found at i:13049 original size:85 final size:85
Alignment explanation
Indices: 12888--13178 Score: 369
Period size: 85 Copynumber: 3.4 Consensus size: 85
12878 CATAAGGAAA
* * * * *
12888 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTTTTATATATGT
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCTTGTGTTATATATGT
12953 GTTTGGGGACTTTGATATAG
66 GTTTGGGGACTTTGATATAG
*
12973 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCTTGTGTTATATATG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAAATGCCCTTGTGTTATATATG
13037 TGTTTGGGGACTTTG-TAATAG
65 TGTTTGGGGACTTTGAT-ATAG
* * * *
13058 AATTGCCCCTGTGTTATATATGTTTTTGGGGACTTGGGTATAG--ATG-CCTCTGTGTTATATAT
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCT-TGTGTTATATAT
*
13120 GTGTTTGAGGACTTTTGGA-ATAG
64 GTGTTTGGGGAC-TTT-GATATAG
*
13143 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 -AATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
13179 TTGGTTATTG
Statistics
Matches: 185, Mismatches: 12, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
83 3 0.02
84 58 0.31
85 85 0.46
86 12 0.06
87 27 0.15
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (85 bp):
AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCTTGTGTTATATATGT
GTTTGGGGACTTTGATATAG
Found at i:14335 original size:2 final size:2
Alignment explanation
Indices: 14328--14365 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14318 GTTAATATGC
14328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14366 TGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.