Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018229.1 Corchorus olitorius cultivar O-4 contig18262, 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: 14284
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:295 original size:15 final size:16

Alignment explanation


    Indices: 262--301  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        252 TTACTTTGCT

                            
        262 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
        278 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
        293 TTGCTTTCT
          1 TTGTTTTCT

        302 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:2163 original size:41 final size:41

Alignment explanation


    Indices: 2118--2248  Score: 208
    Period size: 41  Copynumber: 3.2  Consensus size: 41

       2108 AATAAGGATC

                    *                                
       2118 AAATTGAAACAAATAGTAAATAGAATCCTAAATCAGGGACT
          1 AAATTGAATCAAATAGTAAATAGAATCCTAAATCAGGGACT

                  **                        *        
       2159 AAATTGTGTCAAATAGTAAATAGAATCCTAAAGCAGGGACT
          1 AAATTGAATCAAATAGTAAATAGAATCCTAAATCAGGGACT

                  **                                 
       2200 AAATTGTGTCAAATAGTAAATAGAATCCTAAATCAGGGACT
          1 AAATTGAATCAAATAGTAAATAGAATCCTAAATCAGGGACT

                    
       2241 AAATTGAA
          1 AAATTGAA

       2249 CACGAAAACA


Statistics
Matches: 83,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  41   83  1.00

ACGTcount: A:0.47, C:0.11, G:0.17, T:0.24


Consensus pattern (41 bp):   
AAATTGAATCAAATAGTAAATAGAATCCTAAATCAGGGACT

Found at i:5016 original size:46 final size:46

Alignment explanation


    Indices: 4960--5065  Score: 212
    Period size: 46  Copynumber: 2.3  Consensus size: 46

       4950 AATGCAATCT

                                                          
       4960 AAATGACCAAGATGAGTTAGCTAATCTAAAACTAAAAATGAACTTA
          1 AAATGACCAAGATGAGTTAGCTAATCTAAAACTAAAAATGAACTTA

                                                          
       5006 AAATGACCAAGATGAGTTAGCTAATCTAAAACTAAAAATGAACTTA
          1 AAATGACCAAGATGAGTTAGCTAATCTAAAACTAAAAATGAACTTA

                          
       5052 AAATGACCAAGATG
          1 AAATGACCAAGATG

       5066 TCCCTGAATG


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   60  1.00

ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23


Consensus pattern (46 bp):   
AAATGACCAAGATGAGTTAGCTAATCTAAAACTAAAAATGAACTTA

Found at i:8045 original size:30 final size:30

Alignment explanation


    Indices: 7987--8078  Score: 141
    Period size: 30  Copynumber: 3.1  Consensus size: 30

       7977 AAGTTGTCCT

                    *    *                 
       7987 ATTTGATTTTTAAGGTTTGTGAAGCTCTCCC
          1 ATTTGATTCTTAATGTTTGTG-AGCTCTCCC

                                          
       8018 ATTTGATTCTTAATGTTTGTGAGCTCTCCC
          1 ATTTGATTCTTAATGTTTGTGAGCTCTCCC

                             *            
       8048 ATTTGATTCTTAATGTTAGTGAGCTC-CCC
          1 ATTTGATTCTTAATGTTTGTGAGCTCTCCC

              
       8077 AT
          1 AT

       8079 CATGTCTTAA


Statistics
Matches: 58,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  29    5  0.09
  30   34  0.59
  31   19  0.33

ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45


Consensus pattern (30 bp):   
ATTTGATTCTTAATGTTTGTGAGCTCTCCC

Found at i:8086 original size:28 final size:29

Alignment explanation


    Indices: 8009--8088  Score: 92
    Period size: 30  Copynumber: 2.7  Consensus size: 29

       7999 AGGTTTGTGA

                       *              *   
       8009 AGCTCTCCCATTTGATTCTTAATGTTTGTG
          1 AGCTCTCCCATATGA-TCTTAATGTTAGTG

                       *                  
       8039 AGCTCTCCCATTTGATTCTTAATGTTAGTG
          1 AGCTCTCCCATATGA-TCTTAATGTTAGTG

                                  
       8069 AGCTC-CCCATCATG-TCTTAA
          1 AGCTCTCCCAT-ATGATCTTAA

       8089 AGGTCTCATT


Statistics
Matches: 47,  Mismatches: 2, Indels: 4
        0.89            0.04        0.08

Matches are distributed among these distances:
  28    6  0.13
  29    5  0.11
  30   36  0.77

ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41


Consensus pattern (29 bp):   
AGCTCTCCCATATGATCTTAATGTTAGTG
Done.