Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018085.1 Corchorus olitorius cultivar O-4 contig18118, 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: 1708
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30


Found at i:366 original size:22 final size:21

Alignment explanation


    Indices: 315--356  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        305 GTAGAGACTA

                                 
        315 ATGAAATTTGGTCAAAAAGGG
          1 ATGAAATTTGGTCAAAAAGGG

                                  
        336 ATGAAATTTGG-CTAAAAAGGG
          1 ATGAAATTTGGTC-AAAAAGGG

        357 GCTGGAATTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20    1  0.05
  21   19  0.95

ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24


Consensus pattern (21 bp):   
ATGAAATTTGGTCAAAAAGGG

Found at i:1278 original size:32 final size:32

Alignment explanation


    Indices: 1214--1278  Score: 78
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1204 TCTTTTGTGT

                       *     **             
       1214 AAAAAATTACCGTTATAGTCTTAATCGATAAA
          1 AAAAAATTACCATTATACCCTTAATCGATAAA

                                    *        
       1246 AAAAAATTACCATTATGACCCTTAGTCG-TAAA
          1 AAAAAATTACCATTAT-ACCCTTAATCGATAAA

             
       1278 A
          1 A

       1279 TTTACGCAAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  32   20  0.71
  33    8  0.29

ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29


Consensus pattern (32 bp):   
AAAAAATTACCATTATACCCTTAATCGATAAA

Found at i:1569 original size:27 final size:28

Alignment explanation


    Indices: 1501--1575  Score: 84
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       1491 TTAAGATATC

                    *                   
       1501 AAAATTACTGTTTTGCCCTTGGTCAGCT
          1 AAAATTACAGTTTTGCCCTTGGTCAGCT

                           *         *    
       1529 AAAATTACCA-TTTTACCCTTGGT-TGACT
          1 AAAATTA-CAGTTTTGCCCTTGGTCAG-CT

                                
       1557 -AAATTACAGTTTTGCCCTT
          1 AAAATTACAGTTTTGCCCTT

       1576 AAATGCCGGA


Statistics
Matches: 40,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  26    2  0.05
  27   16  0.40
  28   21  0.52
  29    1  0.03

ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40


Consensus pattern (28 bp):   
AAAATTACAGTTTTGCCCTTGGTCAGCT
Done.