Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008542.1 Corchorus olitorius cultivar O-4 contig08569, 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, 668

Length: 1114
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39


Found at i:956 original size:31 final size:31

Alignment explanation


    Indices: 916--1080  Score: 148
    Period size: 31  Copynumber: 5.5  Consensus size: 31

        906 TTAGGCTAAC

                                           
        916 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
          1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA

             *                 *          **
        947 TACTCAAATAAGGGCCTGATC-TTT-T-AATT
          1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA

                                      *     
        976 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA

                           *   *          **
       1007 TGCTCAAATAAGGGCTTGATC-TTT-T-AATT
          1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA

                                      *     
       1036 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA

                          
       1067 TGCTCAAATAAGGG
          1 TGCTCAAATAAGGG

       1081 TCTGGCGTCG


Statistics
Matches: 103,  Mismatches: 19, Indels: 24
        0.71            0.13        0.16

Matches are distributed among these distances:
  28    4  0.04
  29   37  0.36
  30    8  0.08
  31   50  0.49
  32    4  0.04

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


Consensus pattern (31 bp):   
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA

Found at i:993 original size:60 final size:60

Alignment explanation


    Indices: 920--1080  Score: 295
    Period size: 60  Copynumber: 2.7  Consensus size: 60

        910 GCTAACTGCT

                                 *      *                               
        920 CAAATAAGGGCCTAACGTTTGTCAAAATACTCAAATAAGGGCCTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

                                                      *                 
        980 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

                                                     
       1040 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG

       1081 TCTGGCGTCG


Statistics
Matches: 98,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  60   98  1.00

ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC

Found at i:1050 original size:29 final size:29

Alignment explanation


    Indices: 951--1052  Score: 109
    Period size: 29  Copynumber: 3.4  Consensus size: 29

        941 TCAAAATACT

                                         
        951 CAAATAAGGGCCTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTGATCTTTTAATTTGGC

                           *       *  **    
        980 CAAATAAGGGCCT-AACGTTTGCCAAAAT-GC
          1 CAAATAAGGGCCTGATC-TTT--TAATTTGGC

                        *                 
       1010 TCAAATAAGGGCTTGATCTTTTAATTTGGC
          1 -CAAATAAGGGCCTGATCTTTTAATTTGGC

                         
       1040 CAAATAAGGGCCT
          1 CAAATAAGGGCCT

       1053 AACGTTTGCC


Statistics
Matches: 57,  Mismatches: 10, Indels: 12
        0.72            0.13        0.15

Matches are distributed among these distances:
  28    2  0.04
  29   31  0.54
  30    4  0.07
  31   18  0.32
  32    2  0.04

ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Consensus pattern (29 bp):   
CAAATAAGGGCCTGATCTTTTAATTTGGC
Done.