Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023387.1 Corchorus olitorius cultivar O-4 contig23420, 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: 2955
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35


Found at i:448 original size:25 final size:24

Alignment explanation


    Indices: 412--458  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        402 TCCTTCTATT

                                    
        412 CATCTATCATCAA-GTTTTTCATC
          1 CATCTATCATCAATGTTTTTCATC

                                    
        435 CATCTCATCCATCAATGTTTTTCA
          1 CATCT-AT-CATCAATGTTTTTCA

        459 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    6  0.29
  26    8  0.38

ACGTcount: A:0.26, C:0.28, G:0.04, T:0.43


Consensus pattern (24 bp):   
CATCTATCATCAATGTTTTTCATC

Found at i:2036 original size:33 final size:33

Alignment explanation


    Indices: 1991--2071  Score: 108
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       1981 GTGTTTTAGA

                   *       *                 
       1991 TGTTGTTAGTGATGATACTAAACCTAATTTAAG
          1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG

                                  *  **    * 
       2024 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG

                           
       2057 TGTTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

       2072 AACAAATTTT


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   42  1.00

ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAACCTAATTTAAG

Found at i:2085 original size:33 final size:33

Alignment explanation


    Indices: 1982--2119  Score: 104
    Period size: 33  Copynumber: 4.2  Consensus size: 33

       1972 TTGCAAAGAG

                    *       *       *       * 
       1982 TGTTTTAGATGTTGTTAGTGATGATACTAAA-CC
          1 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC

             **    *                *         
       2015 TAATTTAAGTGTTGTTTGTGATGACACTAAA-TC
          1 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC

                                            *
       2048 TGTTTTAGGTGTTGTTTGTGATGAAACAAATTT
          1 TGTTTTAGGTGTTGTTTGTGATGAAACAAATTC

                        * **                   
       2081 TGTTTT-GGATGCTAATTGTGATGAAAACAAA-TC
          1 TGTTTTAGG-TGTTGTTTGTGATG-AAACAAATTC

                  
       2114 TGTTTT
          1 TGTTTT

       2120 GGTTGATCAT


Statistics
Matches: 86,  Mismatches: 16, Indels: 6
        0.80            0.15        0.06

Matches are distributed among these distances:
  32    5  0.06
  33   74  0.86
  34    7  0.08

ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTGATGAAACAAATTC
Done.