Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021354.1 Corchorus olitorius cultivar O-4 contig21387, 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: 12849
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:6077 original size:26 final size:26

Alignment explanation


    Indices: 6048--6105  Score: 116
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       6038 CTAAATATCC

                                      
       6048 AATAAGGGATATTTGTATAAGTTTTG
          1 AATAAGGGATATTTGTATAAGTTTTG

                                      
       6074 AATAAGGGATATTTGTATAAGTTTTG
          1 AATAAGGGATATTTGTATAAGTTTTG

                  
       6100 AATAAG
          1 AATAAG

       6106 TTTAACAAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   32  1.00

ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40


Consensus pattern (26 bp):   
AATAAGGGATATTTGTATAAGTTTTG

Found at i:6093 original size:15 final size:15

Alignment explanation


    Indices: 6049--6094  Score: 55
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       6039 TAAATATCCA

                           
       6049 ATAAGGGATATTTGT
          1 ATAAGGGATATTTGT

                          *
       6064 ATAA--G-T-TTTGA
          1 ATAAGGGATATTTGT

                           
       6075 ATAAGGGATATTTGT
          1 ATAAGGGATATTTGT

                 
       6090 ATAAG
          1 ATAAG

       6095 TTTTGAATAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 8
        0.71            0.06        0.23

Matches are distributed among these distances:
  11    8  0.32
  12    1  0.04
  13    2  0.08
  14    1  0.04
  15   13  0.52

ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39


Consensus pattern (15 bp):   
ATAAGGGATATTTGT

Found at i:6216 original size:20 final size:20

Alignment explanation


    Indices: 6191--6233  Score: 86
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6181 AAATGGATAT

                                
       6191 TTTGCTTCTTTGCTTTTTTC
          1 TTTGCTTCTTTGCTTTTTTC

                                
       6211 TTTGCTTCTTTGCTTTTTTC
          1 TTTGCTTCTTTGCTTTTTTC

               
       6231 TTT
          1 TTT

       6234 TTGTTTCAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.00, C:0.19, G:0.09, T:0.72


Consensus pattern (20 bp):   
TTTGCTTCTTTGCTTTTTTC

Found at i:7454 original size:27 final size:29

Alignment explanation


    Indices: 7384--7460  Score: 95
    Period size: 30  Copynumber: 2.7  Consensus size: 29

       7374 ATTTTTCTTT

                   *   *                  
       7384 AAAAAAATATAGTATCATGATTTCATGTCA
          1 AAAAAAAAATATTATCATGATTTCA-GTCA

                                   *     
       7414 AAAAAAAAATATTATCATGATTTGA-TCA
          1 AAAAAAAAATATTATCATGATTTCAGTCA

            *                   
       7442 GAAAAAAAA-ATTATCATGA
          1 AAAAAAAAATATTATCATGA

       7461 GATTTTTTTT


Statistics
Matches: 43,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  27   10  0.23
  28   11  0.26
  30   22  0.51

ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30


Consensus pattern (29 bp):   
AAAAAAAAATATTATCATGATTTCAGTCA
Done.