Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024090.1 Corchorus olitorius cultivar O-4 contig24123, 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: 16882
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:8342 original size:42 final size:43

Alignment explanation


    Indices: 8285--8380  Score: 115
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       8275 AAAGTGCATT

                      *               *     *          
       8285 ACCTAA-ATTTTA-CTCCATCTCTAGGTAATTTATCAAAATAA
          1 ACCTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAA

             *                  *                        
       8326 AGCTAATATTCTACTCCTCCTTCTCTAGATAATTCATCAAAATAA
          1 ACCTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAA

                      
       8371 ACCTAATATT
          1 ACCTAATATT

       8381 AATTGTTGTT


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  41    5  0.11
  42    5  0.11
  45   35  0.78

ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36


Consensus pattern (43 bp):   
ACCTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAA

Found at i:9581 original size:21 final size:22

Alignment explanation


    Indices: 9556--9609  Score: 74
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       9546 CCTTATATAA

                          * *     
       9556 ATTAAGTTTTTCA-GTCACCTT
          1 ATTAAGTTTTTCACCTAACCTT

                       *          
       9577 ATTAAGTTTTTTACCTAACCTT
          1 ATTAAGTTTTTCACCTAACCTT

                       
       9599 ATTAAGTTTTT
          1 ATTAAGTTTTT

       9610 AGTAATCTTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  21   12  0.41
  22   17  0.59

ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52


Consensus pattern (22 bp):   
ATTAAGTTTTTCACCTAACCTT

Found at i:9619 original size:20 final size:20

Alignment explanation


    Indices: 9556--9723  Score: 76
    Period size: 21  Copynumber: 8.2  Consensus size: 20

       9546 CCTTATATAA

                           * *   
       9556 ATTAAGTTTTTCAGTCACCTT
          1 ATTAAGTTTTT-AGTAATCTT

                          *   *   
       9577 ATTAAGTTTTTTACCTAACCTT
          1 ATTAAG-TTTTTA-GTAATCTT

                                
       9599 ATTAAGTTTTTAGTAATCTT
          1 ATTAAGTTTTTAGTAATCTT

               **  *              
       9619 ATTGTGAATTTTAG-AAGTCTT
          1 ATTAAG-TTTTTAGTAA-TCTT

                         *       
       9640 ATTAAGCTTTTTAATAA-CTT
          1 ATTAAG-TTTTTAGTAATCTT

                 *        *       
       9660 -TATAGGTTTTTCAATAATCTT
          1 AT-TAAGTTTTT-AGTAATCTT

              * *  *        *   
       9681 A-GAGGTATTTAGTAACCTT
          1 ATTAAGTTTTTAGTAATCTT

             *       *       *  
       9700 AATAA-TTTGTAGTAATGTT
          1 ATTAAGTTTTTAGTAATCTT

                 
       9719 ATTAA
          1 ATTAA

       9724 TATTGTAGTA


Statistics
Matches: 113,  Mismatches: 24, Indels: 22
        0.71            0.15        0.14

Matches are distributed among these distances:
  19   28  0.25
  20   31  0.27
  21   35  0.31
  22   19  0.17

ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48


Consensus pattern (20 bp):   
ATTAAGTTTTTAGTAATCTT

Found at i:9712 original size:19 final size:20

Alignment explanation


    Indices: 9686--9735  Score: 59
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       9676 ATCTTAGAGG

                                
       9686 TATT-TAGTAACCTTAATAA
          1 TATTGTAGTAACCTTAATAA

                       **   *   
       9705 T-TTGTAGTAATGTTATTAA
          1 TATTGTAGTAACCTTAATAA

                        
       9724 TATTGTAGTAAC
          1 TATTGTAGTAAC

       9736 TTTATTAAAC


Statistics
Matches: 25,  Mismatches: 4, Indels: 3
        0.78            0.12        0.09

Matches are distributed among these distances:
  18    2  0.08
  19   14  0.56
  20    9  0.36

ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46


Consensus pattern (20 bp):   
TATTGTAGTAACCTTAATAA

Found at i:9731 original size:20 final size:19

Alignment explanation


    Indices: 9690--9743  Score: 65
    Period size: 20  Copynumber: 2.8  Consensus size: 19

       9680 TAGAGGTATT

                   *   *       
       9690 TAGTAACCTTAATAATTTG
          1 TAGTAACTTTATTAATTTG

                                 
       9709 TAGTAA-TGTTATTAATATTG
          1 TAGTAACT-TTATTAAT-TTG

                           
       9729 TAGTAACTTTATTAA
          1 TAGTAACTTTATTAA

       9744 ACTTTTTTAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  19   13  0.43
  20   16  0.53
  21    1  0.03

ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46


Consensus pattern (19 bp):   
TAGTAACTTTATTAATTTG

Found at i:11140 original size:2 final size:2

Alignment explanation


    Indices: 11128--11201  Score: 112
    Period size: 2  Copynumber: 37.0  Consensus size: 2

      11118 AATAATATAA

                     *                                                  * 
      11128 CT CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

               *           *                               
      11170 CT GT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

      11202 ATATATATAT


Statistics
Matches: 64,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   64  1.00

ACGTcount: A:0.01, C:0.45, G:0.03, T:0.51


Consensus pattern (2 bp):   
CT

Done.