Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013521.1 Corchorus olitorius cultivar O-4 contig13554, 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: 7601
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:3579 original size:20 final size:21

Alignment explanation


    Indices: 3537--3579  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3527 TCCTTTGTTG

                                 
       3537 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGGGCTTCAA

                     *        *  
       3558 ATGATCTCCGAT-GGCTTTAA
          1 ATGATCTCCAATGGGCTTCAA

              
       3578 AT
          1 AT

       3580 TCTTCAAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGGGCTTCAA

Found at i:5599 original size:33 final size:33

Alignment explanation


    Indices: 5562--5747  Score: 205
    Period size: 33  Copynumber: 5.6  Consensus size: 33

       5552 AGAATTTGTT

                                              
       5562 TCATCACAAACAACAC-CTAAAACAGATTTAGTG
          1 TCATCACAAACAACACTC-AAAACAGATTTAGTG

                                 **  *      *
       5595 TCATCACAAACAACACTCAAATTAGTTTTAGTA
          1 TCATCACAAACAACACTCAAAACAGATTTAGTG

                   *            *             
       5628 TCATCACTAACAACA-TCTAGAACAGATTTAGTG
          1 TCATCACAAACAACACTC-AAAACAGATTTAGTG

                 *               **  *      *
       5661 TCATCGCAAACAACACTCAAATTAGGTTTAGTA
          1 TCATCACAAACAACACTCAAAACAGATTTAGTG

                   *                     *   
       5694 TCATCACTAACAACACTCAAAACAGATTTCGTG
          1 TCATCACAAACAACACTCAAAACAGATTTAGTG

                **               
       5727 TCATTGCAAACAACACTCAAA
          1 TCATCACAAACAACACTCAAA

       5748 TTAGGTTCAA


Statistics
Matches: 123,  Mismatches: 27, Indels: 6
        0.79            0.17        0.04

Matches are distributed among these distances:
  32    2  0.02
  33  118  0.96
  34    3  0.02

ACGTcount: A:0.42, C:0.24, G:0.09, T:0.25


Consensus pattern (33 bp):   
TCATCACAAACAACACTCAAAACAGATTTAGTG

Found at i:5752 original size:66 final size:67

Alignment explanation


    Indices: 5562--5754  Score: 311
    Period size: 66  Copynumber: 2.9  Consensus size: 67

       5552 AGAATTTGTT

                   *                               *                   *     
       5562 TCATCACAAACAACAC-CTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAG
          1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG

              
       5626 TA
         66 TA

                                *                                            
       5628 TCATCACTAACAACA-TCTAGAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
          1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG

              
       5692 TA
         66 TA

                                          *       *                       
       5694 TCATCACTAACAACACTC-AAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT

       5755 CAAAATTACT


Statistics
Matches: 118,  Mismatches: 7, Indels: 4
        0.91            0.05        0.03

Matches are distributed among these distances:
  66  116  0.98
  67    2  0.02

ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26


Consensus pattern (67 bp):   
TCATCACTAACAACACTCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
TA
Done.