Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024363.1 Corchorus olitorius cultivar O-4 contig24396, 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: 36347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:17563 original size:11 final size:11

Alignment explanation


    Indices: 17539--17573  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      17529 TTGATAGCGC

                       
      17539 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
      17550 AACGAAAACGA
          1 AACAAAAACAA

                       
      17561 AACAAAAACAA
          1 AACAAAAACAA

              
      17572 AA
          1 AA

      17574 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:17565 original size:16 final size:16

Alignment explanation


    Indices: 17544--17602  Score: 50
    Period size: 16  Copynumber: 3.7  Consensus size: 16

      17534 AGCGCAACAA

                            
      17544 AAACAAAACGAAAACG
          1 AAACAAAACGAAAACG

                       *      
      17560 AAACAAAAACAAAAAAC-
          1 AAAC-AAAAC-GAAAACG

             *              
      17577 AGA-AAAACGAAAACG
          1 AAACAAAACGAAAACG

             *  *      
      17592 ATACCAAACGA
          1 AAACAAAACGA

      17603 CCCCTATTAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  14    5  0.15
  15    7  0.21
  16   10  0.29
  17    7  0.21
  18    5  0.15

ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02


Consensus pattern (16 bp):   
AAACAAAACGAAAACG

Found at i:22531 original size:34 final size:34

Alignment explanation


    Indices: 22467--22533  Score: 109
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      22457 TCTTCCTTTG

                                     *        
      22467 ATTGGATCAGATCTGTGAGATCTGTTTTTGATTA
          1 ATTGGATCAGATCTGTGAGATCTGTCTTTGATTA

                                              
      22501 ATTGGATCAGATCTGTGAGATCT-TCCTTTGATT
          1 ATTGGATCAGATCTGTGAGATCTGT-CTTTGATT

      22534 GTTATTTATG


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  33    1  0.03
  34   30  0.97

ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43


Consensus pattern (34 bp):   
ATTGGATCAGATCTGTGAGATCTGTCTTTGATTA

Found at i:23111 original size:2 final size:2

Alignment explanation


    Indices: 23104--23129  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      23094 ACATTTACCC

                                                  
      23104 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

      23130 TATCAAAACC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:35474 original size:121 final size:127

Alignment explanation


    Indices: 35233--35482  Score: 377
    Period size: 121  Copynumber: 2.0  Consensus size: 127

      35223 TAAGAAATAA

                                                      *                      
      35233 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
          1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-

                                                                    *        
      35298 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTGAATAAAACTGTAAAAGTA
         62 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAAAAGTA

             
      35363 T
        127 T

                                                                             
      35364 ATTTAAAAAATTC-TA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
          1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT

                                             *          * *             
      35424 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
         66 AAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAAAAGT

      35483 TTAAACAATG


Statistics
Matches: 114,  Mismatches: 5, Indels: 10
        0.88            0.04        0.08

Matches are distributed among these distances:
 121   53  0.46
 122    2  0.02
 123    2  0.02
 125    2  0.02
 129   40  0.35
 130    2  0.02
 131   13  0.11

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38


Consensus pattern (127 bp):   
ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAGTTGAATAAAACTATAAAAGTAT
Done.