Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013063.1 Corchorus capsularis cultivar CVL-1 contig13084, 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: 25880
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:10115 original size:19 final size:18

Alignment explanation


    Indices: 10082--10117  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10072 TTGAAATAAT

                              
      10082 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      10100 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      10118 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:11888 original size:21 final size:21

Alignment explanation


    Indices: 11819--11890  Score: 56
    Period size: 21  Copynumber: 3.3  Consensus size: 21

      11809 CTGGATAGCA

                         *       
      11819 TCAACAACACGCGTAAAGATG
          1 TCAACAACACGCGCAAAGATG

                    * ***         *
      11840 TCAACAAGGAATTGACAAA-ATT
          1 TCAACAA-CACGCG-CAAAGATG

                                  
      11862 TCCAACAACACGCGCAAAGATG
          1 T-CAACAACACGCGCAAAGATG

                   
      11884 TCAACAA
          1 TCAACAA

      11891 GGAATTGAAG


Statistics
Matches: 36,  Mismatches: 11, Indels: 8
        0.65            0.20        0.15

Matches are distributed among these distances:
  21   17  0.47
  22   10  0.28
  23    9  0.25

ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15


Consensus pattern (21 bp):   
TCAACAACACGCGCAAAGATG

Found at i:14073 original size:19 final size:18

Alignment explanation


    Indices: 14040--14075  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      14030 TTGAATTAAT

                              
      14040 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      14058 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      14076 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:23312 original size:27 final size:31

Alignment explanation


    Indices: 23268--23332  Score: 93
    Period size: 29  Copynumber: 2.2  Consensus size: 31

      23258 AAAACAGAAT

                                           
      23268 TTTTTTTTTCAAATCGCAAACCCT-A-AATA
          1 TTTTTTTTTCAAATCGCAAACCCTAATAATA

                       *                   
      23297 TTTTTTTTTC-GA-CGCAAACCCTAATAATA
          1 TTTTTTTTTCAAATCGCAAACCCTAATAATA

                   
      23326 TTTTTTT
          1 TTTTTTT

      23333 AAATTGCAAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 4
        0.87            0.03        0.11

Matches are distributed among these distances:
  27   10  0.30
  28    2  0.06
  29   21  0.64

ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48


Consensus pattern (31 bp):   
TTTTTTTTTCAAATCGCAAACCCTAATAATA

Found at i:23341 original size:28 final size:28

Alignment explanation


    Indices: 23270--23343  Score: 80
    Period size: 27  Copynumber: 2.6  Consensus size: 28

      23260 AACAGAATTT

                                        *
      23270 TTTTTTTCAAATCGCAAACCCTAAATATT
          1 TTTTTTT-AAATCGCAAACCCTAAATATA

                   **                    
      23299 TTTTTTTCGA-CGCAAACCCT-AATAATA
          1 TTTTTTTAAATCGCAAACCCTAAAT-ATA

                       *      
      23326 TTTTTTTAAATTGCAAAC
          1 TTTTTTTAAATCGCAAAC

      23344 TTTTTTTTAA


Statistics
Matches: 37,  Mismatches: 6, Indels: 5
        0.77            0.12        0.10

Matches are distributed among these distances:
  26    3  0.08
  27   20  0.54
  28    7  0.19
  29    7  0.19

ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42


Consensus pattern (28 bp):   
TTTTTTTAAATCGCAAACCCTAAATATA
Done.