Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001258.1 Corchorus capsularis cultivar CVL-1 contig01258, 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: 1934
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35


Found at i:232 original size:26 final size:26

Alignment explanation


    Indices: 203--258  Score: 112
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        193 AATATTTTAT

                                      
        203 TAAATAAGAATATATATATATATATG
          1 TAAATAAGAATATATATATATATATG

                                      
        229 TAAATAAGAATATATATATATATATG
          1 TAAATAAGAATATATATATATATATG

                
        255 TAAA
          1 TAAA

        259 AATTTTATTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   30  1.00

ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38


Consensus pattern (26 bp):   
TAAATAAGAATATATATATATATATG

Found at i:281 original size:7 final size:7

Alignment explanation


    Indices: 269--309  Score: 50
    Period size: 7  Copynumber: 6.1  Consensus size: 7

        259 AATTTTATTT

                   
        269 TAATATA
          1 TAATATA

                   
        276 TAATATA
          1 TAATATA

              *    
        283 TATTAT-
          1 TAATATA

                  *
        289 TAATATG
          1 TAATATA

                   
        296 TAATATA
          1 TAATATA

                   
        303 T-ATATA
          1 TAATATA

             
        309 T
          1 T

        310 GTGTGTAATA


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
   6   11  0.37
   7   19  0.63

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (7 bp):   
TAATATA

Found at i:293 original size:20 final size:19

Alignment explanation


    Indices: 264--305  Score: 66
    Period size: 20  Copynumber: 2.2  Consensus size: 19

        254 GTAAAAATTT

                               
        264 TATTTTAATATATAATATA
          1 TATTTTAATATATAATATA

                        *       
        283 TATTATTAATATGTAATATA
          1 TATT-TTAATATATAATATA

               
        303 TAT
          1 TAT

        306 ATATGTGTGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  19    4  0.19
  20   17  0.81

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52


Consensus pattern (19 bp):   
TATTTTAATATATAATATA

Found at i:1651 original size:2 final size:2

Alignment explanation


    Indices: 1644--1677  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1634 AAATGGAATC

                                                              
       1644 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

       1678 CACTAGTATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Done.