Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023616.1 Corchorus olitorius cultivar O-4 contig23649, 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: 13622
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1746 original size:17 final size:17

Alignment explanation


    Indices: 1724--1759  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1714 TGATTTGTAA

                             
       1724 AGTTTGTTACACCAGAT
          1 AGTTTGTTACACCAGAT

                     *  *    
       1741 AGTTTGTTATACTAGAT
          1 AGTTTGTTACACCAGAT

              
       1758 AG
          1 AG

       1760 CTCTTTGTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39


Consensus pattern (17 bp):   
AGTTTGTTACACCAGAT

Found at i:7194 original size:14 final size:15

Alignment explanation


    Indices: 7164--7196  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       7154 AAACTCAGAC

                  *        
       7164 AAAAATTCAACGAAA
          1 AAAAATCCAACGAAA

                           
       7179 AAAAATCCAACGAAA
          1 AAAAATCCAACGAAA

               
       7194 AAA
          1 AAA

       7197 TAAAGCCAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.70, C:0.15, G:0.06, T:0.09


Consensus pattern (15 bp):   
AAAAATCCAACGAAA

Found at i:7339 original size:22 final size:21

Alignment explanation


    Indices: 7310--7362  Score: 54
    Period size: 22  Copynumber: 2.5  Consensus size: 21

       7300 TTTTCCGACC

                      *           
       7310 AAGA-AAGAATGGAGAAAACAA
          1 AAGAGAAGAAAGGAGAAAA-AA

                         *       
       7331 AAGAGAAGAAAGGGGAAAAAA
          1 AAGAGAAGAAAGGAGAAAAAA

            *          
       7352 GAGAGAGAGAA
          1 AAGAGA-AGAA

       7363 CCTGGTTGTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  21   11  0.41
  22   16  0.59

ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02


Consensus pattern (21 bp):   
AAGAGAAGAAAGGAGAAAAAA

Found at i:9964 original size:42 final size:42

Alignment explanation


    Indices: 9897--9978  Score: 119
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       9887 TATTACCTTT

                     *                        *       
       9897 GAGAGATTGTCCTTGTGTTACATGTGCTTAGGGATTTTGAGA
          1 GAGAGATTGCCCTTGTGTTACATGTGCTTAGGGACTTTGAGA

                *               *     *             
       9939 GAGATATTGCCCTTGTGTTATATGTGTTTAGGGACTTTGA
          1 GAGAGATTGCCCTTGTGTTACATGTGCTTAGGGACTTTGA

       9979 TTATTGGGTA


Statistics
Matches: 35,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  42   35  1.00

ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40


Consensus pattern (42 bp):   
GAGAGATTGCCCTTGTGTTACATGTGCTTAGGGACTTTGAGA
Done.