Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001994.1 Corchorus olitorius cultivar O-4 contig01994, 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: 2901
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36


Found at i:1329 original size:31 final size:31

Alignment explanation


    Indices: 1252--1347  Score: 104
    Period size: 31  Copynumber: 3.1  Consensus size: 31

       1242 TGGTTCATTA

                          *                
       1252 AGTCCATAACATTGTAAAATCGGCTAAAATC
          1 AGTCCATAACATTGCAAAATCGGCTAAAATC

             *  *     *                  *  
       1283 AATCTATAACGTTGCAAAATCGGC-ACAAGTC
          1 AGTCCATAACATTGCAAAATCGGCTA-AAATC

                 *                *  *     
       1314 AGTCCCTAACATTGCAAAATCGTCTCAAATC
          1 AGTCCATAACATTGCAAAATCGGCTAAAATC

               
       1345 AGT
          1 AGT

       1348 ATCTAAAATT


Statistics
Matches: 51,  Mismatches: 12, Indels: 4
        0.76            0.18        0.06

Matches are distributed among these distances:
  30    1  0.02
  31   50  0.98

ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25


Consensus pattern (31 bp):   
AGTCCATAACATTGCAAAATCGGCTAAAATC

Found at i:1656 original size:12 final size:12

Alignment explanation


    Indices: 1611--1673  Score: 62
    Period size: 12  Copynumber: 5.4  Consensus size: 12

       1601 GGGATTACTT

                        
       1611 TATATAT-AT-A
          1 TATATATAATAA

                *        
       1621 TATAAATAAATAA
          1 TATATAT-AATAA

                *        
       1634 -ATAAATAAATAA
          1 TATATAT-AATAA

                        
       1646 TATATATAATAA
          1 TATATATAATAA

                        
       1658 TATA-ATAATAA
          1 TATATATAATAA

                 
       1669 TATAT
          1 TATAT

       1674 TTAGATATAC


Statistics
Matches: 46,  Mismatches: 2, Indels: 8
        0.82            0.04        0.14

Matches are distributed among these distances:
  10    6  0.13
  11   11  0.24
  12   23  0.50
  13    6  0.13

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (12 bp):   
TATATATAATAA

Found at i:1980 original size:30 final size:30

Alignment explanation


    Indices: 1944--2032  Score: 169
    Period size: 30  Copynumber: 3.0  Consensus size: 30

       1934 TCACGGAATG

                                          
       1944 TGAGTTTTCTTTGTAATTTATTTGTTTGTT
          1 TGAGTTTTCTTTGTAATTTATTTGTTTGTT

                             *            
       1974 TGAGTTTTCTTTGTAATCTATTTGTTTGTT
          1 TGAGTTTTCTTTGTAATTTATTTGTTTGTT

                                         
       2004 TGAGTTTTCTTTGTAATTTATTTGTTTGT
          1 TGAGTTTTCTTTGTAATTTATTTGTTTGT

       2033 GTATTTAGTA


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   57  1.00

ACGTcount: A:0.13, C:0.04, G:0.17, T:0.65


Consensus pattern (30 bp):   
TGAGTTTTCTTTGTAATTTATTTGTTTGTT

Found at i:2031 original size:15 final size:15

Alignment explanation


    Indices: 1953--2032  Score: 51
    Period size: 15  Copynumber: 5.3  Consensus size: 15

       1943 GTGAGTTTTC

                           
       1953 TTTGTAATTTATTTG
          1 TTTGTAATTTATTTG

                     *      *
       1968 TTTGT--TTGAGTTTTC
          1 TTTGTAATTTA--TTTG

                    *      
       1983 TTTGTAATCTATTTG
          1 TTTGTAATTTATTTG

                     *      *
       1998 TTTGT--TTGAGTTTTC
          1 TTTGTAATTTA--TTTG

                           
       2013 TTTGTAATTTATTTG
          1 TTTGTAATTTATTTG

                 
       2028 TTTGT
          1 TTTGT

       2033 GTATTTAGTA


Statistics
Matches: 47,  Mismatches: 10, Indels: 16
        0.64            0.14        0.22

Matches are distributed among these distances:
  13    5  0.11
  15   37  0.79
  17    5  0.11

ACGTcount: A:0.14, C:0.04, G:0.16, T:0.66


Consensus pattern (15 bp):   
TTTGTAATTTATTTG
Done.