Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014869.1 Corchorus olitorius cultivar O-4 contig14902, 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: 14014
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32


Found at i:1159 original size:15 final size:15

Alignment explanation


    Indices: 1139--1170  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1129 CCTTGGGGGT

                           
       1139 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                           
       1154 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

              
       1169 TC
          1 TC

       1171 CACTTAGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:1871 original size:33 final size:32

Alignment explanation


    Indices: 1768--1896  Score: 100
    Period size: 33  Copynumber: 3.9  Consensus size: 32

       1758 CCTGATTTGA

                      **             *        
       1768 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATTTG-TTTAG

            *       *       *       * **    *
       1801 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAA-TTTGTTTAG

                                             
       1834 GTGTTGTTTGTGATGACACTAAATTTGTTGTAG
          1 GTGTTGTTTGTGATGACACTAAATTTGTT-TAG

                            *              
       1867 GTGTTGTTTGTGATGAAAC-AAATTCTGTTT
          1 GTGTTGTTTGTGATGACACTAAATT-TGTTT

       1897 TGGATGCTAA


Statistics
Matches: 74,  Mismatches: 18, Indels: 9
        0.73            0.18        0.09

Matches are distributed among these distances:
  32    9  0.12
  33   64  0.86
  34    1  0.01

ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43


Consensus pattern (32 bp):   
GTGTTGTTTGTGATGACACTAAATTTGTTTAG

Found at i:1872 original size:66 final size:66

Alignment explanation


    Indices: 1756--1882  Score: 166
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1746 AGTAATTCTG

                 *    *                              *                       
       1756 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTGTAGATGTTGTTAGTGATGATACT

             
       1821 A
         66 A

                                  **             *        *       *       
       1822 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTGTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTGTAGATGTTGTTAGTGATGA

       1883 AACAAATTCT


Statistics
Matches: 52,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  66   51  0.98
  67    1  0.02

ACGTcount: A:0.26, C:0.08, G:0.24, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTGTAGATGTTGTTAGTGATGATACT
A

Found at i:10952 original size:32 final size:32

Alignment explanation


    Indices: 10908--11004  Score: 124
    Period size: 32  Copynumber: 3.0  Consensus size: 32

      10898 TTTTTGCAAA

                   *      *                 
      10908 TAGTGGCGTTTATTCAGTAAAACGCCACTAAT
          1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT

                          *                 
      10940 TAGTGGCATTTATTGAGTAAAACGCCACTAAT
          1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT

                    *     *            *     
      10972 TAGTGGCGTTTTATGAAG-AAAACGCCCCTAAT
          1 TAGTGGC-ATTTATTAAGTAAAACGCCACTAAT

             
      11004 T
          1 T

      11005 TGCAATCCAG


Statistics
Matches: 58,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  32   51  0.88
  33    7  0.12

ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31


Consensus pattern (32 bp):   
TAGTGGCATTTATTAAGTAAAACGCCACTAAT

Found at i:11757 original size:15 final size:15

Alignment explanation


    Indices: 11737--11803  Score: 77
    Period size: 15  Copynumber: 4.7  Consensus size: 15

      11727 TGAAGTTGGT

                           
      11737 GATGATGCAAATGTA
          1 GATGATGCAAATGTA

                           
      11752 GATGATGCAAATGTA
          1 GATGATGCAAATGTA

             *       **    
      11767 GGTGAT---TTTGTA
          1 GATGATGCAAATGTA

                           
      11779 GATGATGCAAATGTA
          1 GATGATGCAAATGTA

             *        
      11794 GGTGATGCAA
          1 GATGATGCAA

      11804 GGGACGAAGA


Statistics
Matches: 42,  Mismatches: 7, Indels: 6
        0.76            0.13        0.11

Matches are distributed among these distances:
  12    9  0.21
  15   33  0.79

ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30


Consensus pattern (15 bp):   
GATGATGCAAATGTA

Found at i:11786 original size:27 final size:27

Alignment explanation


    Indices: 11748--11799  Score: 104
    Period size: 27  Copynumber: 1.9  Consensus size: 27

      11738 ATGATGCAAA

                                       
      11748 TGTAGATGATGCAAATGTAGGTGATTT
          1 TGTAGATGATGCAAATGTAGGTGATTT

                                     
      11775 TGTAGATGATGCAAATGTAGGTGAT
          1 TGTAGATGATGCAAATGTAGGTGAT

      11800 GCAAGGGACG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35


Consensus pattern (27 bp):   
TGTAGATGATGCAAATGTAGGTGATTT
Done.