Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012098.1 Corchorus olitorius cultivar O-4 contig12131, 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: 9455
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:2819 original size:21 final size:21

Alignment explanation


    Indices: 2794--2865  Score: 72
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2784 CTGTAAATGC

                            *    
       2794 ATAGTCAAACCCTAAATTTTG
          1 ATAGTCAAACCCTAAAGTTTG

                 *   * *      * *
       2815 ATAGTTAAATCTTAAAGTCTA
          1 ATAGTCAAACCCTAAAGTTTG

                 *      *        
       2836 ATAGTAAAACCCCAAAGTTTG
          1 ATAGTCAAACCCTAAAGTTTG

                     
       2857 ATAGTCAAA
          1 ATAGTCAAA

       2866 ACACGTTAAA


Statistics
Matches: 38,  Mismatches: 13, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  21   38  1.00

ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31


Consensus pattern (21 bp):   
ATAGTCAAACCCTAAAGTTTG

Found at i:4189 original size:6 final size:7

Alignment explanation


    Indices: 4172--4197  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

       4162 TTACAAATAG

                   
       4172 TTTTTCA
          1 TTTTTCA

                   
       4179 TTTTTCA
          1 TTTTTCA

                   
       4186 TTTTTCA
          1 TTTTTCA

                 
       4193 TTTTT
          1 TTTTT

       4198 TATTGATTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77


Consensus pattern (7 bp):   
TTTTTCA

Found at i:5591 original size:55 final size:55

Alignment explanation


    Indices: 5530--5642  Score: 217
    Period size: 55  Copynumber: 2.1  Consensus size: 55

       5520 ATGTACTCAC

                                                   *               
       5530 CTTTTTTCCATCACATTCTGTCAACCATTTACATATTCAGTTGCAAATACATGTA
          1 CTTTTTTCCATCACATTCTGTCAACCATTTACATATTCAATTGCAAATACATGTA

                                                                   
       5585 CTTTTTTCCATCACATTCTGTCAACCATTTACATATTCAATTGCAAATACATGTA
          1 CTTTTTTCCATCACATTCTGTCAACCATTTACATATTCAATTGCAAATACATGTA

               
       5640 CTT
          1 CTT

       5643 GCATAATAAT


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  55   57  1.00

ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41


Consensus pattern (55 bp):   
CTTTTTTCCATCACATTCTGTCAACCATTTACATATTCAATTGCAAATACATGTA

Found at i:7730 original size:21 final size:21

Alignment explanation


    Indices: 7704--7774  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       7694 TGCTAGGAGT

                                  
       7704 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       7725 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7746 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7767 TCATTGGA
          1 TCATTGGA

       7775 ATTGCCTAAG


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    2  0.04
  21   46  0.96

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC
Done.