Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011945.1 Corchorus capsularis cultivar CVL-1 contig11966, 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: 3895
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27


Found at i:1377 original size:38 final size:38

Alignment explanation


    Indices: 1319--1497  Score: 288
    Period size: 38  Copynumber: 4.7  Consensus size: 38

       1309 ACAATCACAA

                *                   *             
       1319 TCTTGCCAACAG-TTAACCCCCTGGGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                  
       1356 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                   
       1394 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAA-CAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *                      *      
       1433 TCTTACCATCAGTTTAACCCCCTGAGGCACGAGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *            *     
       1471 TCTTACCATCAGTTTAACCCCATGAGG
          1 TCTTACCAACAGTTTAACCCCCTGAGG

       1498 TGCGGATCCA


Statistics
Matches: 135,  Mismatches: 5, Indels: 3
        0.94            0.03        0.02

Matches are distributed among these distances:
  37   11  0.08
  38   87  0.64
  39   37  0.27

ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23


Consensus pattern (38 bp):   
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

Found at i:1458 original size:77 final size:77

Alignment explanation


    Indices: 1319--1497  Score: 292
    Period size: 77  Copynumber: 2.4  Consensus size: 77

       1309 ACAATCACAA

                *                    *                                       
       1319 TCTTGCCAA-CAG-TTAACCCCCTGGGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAG
          1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAG

                 *      
       1382 GCACGGGTCCAC
         66 GCACGAGTCCAC

                                                           *                 
       1394 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGTTTAACCCCCTGAG
          1 TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAG

                        
       1459 GCACGAGTCCAC
         66 GCACGAGTCCAC

                                  *     
       1471 TCTTACC-ATCAGTTTAACCCCATGAGG
          1 TCTTACCAATCAGTTTAACCCCCTGAGG

       1498 TGCGGATCCA


Statistics
Matches: 97,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
  75    8  0.08
  76   22  0.23
  77   67  0.69

ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23


Consensus pattern (77 bp):   
TCTTACCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAG
GCACGAGTCCAC

Found at i:1715 original size:15 final size:16

Alignment explanation


    Indices: 1686--1719  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       1676 TCCATAAATC

                      *     
       1686 AATTCATAATTCATAT
          1 AATTCATAATACATAT

                            
       1702 AATT-ATAATACATAT
          1 AATTCATAATACATAT

               
       1717 AAT
          1 AAT

       1720 ATTTGAAAAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   13  0.76
  16    4  0.24

ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41


Consensus pattern (16 bp):   
AATTCATAATACATAT
Done.