Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003230.1 Corchorus capsularis cultivar CVL-1 contig03238, 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, 713

Length: 1189
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44


Found at i:110 original size:13 final size:13

Alignment explanation


    Indices: 92--116  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         82 TAAAGGCATT

                         
         92 TATTGCATTAATA
          1 TATTGCATTAATA

                        
        105 TATTGCATTAAT
          1 TATTGCATTAAT

        117 TTTCCTGGCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48


Consensus pattern (13 bp):   
TATTGCATTAATA

Found at i:280 original size:32 final size:32

Alignment explanation


    Indices: 244--345  Score: 99
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        234 TTTCTTTCTA

                                            
        244 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT
          1 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT

                 *                       *   *
        276 CATTGTG-TTTCTCATTTACTTA-TTA--CT-AA
          1 CATTGGGTTTTC-CATTT-CTTAGTTATGTTCAT

                  *                         
        305 C-TTGGATTTTCCATTTCTTAGTTATGTTCAT
          1 CATTGGGTTTTCCATTTCTTAGTTATGTTCAT

                 *    
        336 CATTGTGTTT
          1 CATTGGGTTT

        346 CTCATATACT


Statistics
Matches: 53,  Mismatches: 9, Indels: 16
        0.68            0.12        0.21

Matches are distributed among these distances:
  27    4  0.08
  28   11  0.21
  29    6  0.11
  30    2  0.04
  31    6  0.11
  32   20  0.38
  33    4  0.08

ACGTcount: A:0.18, C:0.16, G:0.13, T:0.54


Consensus pattern (32 bp):   
CATTGGGTTTTCCATTTCTTAGTTATGTTCAT

Found at i:344 original size:60 final size:60

Alignment explanation


    Indices: 246--368  Score: 219
    Period size: 60  Copynumber: 2.0  Consensus size: 60

        236 TCTTTCTACA

                *                                        *              
        246 TTGGGTTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATTTACTTATTACTAAC
          1 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC

                                                                   *    
        306 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTAGTAAC
          1 TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC

               
        366 TTG
          1 TTG

        369 CAATTGATGT


Statistics
Matches: 60,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  60   60  1.00

ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53


Consensus pattern (60 bp):   
TTGGATTTTCCATTTCTTAGTTATGTTCATCATTGTGTTTCTCATATACTTATTACTAAC

Found at i:1173 original size:24 final size:28

Alignment explanation


    Indices: 1127--1183  Score: 86
    Period size: 24  Copynumber: 2.2  Consensus size: 28

       1117 TGTTCTACCG

                                        
       1127 TTTTTTATTCTCACAAAATTTCTAATGT
          1 TTTTTTATTCTCACAAAATTTCTAATGT

                                        
       1155 TTTTTTATT-T-A-AAAA-TTCTAATGT
          1 TTTTTTATTCTCACAAAATTTCTAATGT

                 
       1179 TTTTT
          1 TTTTT

       1184 CTACTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  24   14  0.48
  25    4  0.14
  26    1  0.03
  27    1  0.03
  28    9  0.31

ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60


Consensus pattern (28 bp):   
TTTTTTATTCTCACAAAATTTCTAATGT
Done.