Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019313.1 Corchorus olitorius cultivar O-4 contig19346, 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: 9555
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33


Found at i:205 original size:22 final size:22

Alignment explanation


    Indices: 163--205  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        153 TTTCTGATTA

                           **     
        163 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
        185 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

        206 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG

Found at i:587 original size:69 final size:69

Alignment explanation


    Indices: 455--758  Score: 493
    Period size: 69  Copynumber: 4.4  Consensus size: 69

        445 CTGTCTCATG

                                                                             
        455 TGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT-TGTGGCTTGGATGGAACCAAGGCTTGAACTGA
          1 TGGAAACGAGTTTGGCTTGTGGAAAAG--CCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGA

                  
        519 CTCGTA
         64 CTCGTA

                                          *                                  
        525 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAACTGACT
          1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACT

                
        590 CGTA
         66 CGTA

                                                                 *     *     
        594 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGATTGAATTGACT
          1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACT

            *   
        659 AGTA
         66 CGTA

                                            *                       *   *    
        663 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAAACCGACT
          1 TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACT

                
        728 CGTA
         66 CGTA

                  *       *   *        
        732 TGGAAATGAGTTTGACTTATGGAAAAG
          1 TGGAAACGAGTTTGGCTTGTGGAAAAG

        759 TCAAAGCATT


Statistics
Matches: 220,  Mismatches: 13, Indels: 3
        0.93            0.06        0.01

Matches are distributed among these distances:
  68    3  0.01
  69  190  0.86
  70   27  0.12

ACGTcount: A:0.28, C:0.15, G:0.31, T:0.27


Consensus pattern (69 bp):   
TGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACT
CGTA

Found at i:1723 original size:49 final size:49

Alignment explanation


    Indices: 1670--1814  Score: 197
    Period size: 49  Copynumber: 3.0  Consensus size: 49

       1660 AATGCCCTTA

                      *    *      *                          
       1670 GAAAAGCGAACTTTGTTCTTGGTCTCACAAATGGAGTGCAATCTTATTT
          1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTT

                                               *      *      
       1719 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATTTTA-TT
          1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTT

                             *                                
       1767 GTAAAAGCGAATTTTGAACTT-GACTCACAAATGG-GATGCAATCTTATT
          1 G-AAAAGCGAATTTTGATCTTGGACTCACAAATGGAG-TGCAATCTTATT

       1815 ATAAAAATTC


Statistics
Matches: 85,  Mismatches: 8, Indels: 6
        0.86            0.08        0.06

Matches are distributed among these distances:
  48   25  0.29
  49   60  0.71

ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33


Consensus pattern (49 bp):   
GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTT

Found at i:8724 original size:21 final size:21

Alignment explanation


    Indices: 8698--8739  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8688 GCATCTTAGG

                                 
       8698 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                                 
       8719 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

       8740 TTCTTCCTTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC
Done.