Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022347.1 Corchorus olitorius cultivar O-4 contig22380, 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: 15825
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31


Found at i:338 original size:35 final size:35

Alignment explanation


    Indices: 236--339  Score: 176
    Period size: 33  Copynumber: 3.0  Consensus size: 35

        226 AATGCAATCC

                      *                        
        236 AATACATGCAGTGCCAAGCAAAGAAAATCAAAATA
          1 AATACATGCAATGCCAAGCAAAGAAAATCAAAATA

                          *                    
        271 AATACATGCAATG-TAAGCAAA-AAAATCAAAATA
          1 AATACATGCAATGCCAAGCAAAGAAAATCAAAATA

                                               
        304 AATACATGCAATGCCAAGCAAAGAAAATCAAAATA
          1 AATACATGCAATGCCAAGCAAAGAAAATCAAAATA

             
        339 A
          1 A

        340 TGCATGAGGC


Statistics
Matches: 64,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  33   25  0.39
  34   14  0.22
  35   25  0.39

ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15


Consensus pattern (35 bp):   
AATACATGCAATGCCAAGCAAAGAAAATCAAAATA

Found at i:756 original size:28 final size:28

Alignment explanation


    Indices: 688--818  Score: 154
    Period size: 28  Copynumber: 4.6  Consensus size: 28

        678 AGTACTAGAG

                                  **       
        688 ATGACCCAAAATGCCCCCTGGATGTGCTAAA
          1 ATGA-CCAAAATG-CCCCTGGACATGC-AAA

              *                 *       
        719 ATTACCAAAATGCCCCTGGATATGCAAA
          1 ATGACCAAAATGCCCCTGGACATGCAAA

                              *         
        747 ATGACCAAAATGCCCCTGAACATGCAAA
          1 ATGACCAAAATGCCCCTGGACATGCAAA

                        *  *            
        775 ATGACCAAAATGTCCTTGGACATGCAAA
          1 ATGACCAAAATGCCCCTGGACATGCAAA

                **          
        803 ATGATTAAAATGCCCC
          1 ATGACCAAAATGCCCC

        819 CTTAAGTGAC


Statistics
Matches: 88,  Mismatches: 12, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  28   65  0.74
  29   12  0.14
  30    8  0.09
  31    3  0.03

ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20


Consensus pattern (28 bp):   
ATGACCAAAATGCCCCTGGACATGCAAA

Found at i:1120 original size:36 final size:36

Alignment explanation


    Indices: 1078--1314  Score: 337
    Period size: 35  Copynumber: 6.7  Consensus size: 36

       1068 GTTCATATTA

                                    *             
       1078 AAGATGCTACACCGAGTCATCTGAGATCATT-T-TTTG
          1 AAGATGCTACACCGAGTCATCTGAAAT--TTGTCTTTG

                                    *             
       1114 AAGATGCTACACCGAGTCATCTGAGATCATT-T-TTTG
          1 AAGATGCTACACCGAGTCATCTGAAAT--TTGTCTTTG

                                        *       
       1150 AAGATGCTACACCGAGTCATCTG-AATTCGTCTTTG
          1 AAGATGCTACACCGAGTCATCTGAAATTTGTCTTTG

                    *          *                
       1185 AAGATGCTGCACCGAGTCAACT-AAATTTGTCTTTG
          1 AAGATGCTACACCGAGTCATCTGAAATTTGTCTTTG

                                                
       1220 AAGATGCTACACCGAGTCATCT-AAATTTGTCTTTG
          1 AAGATGCTACACCGAGTCATCTGAAATTTGTCTTTG

                                                
       1255 AAGATGCTACACCGAGTCATCT-AAATTTGTCTTTG
          1 AAGATGCTACACCGAGTCATCTGAAATTTGTCTTTG

                                     
       1290 AAGATGCTACACCGAGTCATCTGAA
          1 AAGATGCTACACCGAGTCATCTGAA

       1315 TTCCTGAGAA


Statistics
Matches: 190,  Mismatches: 7, Indels: 8
        0.93            0.03        0.04

Matches are distributed among these distances:
  33    1  0.01
  34    1  0.01
  35  127  0.67
  36   61  0.32

ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32


Consensus pattern (36 bp):   
AAGATGCTACACCGAGTCATCTGAAATTTGTCTTTG

Found at i:1810 original size:2 final size:2

Alignment explanation


    Indices: 1803--1833  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1793 AGATATAAAC

                                                          
       1803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1834 TAACAAAAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.