Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013966.1 Corchorus olitorius cultivar O-4 contig13999, 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: 17624
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27


Found at i:1264 original size:30 final size:29

Alignment explanation


    Indices: 1225--1344  Score: 116
    Period size: 29  Copynumber: 4.1  Consensus size: 29

       1215 TGAATGGCTT

                *         *               
       1225 CGTCTTGGACATTGGCACATGAACGACGAA
          1 CGTCCTGGACATTGCCACATGAAC-ACGAA

                             *           
       1255 CGTCCTGGACATTGCCAAATGAACACGAA
          1 CGTCCTGGACATTGCCACATGAACACGAA

              *          *      *       **
       1284 CGCCCTGGACATTACCATC-GGAACACGTT
          1 CGTCCTGGACATTGCCA-CATGAACACGAA

                      *        *          
       1313 CGTCCTGGACTTTGCCACAGGAACGACGAA
          1 CGTCCTGGACATTGCCACATGAAC-ACGAA

              
       1343 CG
          1 CG

       1345 CTAGGATCTT


Statistics
Matches: 73,  Mismatches: 14, Indels: 6
        0.78            0.15        0.06

Matches are distributed among these distances:
  28    1  0.01
  29   46  0.63
  30   26  0.36

ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18


Consensus pattern (29 bp):   
CGTCCTGGACATTGCCACATGAACACGAA

Found at i:2422 original size:2 final size:2

Alignment explanation


    Indices: 2415--2445  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2405 GGCATCAACA

                                                          
       2415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2446 AAAGATATTA


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


Consensus pattern (2 bp):   
AT

Found at i:14296 original size:77 final size:76

Alignment explanation


    Indices: 14168--14343  Score: 291
    Period size: 77  Copynumber: 2.3  Consensus size: 76

      14158 TGATGGAACG

                   *                                                         
      14168 GTCTCAATAGAGACGATCGTTTCATTTACTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGT
          1 GTCTCAAAAGAGACGATCGTTTCATTTACTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGT

                       
      14233 TTGTGACGAAA
         66 TTGTGACGAAA

                                  *                         *                
      14244 GTCTCAAAAGAGACGATCGTTTTATTTTTA-TTTTATACGGGGACACCGAGGTTGGTGTTCGGCC
          1 GTCTCAAAAGAGACGATCGTTTCA--TTTACTTTTATACGGGGACACCAAGGTTGGTGTTCGGCC

                         
      14308 GTTTGTGACGAAA
         64 GTTTGTGACGAAA

                    *              
      14321 GTCTCAAAGGAGACGATCGTTTC
          1 GTCTCAAAAGAGACGATCGTTTC

      14344 GTTTTTTCCA


Statistics
Matches: 93,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
  76   22  0.24
  77   67  0.72
  78    4  0.04

ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32


Consensus pattern (76 bp):   
GTCTCAAAAGAGACGATCGTTTCATTTACTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGT
TTGTGACGAAA

Done.