Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023277.1 Corchorus olitorius cultivar O-4 contig23310, 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: 2571
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:109 original size:15 final size:15

Alignment explanation


    Indices: 79--120  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

         69 TTACTTTGCT

                            
         79 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
         95 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        110 TTGCTTTCTGT
          1 TTGTTTTCTGT

        121 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:818 original size:12 final size:12

Alignment explanation


    Indices: 801--831  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

        791 TACCCTATGT

                        
        801 AAACACGACACG
          1 AAACACGACACG

                        
        813 AAACACGACACG
          1 AAACACGACACG

            *      
        825 GAACACG
          1 AAACACG

        832 GATTGCCAGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG

Found at i:1236 original size:31 final size:31

Alignment explanation


    Indices: 1201--1267  Score: 75
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1191 TGCGTTTTTT

                         *                   
       1201 AATTTATTAGTT-TTACGTTTTT-GTAAAAAAA
          1 AATTTATT-GTTCCTACGTTTTTAG-AAAAAAA

                 *        *                
       1232 AATTTCTTGTTCCTGCGTTTTTAGAAAAAAA
          1 AATTTATTGTTCCTACGTTTTTAGAAAAAAA

                 
       1263 AATTT
          1 AATTT

       1268 TTCATTATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  30    3  0.10
  31   27  0.87
  32    1  0.03

ACGTcount: A:0.36, C:0.07, G:0.10, T:0.46


Consensus pattern (31 bp):   
AATTTATTGTTCCTACGTTTTTAGAAAAAAA
Done.