Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023236.1 Corchorus olitorius cultivar O-4 contig23269, 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: 29192
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:6326 original size:16 final size:15

Alignment explanation


    Indices: 6288--6329  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6278 ACAGAGGTTG

                           
       6288 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       6303 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6318 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6330 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:16851 original size:18 final size:18

Alignment explanation


    Indices: 16828--16864  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      16818 CTCCTCTTGC

                     *        
      16828 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
      16846 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
      16864 A
          1 A

      16865 ACTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:17805 original size:21 final size:21

Alignment explanation


    Indices: 17752--17806  Score: 92
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      17742 GGCTTGGAAT

                       *         
      17752 GGTGATGGCACAGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                                 
      17773 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *        
      17794 GGTGGTGGCACGG
          1 GGTGATGGCACGG

      17807 TGAATGGATG


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.15, C:0.22, G:0.49, T:0.15


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC

Found at i:27453 original size:15 final size:15

Alignment explanation


    Indices: 27433--27474  Score: 59
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      27423 CGCTCAAATA

                           
      27433 TCGGGTCATTTGGGT
          1 TCGGGTCATTTGGGT

                             
      27448 TCGGGTCAATTCTGGGT
          1 TCGGGTC-ATT-TGGGT

                       
      27465 T-GGGTCATTT
          1 TCGGGTCATTT

      27475 TCGGTTTCGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  14    1  0.04
  15   10  0.40
  16    8  0.32
  17    6  0.24

ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40


Consensus pattern (15 bp):   
TCGGGTCATTTGGGT

Found at i:27471 original size:16 final size:16

Alignment explanation


    Indices: 27433--27487  Score: 60
    Period size: 16  Copynumber: 3.4  Consensus size: 16

      27423 CGCTCAAATA

                            
      27433 TCGGGTC-ATTTGGGT
          1 TCGGGTCAATTTGGGT

                             
      27448 TCGGGTCAATTCTGGGT
          1 TCGGGTCAATT-TGGGT

                    *      * 
      27465 T-GGGTCATTTTCGGTT
          1 TCGGGTCAATTT-GGGT

                   
      27481 TCGGGTC
          1 TCGGGTC

      27488 GTACGGTTCG


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  15    8  0.24
  16   15  0.44
  17   11  0.32

ACGTcount: A:0.07, C:0.16, G:0.36, T:0.40


Consensus pattern (16 bp):   
TCGGGTCAATTTGGGT

Found at i:28085 original size:2 final size:2

Alignment explanation


    Indices: 28073--28106  Score: 52
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      28063 GTCTCTGATT

                                                               
      28073 TA TA CTA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
          1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      28107 ATAGACTTTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    1  0.03
   2   27  0.90
   3    2  0.07

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.