Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009102.1 Corchorus olitorius cultivar O-4 contig09130, 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, 743

Length: 1239
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25


Found at i:53 original size:35 final size:33

Alignment explanation


    Indices: 1--87  Score: 156
    Period size: 35  Copynumber: 2.6  Consensus size: 33

                                             
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGG
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGG

                                               
         34 ACTTGCTCGATGGTCACTCGGCCTTGGCACTCGGG
          1 ACTTGC-CGATGG-CACTCGGCCTTGGCACTCGGG

                               
         69 ACTTGCCGATGGCACTCGG
          1 ACTTGCCGATGGCACTCGG

         88 GACTTGCCGA


Statistics
Matches: 52,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
  33   13  0.25
  34   12  0.23
  35   27  0.52

ACGTcount: A:0.13, C:0.32, G:0.32, T:0.23


Consensus pattern (33 bp):   
ACTTGCCGATGGCACTCGGCCTTGGCACTCGGG

Found at i:83 original size:20 final size:20

Alignment explanation


    Indices: 58--233  Score: 164
    Period size: 20  Copynumber: 9.5  Consensus size: 20

         48 CACTCGGCCT

                                
         58 TGGCACTCGGGACTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                                
         78 TGGCACTCGGGACTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                     **        *
         98 TGGCACTCGACACTTGCCGG
          1 TGGCACTCGGGACTTGCCGA

                      *         
        118 TGGCACTCGGCACTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                          *    *
        138 TGGCACT----A--GGCC-T
          1 TGGCACTCGGGACTTGCCGA

                      *         
        151 TGGCACTCGGCACTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                          *    *
        171 TGGCACT----A--GGCC-T
          1 TGGCACTCGGGACTTGCCGA

                        *       
        184 TGGCACTCGGGAGTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                                
        204 TGGCACTCGGGACTTGCCGA
          1 TGGCACTCGGGACTTGCCGA

                      
        224 TGGCACTCGG
          1 TGGCACTCGG

        234 CCTTGACACT


Statistics
Matches: 128,  Mismatches: 14, Indels: 28
        0.75            0.08        0.16

Matches are distributed among these distances:
  13   14  0.11
  14    6  0.05
  16    2  0.02
  17    2  0.02
  19    6  0.05
  20   98  0.77

ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20


Consensus pattern (20 bp):   
TGGCACTCGGGACTTGCCGA

Found at i:113 original size:40 final size:38

Alignment explanation


    Indices: 58--238  Score: 159
    Period size: 33  Copynumber: 4.9  Consensus size: 38

         48 CACTCGGCCT

                                          *         
         58 TGGCACTCGGGACTTGCCGATGGCACTCGGGACTTGCCGA
          1 TGGCACTC--GACTTGCCGATGGCACTCGGCACTTGCCGA

                               *                    
         98 TGGCACTCGACACTTGCCGGTGGCACTCGGCACTTGCCGA
          1 TGGCACTCG--ACTTGCCGATGGCACTCGGCACTTGCCGA

                        *    *                    
        138 TGGCACT--A--GGCC-TTGGCACTCGGCACTTGCCGA
          1 TGGCACTCGACTTGCCGATGGCACTCGGCACTTGCCGA

                        *    *          * *       
        171 TGGCACT--A--GGCC-TTGGCACTCGGGAGTTGCCGA
          1 TGGCACTCGACTTGCCGATGGCACTCGGCACTTGCCGA

                                                
        204 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CTTG
          1 TGGCACTC--GACTTGCCGATGGCACTCGGCACTTG

        239 ACACTCGGGA


Statistics
Matches: 122,  Mismatches: 10, Indels: 19
        0.81            0.07        0.13

Matches are distributed among these distances:
  33   58  0.48
  34    3  0.02
  36    1  0.01
  37    1  0.01
  38    1  0.01
  39    6  0.05
  40   52  0.43

ACGTcount: A:0.14, C:0.31, G:0.33, T:0.21


Consensus pattern (38 bp):   
TGGCACTCGACTTGCCGATGGCACTCGGCACTTGCCGA

Found at i:160 original size:33 final size:33

Alignment explanation


    Indices: 118--210  Score: 168
    Period size: 33  Copynumber: 2.8  Consensus size: 33

        108 CACTTGCCGG

                                             
        118 TGGCACTCGGCACTTGCCGATGGCACTAGGCCT
          1 TGGCACTCGGCACTTGCCGATGGCACTAGGCCT

                                             
        151 TGGCACTCGGCACTTGCCGATGGCACTAGGCCT
          1 TGGCACTCGGCACTTGCCGATGGCACTAGGCCT

                      * *              
        184 TGGCACTCGGGAGTTGCCGATGGCACT
          1 TGGCACTCGGCACTTGCCGATGGCACT

        211 CGGGACTTGC


Statistics
Matches: 58,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   58  1.00

ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22


Consensus pattern (33 bp):   
TGGCACTCGGCACTTGCCGATGGCACTAGGCCT

Found at i:208 original size:53 final size:53

Alignment explanation


    Indices: 1--260  Score: 280
    Period size: 53  Copynumber: 4.9  Consensus size: 53

                                                                   
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCTCGATGGTCACTCGGC
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGC-CGATGG-CACTCGGC

                 *        *    *    *                             * 
         56 -CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGGACTTGCCGATGGCACTCGAC
          1 ACTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGACTTGCCGATGGCACTCGGC

                    *                *        *    *    *           
        109 ACTTGCCGGTGGCACTCGGCACTTGCCGA-T-GGCACTAGGCC-TTGGCACTCGGC
          1 ACTTGCCGATGGCACTCGGC-CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGC

                            *                 *                 *
        162 ACTTGCCGATGGCACTAGGCCTTGGCACTCGGGAGTTGCCGATGGCACTCGGG
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGC

                                    *                     
        215 ACTTGCCGATGGCACTCGGCCTTGACACTCGGGACTTGCCGATGGC
          1 ACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGC

        261 GCTTGGCAAC


Statistics
Matches: 167,  Mismatches: 26, Indels: 26
        0.76            0.12        0.12

Matches are distributed among these distances:
  51    1  0.01
  52    9  0.05
  53  103  0.62
  54   30  0.18
  55   24  0.14

ACGTcount: A:0.14, C:0.32, G:0.32, T:0.22


Consensus pattern (53 bp):   
ACTTGCCGATGGCACTCGGCCTTGGCACTCGGGACTTGCCGATGGCACTCGGC
Done.