Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023144.1 Corchorus olitorius cultivar O-4 contig23177, 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: 18614
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:724 original size:25 final size:26

Alignment explanation


    Indices: 661--727  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

        651 CTAGAAAATT

                           *          
        661 TGAAAAACTTTGATGGATGAGATAGA
          1 TGAAAAACTTTGATGAATGAGATAGA

                                   *  
        687 TGAAAAACTTTGATGAATGAGATGGA
          1 TGAAAAACTTTGATGAATGAGATAGA

                            
        713 TGAAAAAC-TTGATGA
          1 TGAAAAACTTTGATGA

        728 CAGATGAATA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  25    7  0.18
  26   32  0.82

ACGTcount: A:0.43, C:0.04, G:0.25, T:0.27


Consensus pattern (26 bp):   
TGAAAAACTTTGATGAATGAGATAGA

Found at i:6348 original size:2 final size:2

Alignment explanation


    Indices: 6341--6378  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       6331 AGGTTATCAT

                                          *                         
       6341 TA TA TA TA TA TA TA TA TA TA CA 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 TA TA

       6379 GAGGTATAAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:6408 original size:16 final size:16

Alignment explanation


    Indices: 6382--6421  Score: 64
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6372 ATATATAGAG

                            
       6382 GTATA-ATAAGTATAA
          1 GTATAGATAAGTATAA

                           *
       6397 GTATAGATAAGTATAG
          1 GTATAGATAAGTATAA

                     
       6413 GTATAGATA
          1 GTATAGATA

       6422 GATAGATACT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15    5  0.22
  16   18  0.78

ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33


Consensus pattern (16 bp):   
GTATAGATAAGTATAA

Found at i:7226 original size:14 final size:15

Alignment explanation


    Indices: 7207--7236  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       7197 AACTAGGAAA

                           
       7207 AATAAAT-AACAAGG
          1 AATAAATAAACAAGG

                           
       7221 AATAAATAAACAAGG
          1 AATAAATAAACAAGG

             
       7236 A
          1 A

       7237 TTGGACTTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13


Consensus pattern (15 bp):   
AATAAATAAACAAGG

Found at i:10636 original size:2 final size:2

Alignment explanation


    Indices: 10631--10660  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      10621 TTTTTTCTTA

                                                        
      10631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      10661 TTTGTTTCTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:15696 original size:19 final size:18

Alignment explanation


    Indices: 15672--15710  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      15662 TTGAAGATTT

                               
      15672 ATTGAAGATAATTTGAAGA
          1 ATTGAAGATAA-TTGAAGA

                     *        
      15691 ATTGAAGATGATTGAAGA
          1 ATTGAAGATAATTGAAGA

              
      15709 AT
          1 AT

      15711 ATCTCAAGAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    9  0.47
  19   10  0.53

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (18 bp):   
ATTGAAGATAATTGAAGA
Done.