Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004724.1 Corchorus capsularis cultivar CVL-1 contig04740, 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, 840

Length: 1401
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26


Found at i:618 original size:48 final size:48

Alignment explanation


    Indices: 542--654  Score: 183
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        532 TGGATTTCTA

                         *                                  
        542 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                                          *              *   
        590 -TTTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGC
          1 ATTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                             
        638 ATTTTGGCCAATTTTTG
          1 ATTTTGGCCAATTTTTG

        655 CCCCCGAAGC


Statistics
Matches: 60,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  47    4  0.07
  48   52  0.87
  49    4  0.07

ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37


Consensus pattern (48 bp):   
ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

Found at i:718 original size:77 final size:78

Alignment explanation


    Indices: 591--745  Score: 206
    Period size: 77  Copynumber: 2.0  Consensus size: 78

        581 ACCTACGGCT

                                        *    ****                            
        591 TTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGCA-TTTTGGCCAATTTTTG
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTTGGCCAATTTTTG

                    *    
        655 CCCCCGAAGCTCA
         66 CCCCCGAAACTCA

                     *          *                                      *     
        668 TTTCGGCCATTTTTTGGGTCTGGAACTCATGATACAAAACCTAAT-GCATTTTTGGCCATTTTTT
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCT-ATGGCATTTTTGGCCAATTTTT

                          
        732 GCCCCCGAAACTCA
         65 GCCCCCGAAACTCA

        746 GCGAACACCT


Statistics
Matches: 67,  Mismatches: 9, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  77   38  0.57
  78   29  0.43

ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35


Consensus pattern (78 bp):   
TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTTGGCCAATTTTTG
CCCCCGAAACTCA

Found at i:1053 original size:32 final size:32

Alignment explanation


    Indices: 964--1054  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        954 GGACACCCTT

                                     *      
        964 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
        996 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
       1028 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

       1055 ATCGGCACTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  31    1  0.02
  32   54  0.96
  33    1  0.02

ACGTcount: A:0.11, C:0.31, G:0.30, T:0.29


Consensus pattern (32 bp):   
CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

Found at i:1054 original size:26 final size:26

Alignment explanation


    Indices: 1042--1124  Score: 166
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       1032 GGCATTCTCC

                                      
       1042 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
       1068 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
       1094 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                 
       1120 GATGG
          1 GATGG

       1125 ATGGCACTTG


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   57  1.00

ACGTcount: A:0.16, C:0.25, G:0.33, T:0.27


Consensus pattern (26 bp):   
GATGGCACTTGGCATCGGCACTTGCT

Found at i:1061 original size:13 final size:13

Alignment explanation


    Indices: 1045--1117  Score: 82
    Period size: 13  Copynumber: 5.6  Consensus size: 13

       1035 ATTCTCCGAT

                         
       1045 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
       1058 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
       1071 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
       1084 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
       1097 GGCACTTGGCATC
          1 GGCACTTGGCATC

                    
       1110 GGCACTTG
          1 GGCACTTG

       1118 CTGATGGATG


Statistics
Matches: 52,  Mismatches: 0, Indels: 16
        0.76            0.00        0.24

Matches are distributed among these distances:
  12    8  0.15
  13   36  0.69
  14    8  0.15

ACGTcount: A:0.15, C:0.27, G:0.32, T:0.26


Consensus pattern (13 bp):   
GGCACTTGGCATC

Found at i:1086 original size:52 final size:51

Alignment explanation


    Indices: 1019--1124  Score: 162
    Period size: 52  Copynumber: 2.1  Consensus size: 51

       1009 CGATGGATCT

                      *                                          
       1019 TGGCCTTGGCGTCGGCA-TT-CTCCGATGGCACTTGGCATCGGCACTTGCTGA
          1 TGGCCTTGGCATCGGCACTTGCT--GATGGCACTTGGCATCGGCACTTGCTGA

                                                                
       1070 TGGCACTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA
          1 TGGC-CTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA

               
       1122 TGG
          1 TGG

       1125 ATGGCACTTG


Statistics
Matches: 51,  Mismatches: 1, Indels: 5
        0.89            0.02        0.09

Matches are distributed among these distances:
  51    4  0.08
  52   43  0.84
  53    2  0.04
  54    2  0.04

ACGTcount: A:0.13, C:0.27, G:0.32, T:0.27


Consensus pattern (51 bp):   
TGGCCTTGGCATCGGCACTTGCTGATGGCACTTGGCATCGGCACTTGCTGA
Done.