Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021205.1 Corchorus olitorius cultivar O-4 contig21238, 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: 3636
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34


Found at i:112 original size:68 final size:68

Alignment explanation


    Indices: 1--422  Score: 718
    Period size: 68  Copynumber: 6.2  Consensus size: 68

                                                  *      *            *      
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGATCGAAGAGTCATTTTCGTCCTTTTGC
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC

               
         66 ATT
         66 ATT

                                                *                  *         
         69 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTTGGTCGAAGGGTCATTTTCATCTTTTTGC
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC

               
        134 ATT
         66 ATT

                            *                                                
        137 TAAGTTTAGTGTTTTCGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC

               
        202 ATT
         66 ATT

                                           *                          *      
        205 TAAGTTTAGTGTTTTCTATTTCCAAAAATACACTTTCGGTCGAAGGGTCATTTTCGTCCTTTTGC
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC

               
        270 ATT
         66 ATT

                         *                                          *        
        273 TAAGTTTAGTGTTGTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTTTGTCTTTTT
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCA--TTTTCGTCTTTTT

                 
        338 GCATT
         64 GCATT

                                                    *              *         
        343 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTTGAAGGGTCATTTTCATCTTTTTGC
          1 TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC

               
        408 ATT
         66 ATT

                        
        411 TAAGTTTAGTGT
          1 TAAGTTTAGTGT

        423 GTCTGTCGCC


Statistics
Matches: 333,  Mismatches: 19, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
  68  269  0.81
  70   64  0.19

ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46


Consensus pattern (68 bp):   
TAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGC
ATT

Found at i:679 original size:13 final size:13

Alignment explanation


    Indices: 661--685  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        651 TTTGGAATTC

                         
        661 CAAATAATATTTT
          1 CAAATAATATTTT

                        
        674 CAAATAATATTT
          1 CAAATAATATTT

        686 AGAACATTGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44


Consensus pattern (13 bp):   
CAAATAATATTTT

Found at i:2707 original size:28 final size:29

Alignment explanation


    Indices: 2643--2719  Score: 88
    Period size: 28  Copynumber: 2.7  Consensus size: 29

       2633 TGTAAAGGCA

                                *        
       2643 TAAAATTACCGTTTTACCCTAAGAATGAG
          1 TAAAATTACCGTTTTACCCTTAGAATGAG

                *                        
       2672 T-AAGTTACCGTTTTACCCTTAGAA-G-G
          1 TAAAATTACCGTTTTACCCTTAGAATGAG

                 *    *           
       2698 TTAAATTTACAGTTTTACCCTT
          1 -TAAAATTACCGTTTTACCCTT

       2720 TTAACATTGT


Statistics
Matches: 42,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  26    1  0.02
  27    2  0.05
  28   38  0.90
  29    1  0.02

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38


Consensus pattern (29 bp):   
TAAAATTACCGTTTTACCCTTAGAATGAG

Found at i:3270 original size:37 final size:37

Alignment explanation


    Indices: 3220--3304  Score: 134
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       3210 CTCGTTGAGG

                             *            *   *  
       3220 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATACTTAAT

                                                 
       3257 AAAATGTTTTATTACTGATTTTATTTAAATACTTAAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATACTTAAT

                 *     
       3294 AAAATATTTTA
          1 AAAATGTTTTA

       3305 ATAAATTATT


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  37   44  1.00

ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53


Consensus pattern (37 bp):   
AAAATGTTTTATTACTGATTTTATTTAAATACTTAAT
Done.