Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009819.1 Corchorus olitorius cultivar O-4 contig09851, 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: 5613
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36


Found at i:2152 original size:31 final size:29

Alignment explanation


    Indices: 2117--2191  Score: 87
    Period size: 29  Copynumber: 2.5  Consensus size: 29

       2107 AAAGTTCAAA

                                           
       2117 TAAGGACCTAACCTTTAGGGAAAAGGTCATT
          1 TAAGGACCTAACCTTTA--GAAAAGGTCATT

                 *   * *                 
       2148 TAAGGGCCTGATCTTTAGAAAAGGTCATT
          1 TAAGGACCTAACCTTTAGAAAAGGTCATT

                *   *      
       2177 TAAGTACCCAACCTT
          1 TAAGGACCTAACCTT

       2192 ACAAAATTGG


Statistics
Matches: 36,  Mismatches: 8, Indels: 2
        0.78            0.17        0.04

Matches are distributed among these distances:
  29   22  0.61
  31   14  0.39

ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28


Consensus pattern (29 bp):   
TAAGGACCTAACCTTTAGAAAAGGTCATT

Found at i:2799 original size:24 final size:24

Alignment explanation


    Indices: 2763--2810  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2753 AGAGGGGCAG

                                    
       2763 CACCACCAACGCCGACAAAAGCAA
          1 CACCACCAACGCCGACAAAAGCAA

                    *               
       2787 CACCACCAGCGCCGACAAAAGCAA
          1 CACCACCAACGCCGACAAAAGCAA

       2811 TGACATCGGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.44, C:0.42, G:0.15, T:0.00


Consensus pattern (24 bp):   
CACCACCAACGCCGACAAAAGCAA

Found at i:3492 original size:2 final size:2

Alignment explanation


    Indices: 3487--3528  Score: 66
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       3477 TTCTAAAGGT

                                                          *     *         
       3487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3529 CTACTTTCAC


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4998 original size:9 final size:9

Alignment explanation


    Indices: 4984--5009  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       4974 GATTCACCCT

                     
       4984 AAACCGACC
          1 AAACCGACC

                     
       4993 AAACCGACC
          1 AAACCGACC

                    
       5002 AAACCGAC
          1 AAACCGAC

       5010 AGGAGAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.46, C:0.42, G:0.12, T:0.00


Consensus pattern (9 bp):   
AAACCGACC
Done.