Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013214.1 Corchorus olitorius cultivar O-4 contig13247, 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: 27457
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:15212 original size:21 final size:21

Alignment explanation


    Indices: 15172--15212  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      15162 ATTTTTATTA

                           *     
      15172 GTATTATTAATAAAATAAATT
          1 GTATTATTAATAAAAGAAATT

                                 
      15193 GTATTA-TAATAATAAGAAAT
          1 GTATTATTAATAA-AAGAAAT

      15213 AAGAAACAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    6  0.33
  21   12  0.67

ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39


Consensus pattern (21 bp):   
GTATTATTAATAAAAGAAATT

Found at i:25569 original size:17 final size:17

Alignment explanation


    Indices: 25547--25581  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      25537 AAGAAACCTG

                             
      25547 TATTATAACTAATCAAT
          1 TATTATAACTAATCAAT

                             
      25564 TATTATAACTAATCAAT
          1 TATTATAACTAATCAAT

             
      25581 T
          1 T

      25582 TGTGGCCAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43


Consensus pattern (17 bp):   
TATTATAACTAATCAAT

Found at i:26381 original size:60 final size:59

Alignment explanation


    Indices: 26250--26387  Score: 161
    Period size: 60  Copynumber: 2.3  Consensus size: 59

      26240 CTAATTGCTC

                   *  *               *           * *   *   *          
      26250 AAATAGGTCCTTAACGTATGCAAAAATCTCAATTTAGGGCTCATGCTTTTAATTCGGTT
          1 AAATAGGACCCTAACGTATGCAAAAAGCTCAATTTAGGACCCATACTTATAATTCGGTT

                  *        *                                        *    
      26309 AAATA-AAGCCCTAAGGTATGCAAAAACGCTCAATTTAGGACCCATACTTATAATTTGGTT
          1 AAATAGGA-CCCTAACGTATGCAAAAA-GCTCAATTTAGGACCCATACTTATAATTCGGTT

                               
      26369 AAATAGGACCCTAACGTAT
          1 AAATAGGACCCTAACGTAT

      26388 ATGAAAATGC


Statistics
Matches: 64,  Mismatches: 12, Indels: 5
        0.79            0.15        0.06

Matches are distributed among these distances:
  59   21  0.33
  60   42  0.66
  61    1  0.02

ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Consensus pattern (59 bp):   
AAATAGGACCCTAACGTATGCAAAAAGCTCAATTTAGGACCCATACTTATAATTCGGTT

Found at i:26575 original size:59 final size:60

Alignment explanation


    Indices: 26458--26593  Score: 154
    Period size: 59  Copynumber: 2.3  Consensus size: 60

      26448 ATACCCTTAT

                        *                                               
      26458 TTGAGCATTTTCGCATAATCTAGGGCCTTATGTAACCAAATTCAAAGCATGAACCCTAAA
          1 TTGAGCATTTTCACATAATCTAGGGCCTTATGTAACCAAATTCAAAGCATGAACCCTAAA

                              *              *                *    **      
      26518 TTGAGCATTTTC-CATACGT-TAGGGTCC-TATTTAACCAAATT-AAACGTATGAGTCCTAAA
          1 TTGAGCATTTTCACATA-ATCTAGGG-CCTTATGTAACCAAATTCAAA-GCATGAACCCTAAA

              *              
      26577 TTCAGCATTTTCACATA
          1 TTGAGCATTTTCACATA

      26594 TGTCAAGGAC


Statistics
Matches: 66,  Mismatches: 6, Indels: 8
        0.82            0.08        0.10

Matches are distributed among these distances:
  58    3  0.05
  59   44  0.67
  60   19  0.29

ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32


Consensus pattern (60 bp):   
TTGAGCATTTTCACATAATCTAGGGCCTTATGTAACCAAATTCAAAGCATGAACCCTAAA

Found at i:27334 original size:20 final size:20

Alignment explanation


    Indices: 27311--27357  Score: 94
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      27301 AAAGTATGTT

                                
      27311 TTTTTTTAAAAAAAAAAGAA
          1 TTTTTTTAAAAAAAAAAGAA

                                
      27331 TTTTTTTAAAAAAAAAAGAA
          1 TTTTTTTAAAAAAAAAAGAA

                   
      27351 TTTTTTT
          1 TTTTTTT

      27358 TTCTATTTAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   27  1.00

ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45


Consensus pattern (20 bp):   
TTTTTTTAAAAAAAAAAGAA
Done.