Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010841.1 Corchorus capsularis cultivar CVL-1 contig10862, 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: 44859
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:127 original size:33 final size:33

Alignment explanation


    Indices: 66--134  Score: 88
    Period size: 33  Copynumber: 2.1  Consensus size: 33

         56 TTTTTTTATT

                                 *            
         66 AGACACATGTTATAAGCTACTGCCAAAAAA-AAA
          1 AGACACATGTTATAAGCTA-TCCCAAAAAATAAA

                                               
         99 AGACACATGTTATAAGCT-TCCCGTAAAAAATAAA
          1 AGACACATGTTATAAGCTATCCC--AAAAAATAAA

              
        133 AG
          1 AG

        135 GGCATATATA


Statistics
Matches: 32,  Mismatches: 1, Indels: 5
        0.84            0.03        0.13

Matches are distributed among these distances:
  31    3  0.09
  33   24  0.75
  34    5  0.16

ACGTcount: A:0.49, C:0.17, G:0.13, T:0.20


Consensus pattern (33 bp):   
AGACACATGTTATAAGCTATCCCAAAAAATAAA

Found at i:26735 original size:6 final size:6

Alignment explanation


    Indices: 26724--26748  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      26714 CTAGGAGTGT

                                         
      26724 CACCGC CACCGC CACCGC CACCGC C
          1 CACCGC CACCGC CACCGC CACCGC C

      26749 GCTTGTACAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00


Consensus pattern (6 bp):   
CACCGC

Found at i:38874 original size:147 final size:147

Alignment explanation


    Indices: 38606--38878  Score: 404
    Period size: 147  Copynumber: 1.9  Consensus size: 147

      38596 CCAGAGTTGC

                             *    *            *                     *       
      38606 TGCTTGCACTTGCAGTGCTGCTGGAGTTAGATTCTGATGCCATGCTCCATTGGTTTTTTGCCCAT
          1 TGCTTGCACTTGCAGTGATGCTAGAGTTAGATTCTAATGCCATGCTCCATTGGTTTTCTGCCCAT

                           *  *      * *                       *             
      38671 TGTTGATGCTCATAAGAATTCTCTTTTTTATAAGCCACTTGCTTACCATGATCATCATCATCATC
         66 TGTTGATGCTCATAACAACTCTCTTCTATATAAGCCACTTGCTTACCATGACCATCATCATCATC

                             
      38736 GTGGGTTTTTTCTAAGT
        131 GTGGGTTTTTTCTAAGT

                  *                                 *     *                  
      38753 TGCTTGTACTTGCAGTGATGCTAGAGTTAGATTCTAATGCTATGCTGCATTGGTTTTCTGCCTC-
          1 TGCTTGCACTTGCAGTGATGCTAGAGTTAGATTCTAATGCCATGCTCCATTGGTTTTCTGCC-CA

              *  *                                                        
      38817 TTTTTTATGCTCATAACAACTCTCTTCTATATAAGCCACTTGCTTACCATGACCATCATCAT
         65 TTGTTGATGCTCATAACAACTCTCTTCTATATAAGCCACTTGCTTACCATGACCATCATCAT

      38879 GGTCGCTTTG


Statistics
Matches: 111,  Mismatches: 14, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
 147  110  0.99
 148    1  0.01

ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40


Consensus pattern (147 bp):   
TGCTTGCACTTGCAGTGATGCTAGAGTTAGATTCTAATGCCATGCTCCATTGGTTTTCTGCCCAT
TGTTGATGCTCATAACAACTCTCTTCTATATAAGCCACTTGCTTACCATGACCATCATCATCATC
GTGGGTTTTTTCTAAGT
Done.