Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009510.1 Corchorus capsularis cultivar CVL-1 contig09531, 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: 27799
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:19404 original size:1 final size:1

Alignment explanation


    Indices: 19398--19436  Score: 78
    Period size: 1  Copynumber: 39.0  Consensus size: 1

      19388 AGAAATTCGG

                                                   
      19398 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      19437 CATGACAAAG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   38  1.00

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


Consensus pattern (1 bp):   
A

Found at i:20209 original size:16 final size:17

Alignment explanation


    Indices: 20180--20229  Score: 50
    Period size: 17  Copynumber: 3.0  Consensus size: 17

      20170 TTTATTAATA

                              
      20180 TATATA-ATTAAATATAT
          1 TATATACATT-AATATAT

                  *        **
      20197 TATATAGA-TAATATCG
          1 TATATACATTAATATAT

                             
      20213 TATATACATTAATATAT
          1 TATATACATTAATATAT

      20230 ATAATATTTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  16   12  0.46
  17   13  0.50
  18    1  0.04

ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44


Consensus pattern (17 bp):   
TATATACATTAATATAT

Found at i:21117 original size:9 final size:8

Alignment explanation


    Indices: 21091--21124  Score: 54
    Period size: 8  Copynumber: 4.5  Consensus size: 8

      21081 TTTGGTATCG

                    
      21091 TTTTC-GT
          1 TTTTCTGT

                    
      21098 TTTTCTGT
          1 TTTTCTGT

                    
      21106 TTTTCTGT
          1 TTTTCTGT

                    
      21114 TTTT-TGT
          1 TTTTCTGT

                
      21121 TTTT
          1 TTTT

      21125 GTTTTGTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   7   12  0.46
   8   14  0.54

ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79


Consensus pattern (8 bp):   
TTTTCTGT

Found at i:24138 original size:12 final size:13

Alignment explanation


    Indices: 24100--24139  Score: 55
    Period size: 12  Copynumber: 3.1  Consensus size: 13

      24090 GAAAAAAAGA

                          
      24100 ATATATTTATATAT
          1 ATATATTTATAT-T

                  *      
      24114 ATATATATATATT
          1 ATATATTTATATT

                         
      24127 -TATATTTATATT
          1 ATATATTTATATT

             
      24139 A
          1 A

      24140 GTAAAAGACA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  12   11  0.48
  13    1  0.04
  14   11  0.48

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57


Consensus pattern (13 bp):   
ATATATTTATATT
Done.