Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009811.1 Corchorus capsularis cultivar CVL-1 contig09832, 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: 1863
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28


Found at i:1086 original size:6 final size:6

Alignment explanation


    Indices: 1077--1111  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       1067 AGATGCACCG

                 *                   *              
       1077 CAATCG CAATCA CAATCA CAATTA CAATCA CAATC
          1 CAATCA CAATCA CAATCA CAATCA CAATCA CAATC

       1112 TTGCCAACAG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20


Consensus pattern (6 bp):   
CAATCA

Found at i:1170 original size:38 final size:38

Alignment explanation


    Indices: 1110--1300  Score: 310
    Period size: 38  Copynumber: 5.0  Consensus size: 38

       1100 ACAATCACAA

                *       *    *                   *
       1110 TCTTGCCAACAGCTTAAACCCCTGAGGCACGGGTCCAT
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                        *               *         
       1148 TCTTACCAACAGCTTAACCCCCTGAGGCGCGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                    *                       *     
       1186 TCTTACCATCAGTTTAACCCCCTGAGGCACGGATCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                  
       1224 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

                                                  
       1262 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
          1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

             
       1300 T
          1 T

       1301 ATGCACAGCC


Statistics
Matches: 143,  Mismatches: 10, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  38  143  1.00

ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21


Consensus pattern (38 bp):   
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC

Done.