Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001210.1 Corchorus capsularis cultivar CVL-1 contig01210, 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: 5357
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:404 original size:30 final size:30

Alignment explanation


    Indices: 370--471  Score: 111
    Period size: 30  Copynumber: 3.4  Consensus size: 30

        360 ACTAATTACT

                                          
        370 CAAATAAGGGCCTAATGTTTGCCGAAATGC
          1 CAAATAAGGGCCTAATGTTTGCCGAAATGC

                    *  * *  *      *   *    
        400 CAAATAAGCGCTTGATCTTT---TAATTTGGC
          1 CAAATAAGGGCCTAATGTTTGCCGAA-AT-GC

                                          
        429 CAAATAAGGGCCTAATGTTTGCCGAAATGC
          1 CAAATAAGGGCCTAATGTTTGCCGAAATGC

                         
        459 CAAATAAGGGCCT
          1 CAAATAAGGGCCT

        472 GATCTTTTAA


Statistics
Matches: 55,  Mismatches: 12, Indels: 10
        0.71            0.16        0.13

Matches are distributed among these distances:
  27    2  0.04
  28    1  0.02
  29   18  0.33
  30   31  0.56
  31    1  0.02
  32    2  0.04

ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26


Consensus pattern (30 bp):   
CAAATAAGGGCCTAATGTTTGCCGAAATGC

Found at i:434 original size:29 final size:29

Alignment explanation


    Indices: 398--560  Score: 118
    Period size: 29  Copynumber: 5.5  Consensus size: 29

        388 TTGCCGAAAT

                      *  *               
        398 GCCAAATAAGCGCTTGATCTTTTAATTTG
          1 GCCAAATAAGGGCCTGATCTTTTAATTTG

                           *  *      *   *  
        427 GCCAAATAAGGGCCTAATGTTTGCCGAA-AT-
          1 GCCAAATAAGGGCCTGATCTTT---TAATTTG

                                         
        457 GCCAAATAAGGGCCTGATCTTTTAATTTG
          1 GCCAAATAAGGGCCTGATCTTTTAATTTG

                     *       *       *  **  
        486 GCCAAATAAAGGCCT-AACATTATAGAAAAT-
          1 GCCAAATAAGGGCCTGATC-TT-T-TAATTTG

                           *              
        516 GCTCAAATAAGGGCCCGATCTTTTAATTTG
          1 GC-CAAATAAGGGCCTGATCTTTTAATTTG

                *          
        546 GCCAGATAAGGGCCT
          1 GCCAAATAAGGGCCT

        561 AACGTCGTCG


Statistics
Matches: 100,  Mismatches: 23, Indels: 22
        0.69            0.16        0.15

Matches are distributed among these distances:
  27    2  0.02
  28    3  0.03
  29   48  0.48
  30   26  0.26
  31   17  0.17
  32    4  0.04

ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28


Consensus pattern (29 bp):   
GCCAAATAAGGGCCTGATCTTTTAATTTG

Found at i:437 original size:59 final size:59

Alignment explanation


    Indices: 370--588  Score: 273
    Period size: 59  Copynumber: 3.7  Consensus size: 59

        360 ACTAATTACT

                                                  *  *                 
        370 CAAATAAGGGCCTAATGTTTGCCGAAATGCCAAATAAGCGCTTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAATGTTTGCCGAAATGCCAAATAAGGGCCTGATCTTTTAATTTGGC

                                                                       
        429 CAAATAAGGGCCTAATGTTTGCCGAAATGCCAAATAAGGGCCTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAATGTTTGCCGAAATGCCAAATAAGGGCCTGATCTTTTAATTTGGC

                   *       **        *                   *                
        488 CAAATAAAGGCCTAACATTATAG--AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAATGTT-T-GCCGAAATGC-CAAATAAGGGCCTGATCTTTTAATTTGGC

              *            *   * *                    
        548 CAGATAAGGGCCTAACG-TCGTCGAAAATGCTCAAATAAGGG
          1 CAAATAAGGGCCTAATGTTTGCCG-AAATGC-CAAATAAGGG

        589 TCTGGCATCA


Statistics
Matches: 142,  Mismatches: 12, Indels: 11
        0.86            0.07        0.07

Matches are distributed among these distances:
  57    1  0.01
  59   80  0.56
  60   60  0.42
  61    1  0.01

ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26


Consensus pattern (59 bp):   
CAAATAAGGGCCTAATGTTTGCCGAAATGCCAAATAAGGGCCTGATCTTTTAATTTGGC

Found at i:668 original size:31 final size:30

Alignment explanation


    Indices: 632--770  Score: 97
    Period size: 31  Copynumber: 4.6  Consensus size: 30

        622 TCGATGCCAT

                                           
        632 GCCCTTATTTGAGAATTTTGGCAAATGTTAG
          1 GCCCTTATTTGAGAATTTTGGCAAA-GTTAG

                            **    *         
        663 GCCCTTATTTG-GCAAAATT--AAAAGATT-G
          1 GCCCTTATTTGAG-AATTTTGGCAAAG-TTAG

                          *           *    
        691 GACCCTTATTTGAGCATTTTGGCAAACTTAG
          1 G-CCCTTATTTGAGAATTTTGGCAAAGTTAG

            *            *     **          
        722 ACCCTTATTTGAGCATTTTAACAAACGTTAG
          1 GCCCTTATTTGAGAATTTTGGCAAA-GTTAG

            *    *            
        753 ACCCTAATTTGAGCAATT
          1 GCCCTTATTTGAG-AATT

        771 AGCCTAATGT


Statistics
Matches: 85,  Mismatches: 14, Indels: 17
        0.73            0.12        0.15

Matches are distributed among these distances:
  28    3  0.04
  29   18  0.21
  30   26  0.31
  31   35  0.41
  32    3  0.04

ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35


Consensus pattern (30 bp):   
GCCCTTATTTGAGAATTTTGGCAAAGTTAG

Found at i:727 original size:30 final size:31

Alignment explanation


    Indices: 691--767  Score: 120
    Period size: 30  Copynumber: 2.5  Consensus size: 31

        681 TAAAAGATTG

                                **         
        691 GACCCTTATTTGAGCATTTTGGCAAAC-TTA
          1 GACCCTTATTTGAGCATTTTAACAAACGTTA

                                           
        721 GACCCTTATTTGAGCATTTTAACAAACGTTA
          1 GACCCTTATTTGAGCATTTTAACAAACGTTA

                  *         
        752 GACCCTAATTTGAGCA
          1 GACCCTTATTTGAGCA

        768 ATTAGCCTAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 1
        0.91            0.06        0.02

Matches are distributed among these distances:
  30   25  0.58
  31   18  0.42

ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34


Consensus pattern (31 bp):   
GACCCTTATTTGAGCATTTTAACAAACGTTA
Done.