Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022622.1 Corchorus olitorius cultivar O-4 contig22655, 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: 7966
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28


Found at i:4738 original size:11 final size:11

Alignment explanation


    Indices: 4722--4747  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       4712 CTAGCCCTAT

                       
       4722 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       4733 AAAACTAGAAG
          1 AAAACTAGAAG

                
       4744 AAAA
          1 AAAA

       4748 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:7135 original size:16 final size:15

Alignment explanation


    Indices: 7114--7160  Score: 53
    Period size: 16  Copynumber: 3.1  Consensus size: 15

       7104 AGGAATAGGC

                           
       7114 AATCAATCAAAGCAA
          1 AATCAATCAAAGCAA

                      *     
       7129 TAATCAATCAGAGCAA
          1 -AATCAATCAAAGCAA

                            
       7145 AA-CAATGCAAAG-AA
          1 AATCAAT-CAAAGCAA

              
       7159 AA
          1 AA

       7161 AGTAAATGGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  14    8  0.29
  15    6  0.21
  16   14  0.50

ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13


Consensus pattern (15 bp):   
AATCAATCAAAGCAA

Found at i:7600 original size:5 final size:6

Alignment explanation


    Indices: 7585--7618  Score: 50
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       7575 TTGAAATCCT

                                     **            
       7585 AAAAAG AAAAAG AAAAAG AAAACT AAAAAG AAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA

       7619 TCAACATGTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Done.