Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023105.1 Corchorus olitorius cultivar O-4 contig23138, 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: 11118
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:3076 original size:19 final size:19

Alignment explanation


    Indices: 3040--3076  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       3030 TGAATCTGTA

                     *   *     
       3040 ACCGTTTCATCATTGTTTG
          1 ACCGTTTCACCATCGTTTG

                              
       3059 ACCGTTTCACCATCGTTT
          1 ACCGTTTCACCATCGTTT

       3077 TGGGTCCAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43


Consensus pattern (19 bp):   
ACCGTTTCACCATCGTTTG

Found at i:3153 original size:21 final size:19

Alignment explanation


    Indices: 3127--3184  Score: 71
    Period size: 21  Copynumber: 2.9  Consensus size: 19

       3117 GCTGCTTTAA

                                 
       3127 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *           *
       3148 TAATCTAATCTGTACAGTT
          1 TAATCTCATCTGTACAGTC

                     *        
       3167 TAATCTCATATGTACAGT
          1 TAATCTCATCTGTACAGT

       3185 TGCTAAACAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:3172 original size:19 final size:19

Alignment explanation


    Indices: 3127--3185  Score: 73
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       3117 GCTGCTTTAA

                                *
       3127 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--T

                  *            
       3148 TAATCTAATCTGTACAGTT
          1 TAATCTCATCTGTACAGTT

                     *         
       3167 TAATCTCATATGTACAGTT
          1 TAATCTCATCTGTACAGTT

       3186 GCTAAACAGT


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.50
  21   17  0.50

ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTT

Found at i:7305 original size:56 final size:57

Alignment explanation


    Indices: 7219--7329  Score: 188
    Period size: 56  Copynumber: 2.0  Consensus size: 57

       7209 CTTTTCCTTT

                                     *       *                       
       7219 CACACAATAAATATTATAATAAATCCTAT-CCCTCTATCTCTACTTAATTATTCTTC
          1 CACACAATAAATATTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTC

                        *                                          
       7275 CACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCT
          1 CACACAATAAATATTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCT

       7330 ACAAAATAAA


Statistics
Matches: 51,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  56   27  0.53
  57   24  0.47

ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38


Consensus pattern (57 bp):   
CACACAATAAATATTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTC

Found at i:10496 original size:58 final size:57

Alignment explanation


    Indices: 10402--10515  Score: 174
    Period size: 58  Copynumber: 2.0  Consensus size: 57

      10392 ATTAATAAAA

                                                         *           
      10402 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCAAGGCT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT

                *            *            *                     *    
      10459 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACCGAGGC
          1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC

      10516 ATGATGCTAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  57   13  0.25
  58   38  0.75

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Consensus pattern (57 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
Done.