Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002045.1 Corchorus olitorius cultivar O-4 contig02045, 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: 7069
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:1436 original size:21 final size:21

Alignment explanation


    Indices: 1396--1437  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1386 TATAAAAATA

                      *          
       1396 AAATTACAATGATTATAACAT
          1 AAATTACAATAATTATAACAT

                                  
       1417 AAATTACAATAAATTA-AACAT
          1 AAATTACAAT-AATTATAACAT

       1438 GAATCTCCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21   15  0.79
  22    4  0.21

ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31


Consensus pattern (21 bp):   
AAATTACAATAATTATAACAT

Found at i:1500 original size:29 final size:29

Alignment explanation


    Indices: 1458--1516  Score: 102
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       1448 TTCATCTTGA

                                          
       1458 TCTGGATCTGACATTC-TAATATGAATTAG
          1 TCTGGATCTGACA-TCATAATATGAATTAG

                                         
       1487 TCTGGATCTGACATCATAATATGAATTAG
          1 TCTGGATCTGACATCATAATATGAATTAG

             
       1516 T
          1 T

       1517 TAGAGTTTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  28    2  0.07
  29   27  0.93

ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37


Consensus pattern (29 bp):   
TCTGGATCTGACATCATAATATGAATTAG

Found at i:3651 original size:29 final size:30

Alignment explanation


    Indices: 3612--3672  Score: 81
    Period size: 29  Copynumber: 2.1  Consensus size: 30

       3602 TATAAATAAT

                  *                  *     
       3612 ATAATATAATT-ATATAA-TTATATTTATAC
          1 ATAATAAAATTGA-ATAATTTATATGTATAC

                                          
       3641 ATAATAAAATTGAATAATTTATATGTATAC
          1 ATAATAAAATTGAATAATTTATATGTATAC

              
       3671 AT
          1 AT

       3673 TAATTAGAAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29   14  0.50
  30   14  0.50

ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44


Consensus pattern (30 bp):   
ATAATAAAATTGAATAATTTATATGTATAC
Done.