Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011066.1 Corchorus capsularis cultivar CVL-1 contig11087, 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: 16416
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:7319 original size:18 final size:19

Alignment explanation


    Indices: 7278--7319  Score: 50
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       7268 TAACGAAGTC

                      **       
       7278 AATTTTTAGTTTTTACATT
          1 AATTTTTAGTACTTACATT

            *                  
       7297 TATTTTTAGTACTTA-ATT
          1 AATTTTTAGTACTTACATT

                 
       7315 AATTT
          1 AATTT

       7320 ATTTATTTTT


Statistics
Matches: 19,  Mismatches: 4, Indels: 1
        0.79            0.17        0.04

Matches are distributed among these distances:
  18    7  0.37
  19   12  0.63

ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62


Consensus pattern (19 bp):   
AATTTTTAGTACTTACATT

Found at i:9555 original size:33 final size:33

Alignment explanation


    Indices: 9489--9585  Score: 136
    Period size: 28  Copynumber: 3.2  Consensus size: 33

       9479 ATTTTATTCG

                       *                     
       9489 ATTTGGCTCAACTATATTATAAGTAAG----G-
          1 ATTTGGCTCAAGTATATTATAAGTAAGTATAGT

                                             
       9517 ATTTGGCTCAAGTATATTATAAGTAAGTATAGT
          1 ATTTGGCTCAAGTATATTATAAGTAAGTATAGT

                                             
       9550 ATTTGGCTCAAGTATATTAT-A-TAAGTATAGT
          1 ATTTGGCTCAAGTATATTATAAGTAAGTATAGT

                 
       9581 ATTTG
          1 ATTTG

       9586 TTGGCATTAT


Statistics
Matches: 63,  Mismatches: 1, Indels: 7
        0.89            0.01        0.10

Matches are distributed among these distances:
  28   26  0.41
  31   15  0.24
  32    2  0.03
  33   20  0.32

ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40


Consensus pattern (33 bp):   
ATTTGGCTCAAGTATATTATAAGTAAGTATAGT

Found at i:11489 original size:13 final size:13

Alignment explanation


    Indices: 11471--11496  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      11461 AGGTCCTATA

                         
      11471 ATTACAATAGACT
          1 ATTACAATAGACT

                         
      11484 ATTACAATAGACT
          1 ATTACAATAGACT

      11497 CCAAGATAAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31


Consensus pattern (13 bp):   
ATTACAATAGACT

Found at i:12215 original size:16 final size:16

Alignment explanation


    Indices: 12194--12224  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      12184 AAGAAAATTA

                            
      12194 GCAAGAGCAAGTGTTG
          1 GCAAGAGCAAGTGTTG

                           
      12210 GCAAGAGCAAGTGTT
          1 GCAAGAGCAAGTGTT

      12225 TAGCAAGATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19


Consensus pattern (16 bp):   
GCAAGAGCAAGTGTTG

Found at i:12982 original size:1 final size:1

Alignment explanation


    Indices: 12976--13004  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

      12966 TTAGGTATGC

                                         
      12976 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      13005 CAAACAGAAA


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

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:13737 original size:14 final size:14

Alignment explanation


    Indices: 13712--13746  Score: 52
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      13702 ACAAAGGAAA

                           
      13712 GAAAATACAGAGCAT
          1 GAAAA-ACAGAGCAT

            *             
      13727 TAAAAACAGAGCAT
          1 GAAAAACAGAGCAT

                  
      13741 GAAAAA
          1 GAAAAA

      13747 AACAATAATC


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

Matches are distributed among these distances:
  14   14  0.78
  15    4  0.22

ACGTcount: A:0.60, C:0.11, G:0.17, T:0.11


Consensus pattern (14 bp):   
GAAAAACAGAGCAT
Done.