Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018064.1 Corchorus olitorius cultivar O-4 contig18097, 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: 15228
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:2632 original size:92 final size:88

Alignment explanation


    Indices: 2459--2633  Score: 251
    Period size: 92  Copynumber: 1.9  Consensus size: 88

       2449 TCAAGTTCAT

                          *                      *                       *   
       2459 AGTCATGCTTAAGAGAATTGATGTTTTAACCATTTCTTCGTTTAGATTGACTGATCGACCATTCA
          1 AGTCATGCTTAAGAAAATTGATGTTTTAACCATTTCTCCGTTTAGATTGACTGATCGACCAGTCA

                       *           
       2524 CTTATGCTTTATTTTGGTTTGGC
         66 CTTATGCTTTACTTTGGTTTGGC

                                                                  *    *  *  
       2547 AGTCATGCTTAAGAAAATTGATGTTTTAACCACCCTCTTCTCCGTTTAGATTGAGTGATTGATCA
          1 AGTCATGCTTAAGAAAATTGATGTTTTAACCA---T-TTCTCCGTTTAGATTGACTGATCGACCA

                                  
       2612 GTCACTTATGCTTTACTTTGGT
         62 GTCACTTATGCTTTACTTTGGT

       2634 ATCTTTTGAT


Statistics
Matches: 76,  Mismatches: 7, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  88   31  0.41
  91    1  0.01
  92   44  0.58

ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42


Consensus pattern (88 bp):   
AGTCATGCTTAAGAAAATTGATGTTTTAACCATTTCTCCGTTTAGATTGACTGATCGACCAGTCA
CTTATGCTTTACTTTGGTTTGGC

Found at i:3772 original size:15 final size:15

Alignment explanation


    Indices: 3752--3781  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3742 AATAAATGAA

                           
       3752 ATACTCGGGTATCAC
          1 ATACTCGGGTATCAC

                           
       3767 ATACTCGGGTATCAC
          1 ATACTCGGGTATCAC

       3782 GTTACTAGCG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27


Consensus pattern (15 bp):   
ATACTCGGGTATCAC

Found at i:12713 original size:13 final size:13

Alignment explanation


    Indices: 12692--12727  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

      12682 TGGTGGGGGC

                     *   
      12692 AAGAAAAAATA-G
          1 AAGAAAAAAAAGG

                         
      12704 AAGAAAAAAAAGG
          1 AAGAAAAAAAAGG

                       
      12717 AAGAAAAAAAA
          1 AAGAAAAAAAA

      12728 ACATGGGTAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12   10  0.45
  13   12  0.55

ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03


Consensus pattern (13 bp):   
AAGAAAAAAAAGG

Found at i:14245 original size:91 final size:88

Alignment explanation


    Indices: 14072--14246  Score: 242
    Period size: 91  Copynumber: 2.0  Consensus size: 88

      14062 TCAAGTTCAT

                          *                  *  * *                       *  
      14072 AGTCATGCTTAAGAGAATTGATGTTTTAACCATTTTTTTCGTTTAGATTGACTGATCGACCATTC
          1 AGTCATGCTTAAGAAAATTGATGTTTTAACCATCTTCTCCGTTTAGATTGACTGATCGACCAGTC

                        *          
      14137 ACTTATGCTTTATTTTGGTTTGC
         66 ACTTATGCTTTACTTTGGTTTGC

                                                                  *    *  *  
      14160 AGTCATGCTTAAGAAAATTGATGTTTTAACCACCCTCTTCTCCGTTTAGATTGAGTGATTGATCA
          1 AGTCATGCTTAAGAAAATTGATGTTTTAACCA---TCTTCTCCGTTTAGATTGACTGATCGACCA

                                  
      14225 GTCACTTATGCTTTACTTTGGT
         63 GTCACTTATGCTTTACTTTGGT

      14247 ATTTTTTGAT


Statistics
Matches: 75,  Mismatches: 9, Indels: 3
        0.86            0.10        0.03

Matches are distributed among these distances:
  88   31  0.41
  91   44  0.59

ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43


Consensus pattern (88 bp):   
AGTCATGCTTAAGAAAATTGATGTTTTAACCATCTTCTCCGTTTAGATTGACTGATCGACCAGTC
ACTTATGCTTTACTTTGGTTTGC

Found at i:15149 original size:68 final size:69

Alignment explanation


    Indices: 15009--15157  Score: 275
    Period size: 69  Copynumber: 2.2  Consensus size: 69

      14999 TCTCACCATT

                                                   *                         
      15009 CAATTTCAAA-TGTACAACAACACCCATTACTTGAAAAGTATAAGGAAACAGAGCAAAAGAAAAG
          1 CAATTTCAAAGTGTACAACAACACCCATTACTTGAAAAGCATAAGGAAACAGAGCAAAAGAAAAG

                
      15073 ATAG
         66 ATAG

                                                                             
      15077 CAATTTCAAAGTGTACAACAACACCCATTACTTGAAAAGCATAAGGAAACAGAGCAAAAG-AAAG
          1 CAATTTCAAAGTGTACAACAACACCCATTACTTGAAAAGCATAAGGAAACAGAGCAAAAGAAAAG

                
      15141 ATAG
         66 ATAG

                         
      15145 CAATTTCAAAGTG
          1 CAATTTCAAAGTG

      15158 GTTTCATGCC


Statistics
Matches: 79,  Mismatches: 1, Indels: 2
        0.96            0.01        0.02

Matches are distributed among these distances:
  68   31  0.39
  69   48  0.61

ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18


Consensus pattern (69 bp):   
CAATTTCAAAGTGTACAACAACACCCATTACTTGAAAAGCATAAGGAAACAGAGCAAAAGAAAAG
ATAG
Done.