Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024517.1 Corchorus olitorius cultivar O-4 contig24550, 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: 21318
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:3217 original size:11 final size:11

Alignment explanation


    Indices: 3203--3240  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       3193 ATTCATAACA

                       
       3203 AATTTATAATT
          1 AATTTATAATT

                       
       3214 AATTTATAATT
          1 AATTTATAATT

                        
       3225 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       3236 TATTT
          1 AATTT

       3241 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:3963 original size:2 final size:2

Alignment explanation


    Indices: 3956--3987  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3946 TAATCAATGA

                                                           
       3956 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

       3988 GTATGCACCT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:15860 original size:9 final size:10

Alignment explanation


    Indices: 15830--15869  Score: 57
    Period size: 9  Copynumber: 4.1  Consensus size: 10

      15820 TCAATTTTTT

                      
      15830 TTAGTTTTAA
          1 TTAGTTTTAA

                       
      15840 TTAGTTTTTAA
          1 TTAG-TTTTAA

                      
      15851 TTAG-TTTAA
          1 TTAGTTTTAA

                      
      15860 TTA-TTTTAA
          1 TTAGTTTTAA

             
      15869 T
          1 T

      15870 CATTTAAATA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   9   14  0.50
  10    4  0.14
  11   10  0.36

ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62


Consensus pattern (10 bp):   
TTAGTTTTAA

Found at i:16567 original size:1 final size:1

Alignment explanation


    Indices: 16561--16591  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

      16551 TTGTAAATAT

                                           
      16561 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      16592 CCATATCCGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:18321 original size:3 final size:3

Alignment explanation


    Indices: 18313--18365  Score: 106
    Period size: 3  Copynumber: 17.7  Consensus size: 3

      18303 GGAAGGGTAT

                                                                           
      18313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                  
      18361 TTA TT
          1 TTA TT

      18366 TCCTTGAGAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   50  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Done.