Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014450.1 Corchorus capsularis cultivar CVL-1 contig14471, 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: 16216
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:9939 original size:2 final size:2

Alignment explanation


    Indices: 9932--9957  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       9922 ATTCATAAAC

                                                  
       9932 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       9958 CTTGAGGTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14992 original size:3 final size:3

Alignment explanation


    Indices: 14979--15015  Score: 58
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      14969 TTTGTAGAAT

                                                              
      14979 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA T
          1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      15016 ATAATAATAG


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   2    2  0.06
   3   27  0.84
   4    3  0.09

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:16031 original size:2 final size:2

Alignment explanation


    Indices: 16024--16076  Score: 106
    Period size: 2  Copynumber: 26.5  Consensus size: 2

      16014 CATGTTTAGC

                                                                          
      16024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                            
      16066 TA TA TA TA TA T
          1 TA TA TA TA TA T

      16077 TATTACTATT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   51  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:16125 original size:14 final size:14

Alignment explanation


    Indices: 16108--16135  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      16098 AATAATGATC

                          
      16108 AAAAAATCATCAAA
          1 AAAAAATCATCAAA

                          
      16122 AAAAAATCATCAAA
          1 AAAAAATCATCAAA

      16136 TCAGAAAAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14


Consensus pattern (14 bp):   
AAAAAATCATCAAA

Found at i:16172 original size:22 final size:21

Alignment explanation


    Indices: 16154--16208  Score: 69
    Period size: 20  Copynumber: 2.7  Consensus size: 21

      16144 GTGAAAAGAA

                                 
      16154 AAAAGAAA-AAAAAACAAAAG
          1 AAAAGAAATAAAAAACAAAAG

                             *  *
      16174 AAAAGAAATAAAAAAC-TAAT
          1 AAAAGAAATAAAAAACAAAAG

            *              
      16194 TAAAGAAATAAAAAA
          1 AAAAGAAATAAAAAA

      16209 GGAAGAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  20   24  0.77
  21    7  0.23

ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09


Consensus pattern (21 bp):   
AAAAGAAATAAAAAACAAAAG
Done.