Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005872.1 Corchorus olitorius cultivar O-4 contig05897, 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, 629

Length: 1049
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37


Found at i:301 original size:12 final size:12

Alignment explanation


    Indices: 286--310  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        276 TTTTTTCCCC

                        
        286 TCTTTTTTTATT
          1 TCTTTTTTTATT

                        
        298 TCTTTTTTTATT
          1 TCTTTTTTTATT

             
        310 T
          1 T

        311 ATTCCCTTCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84


Consensus pattern (12 bp):   
TCTTTTTTTATT

Found at i:833 original size:14 final size:14

Alignment explanation


    Indices: 814--841  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        804 TATATTAGTA

                          
        814 TTTTCTATTCTATT
          1 TTTTCTATTCTATT

                          
        828 TTTTCTATTCTATT
          1 TTTTCTATTCTATT

        842 AGTATTAGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71


Consensus pattern (14 bp):   
TTTTCTATTCTATT

Found at i:853 original size:5 final size:6

Alignment explanation


    Indices: 838--899  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        828 TTTTCTATTC

                                      *      *                     
        838 TATTAG TATTAG -ATTAG TATT-T TATT-C TATTAG TATTAG -ATTAG
          1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG

                                  
        882 TATTAG -ATTAG TATTAG T
          1 TATTAG TATTAG TATTAG T

        900 TAGTGATCCC


Statistics
Matches: 49,  Mismatches: 3, Indels: 8
        0.82            0.05        0.13

Matches are distributed among these distances:
   5   23  0.47
   6   26  0.53

ACGTcount: A:0.32, C:0.02, G:0.15, T:0.52


Consensus pattern (6 bp):   
TATTAG

Found at i:853 original size:11 final size:11

Alignment explanation


    Indices: 839--903  Score: 54
    Period size: 11  Copynumber: 6.5  Consensus size: 11

        829 TTTCTATTCT

                       
        839 ATTAGTATTAG
          1 ATTAGTATTAG

                     **
        850 ATTAGTATTTT
          1 ATTAGTATTAG

                *      
        861 ATT-CTATTAG
          1 ATTAGTATTAG

                       
        871 --TA-T--TAG
          1 ATTAGTATTAG

                       
        877 ATTAGTATTAG
          1 ATTAGTATTAG

                       
        888 ATTAGTATTAG
          1 ATTAGTATTAG

                  
        899 -TTAGT
          1 ATTAGT

        904 GATCCCGGCT


Statistics
Matches: 43,  Mismatches: 5, Indels: 13
        0.70            0.08        0.21

Matches are distributed among these distances:
   6    3  0.07
   8    4  0.09
   9    1  0.02
  10    9  0.21
  11   26  0.60

ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51


Consensus pattern (11 bp):   
ATTAGTATTAG

Found at i:863 original size:27 final size:27

Alignment explanation


    Indices: 833--885  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        823 CTATTTTTTC

                                       
        833 TATTCTATTAGTATTAGATTAGTATTT
          1 TATTCTATTAGTATTAGATTAGTATTT

                                      
        860 TATTCTATTAGTATTAGATTAGTATT
          1 TATTCTATTAGTATTAGATTAGTATT

        886 AGATTAGTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55


Consensus pattern (27 bp):   
TATTCTATTAGTATTAGATTAGTATTT
Done.