Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017325.1 Corchorus olitorius cultivar O-4 contig17358, 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: 4931
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31


Found at i:694 original size:15 final size:15

Alignment explanation


    Indices: 646--694  Score: 55
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        636 AATTCGTCCC

                         * 
        646 GATGA-AAGCGTCCT
          1 GATGATAAGCGTCTT

            *            *  
        660 AATGATAAGTCGTTTT
          1 GATGATAAG-CGTCTT

                           
        676 GATGATAAGCGTCTT
          1 GATGATAAGCGTCTT

                
        691 GATG
          1 GATG

        695 GTGAGTCGAT


Statistics
Matches: 28,  Mismatches: 5, Indels: 3
        0.78            0.14        0.08

Matches are distributed among these distances:
  14    4  0.14
  15   12  0.43
  16   12  0.43

ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33


Consensus pattern (15 bp):   
GATGATAAGCGTCTT

Found at i:901 original size:53 final size:53

Alignment explanation


    Indices: 841--954  Score: 142
    Period size: 54  Copynumber: 2.1  Consensus size: 53

        831 AATTGCACAT

                                       *                           
        841 GACCATCGGGACCAAAAAT-CATCTCATGACCATC-GGATCAACCTTGGCATCCC
          1 GACCATCGGGACCAAAAATGCATC-C-CGACCATCGGGATCAACCTTGGCATCCC

                       *   ***                                    
        894 GACCATCGGGATCAACCTTGGCATCCCGACCATCGGGATCAACCTTGGCATCCC
          1 GACCATCGGGACCAAAAAT-GCATCCCGACCATCGGGATCAACCTTGGCATCCC

                   
        948 GACCATC
          1 GACCATC

        955 AGGATGCCAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 5
        0.84            0.08        0.08

Matches are distributed among these distances:
  53   22  0.42
  54   27  0.51
  55    4  0.08

ACGTcount: A:0.26, C:0.36, G:0.19, T:0.18


Consensus pattern (53 bp):   
GACCATCGGGACCAAAAATGCATCCCGACCATCGGGATCAACCTTGGCATCCC

Found at i:910 original size:27 final size:27

Alignment explanation


    Indices: 868--959  Score: 168
    Period size: 27  Copynumber: 3.4  Consensus size: 27

        858 ATCATCTCAT

                                       
        868 GACCATC-GGATCAACCTTGGCATCCC
          1 GACCATCGGGATCAACCTTGGCATCCC

                                       
        894 GACCATCGGGATCAACCTTGGCATCCC
          1 GACCATCGGGATCAACCTTGGCATCCC

                                       
        921 GACCATCGGGATCAACCTTGGCATCCC
          1 GACCATCGGGATCAACCTTGGCATCCC

                   *    
        948 GACCATCAGGAT
          1 GACCATCGGGAT

        960 GCCAAAGCCA


Statistics
Matches: 64,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  26    7  0.11
  27   57  0.89

ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18


Consensus pattern (27 bp):   
GACCATCGGGATCAACCTTGGCATCCC

Found at i:1374 original size:46 final size:46

Alignment explanation


    Indices: 1304--1536  Score: 369
    Period size: 46  Copynumber: 5.1  Consensus size: 46

       1294 GCTCTTTGTG

                *                                   *  * *
       1304 ATTTTTCCATCCAGATGGTATAAATTTCTTCACACCATCAGGACCC
          1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

                                                           
       1350 ATATT-TCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA
          1 AT-TTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

                        *                                 
       1396 ATTTCTCCATCCTGATGGTATAAATTTCTTCACACCATCAAGATCA
          1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

                                                          
       1442 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA
          1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

                        *              *            *  *  
       1488 ATTTCTCCATCCTGATGGTATAAATTTATTCACACCATCAGGACCA
          1 ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

               
       1534 ATT
          1 ATT

       1537 CTGCTTTGCC


Statistics
Matches: 176,  Mismatches: 9, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
  45    2  0.01
  46  172  0.98
  47    2  0.01

ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33


Consensus pattern (46 bp):   
ATTTCTCCATCCAGATGGTATAAATTTCTTCACACCATCAAGATCA

Found at i:1469 original size:23 final size:24

Alignment explanation


    Indices: 1304--1514  Score: 87
    Period size: 23  Copynumber: 9.2  Consensus size: 24

       1294 GCTCTTTGTG

                                    
       1304 ATTT-TTCCATCCAGATGGTATAA
          1 ATTTCTTCCATCCAGATGGTATAA

                            *      ***
       1327 ATTTCTTCACA-CCATCA-GG-ACCC
          1 ATTTCTTC-CATCCA-GATGGTATAA

              *                     
       1350 ATAT-TTCCATCCAGATGGTATAA
          1 ATTTCTTCCATCCAGATGGTATAA

                            *  *    * 
       1373 ATTTCTTCACA-CCATCA-AG-ATCA
          1 ATTTCTTC-CATCCA-GATGGTATAA

                         *          
       1396 ATTTC-TCCATCCTGATGGTATAA
          1 ATTTCTTCCATCCAGATGGTATAA

                            *  *    * 
       1419 ATTTCTTCACA-CCATCA-AG-ATCA
          1 ATTTCTTC-CATCCA-GATGGTATAA

                                    
       1442 ATTTC-TCCATCCAGATGGTATAA
          1 ATTTCTTCCATCCAGATGGTATAA

                            *  *    * 
       1465 ATTTCTTCACA-CCATCA-AG-ATCA
          1 ATTTCTTC-CATCCA-GATGGTATAA

                         *          
       1488 ATTTC-TCCATCCTGATGGTATAA
          1 ATTTCTTCCATCCAGATGGTATAA

                
       1511 ATTT
          1 ATTT

       1515 ATTCACACCA


Statistics
Matches: 133,  Mismatches: 31, Indels: 48
        0.63            0.15        0.23

Matches are distributed among these distances:
  21   12  0.09
  22   24  0.18
  23   59  0.44
  24   26  0.20
  25   12  0.09

ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35


Consensus pattern (24 bp):   
ATTTCTTCCATCCAGATGGTATAA
Done.