Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010978.1 Corchorus capsularis cultivar CVL-1 contig10999, 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: 9420
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30


Found at i:181 original size:33 final size:31

Alignment explanation


    Indices: 140--254  Score: 124
    Period size: 33  Copynumber: 3.6  Consensus size: 31

        130 TTAATTGTGA

                                             
        140 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT

             *                               
        173 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT

              *   *   *                     
        206 TGCAAATAATCCTGTTTTTGGTTG-ATAGCAT
          1 TGAAAACAATTCTG-TTTTGGTTGAATAGCAT

                  *  *        
        237 TGAAAATAAATCTGTTTT
          1 TGAAAACAATTCTGTTTT

        255 TTGGTGACGA


Statistics
Matches: 71,  Mismatches: 9, Indels: 7
        0.82            0.10        0.08

Matches are distributed among these distances:
  30    4  0.06
  31   18  0.25
  32    1  0.01
  33   39  0.55
  34    9  0.13

ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41


Consensus pattern (31 bp):   
TGAAAACAATTCTGTTTTGGTTGAATAGCAT

Found at i:7250 original size:17 final size:17

Alignment explanation


    Indices: 7228--7261  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       7218 GAATCGGCTA

                             
       7228 TGAATTTTTGAAGTTTC
          1 TGAATTTTTGAAGTTTC

                        *    
       7245 TGAATTTTTGAATTTTC
          1 TGAATTTTTGAAGTTTC

       7262 AAGAAGGGTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56


Consensus pattern (17 bp):   
TGAATTTTTGAAGTTTC
Done.