Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002286.1 Corchorus capsularis cultivar CVL-1 contig02292, 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, 803

Length: 1339
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34


Found at i:1241 original size:33 final size:31

Alignment explanation


    Indices: 1193--1287  Score: 147
    Period size: 33  Copynumber: 3.0  Consensus size: 31

       1183 TTTGATTTCA

                                           
       1193 TTCTATTTCATTATATGGTATTACATAATTT
          1 TTCTATTTCATTATATGGTATTACATAATTT

                                             
       1224 TTGCTATGTTCATTATATGGTATTACATAA-TT
          1 TT-CTAT-TTCATTATATGGTATTACATAATTT

                                   **      
       1256 TTCTATTTCATTATATGGTATTATGTAATTT
          1 TTCTATTTCATTATATGGTATTACATAATTT

             
       1287 T
          1 T

       1288 GATTTCATTC


Statistics
Matches: 59,  Mismatches: 2, Indels: 6
        0.88            0.03        0.09

Matches are distributed among these distances:
  30   20  0.34
  31    9  0.15
  32    8  0.14
  33   22  0.37

ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55


Consensus pattern (31 bp):   
TTCTATTTCATTATATGGTATTACATAATTT

Found at i:1268 original size:30 final size:30

Alignment explanation


    Indices: 1193--1301  Score: 148
    Period size: 30  Copynumber: 3.6  Consensus size: 30

       1183 TTTGATTTCA

                                           
       1193 TTCTATTTCATTATATGGTATTACATAATTT
          1 TTCTATTTCATTATATGGTATTACATAA-TT

                                            
       1224 TTGCTATGTTCATTATATGGTATTACATAATT
          1 TT-CTAT-TTCATTATATGGTATTACATAATT

                                   **     
       1256 TTCTATTTCATTATATGGTATTATGTAATT
          1 TTCTATTTCATTATATGGTATTACATAATT

               *        *    
       1286 TT-GATTTCATTCTATG
          1 TTCTATTTCATTATATG

       1302 TTCATTATAT


Statistics
Matches: 72,  Mismatches: 4, Indels: 6
        0.88            0.05        0.07

Matches are distributed among these distances:
  29   12  0.17
  30   24  0.33
  31    6  0.08
  32    8  0.11
  33   22  0.31

ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54


Consensus pattern (30 bp):   
TTCTATTTCATTATATGGTATTACATAATT

Found at i:1306 original size:40 final size:39

Alignment explanation


    Indices: 1256--1339  Score: 141
    Period size: 40  Copynumber: 2.1  Consensus size: 39

       1246 TTACATAATT

                                   **              
       1256 TTCTATTTCATTATATGGTATTATGTAATTTTGATTTCA
          1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA

                                                    
       1295 TTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
          1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA

                 
       1335 TTCTA
          1 TTCTA


Statistics
Matches: 42,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  39    6  0.14
  40   36  0.86

ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55


Consensus pattern (39 bp):   
TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
Done.