Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010670.1 Corchorus capsularis cultivar CVL-1 contig10691, 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: 25273
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:5384 original size:33 final size:33

Alignment explanation


    Indices: 5308--5431  Score: 144
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       5298 TAGACAAAGG

                                   *    *     
       5308 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT

                **           *     *         
       5341 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

                                              
       5374 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT

                                     
       5407 GTCGCGTGGCCGGTCTTGTGGCCGG
          1 GTCGCGTGGCCGG--TTGTGGCCGG

       5432 TGTTGCGCGG


Statistics
Matches: 77,  Mismatches: 9, Indels: 8
        0.82            0.10        0.09

Matches are distributed among these distances:
  32    3  0.04
  33   65  0.84
  35    7  0.09
  36    2  0.03

ACGTcount: A:0.07, C:0.27, G:0.42, T:0.23


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

Found at i:8308 original size:33 final size:33

Alignment explanation


    Indices: 8271--8383  Score: 174
    Period size: 33  Copynumber: 3.4  Consensus size: 33

       8261 GCATGGCCAT

                        *  *                  
       8271 GTCGCGTGGCCGTTGATG-GCCGGGCATCTCCAA
          1 GTCGCGTGGCCGGTGTTGCG-CGGGCATCTCCAA

                 *                  *        
       8304 GTCGCATGGCCGGTGTTGCGCGGGTATCTCCAA
          1 GTCGCGTGGCCGGTGTTGCGCGGGCATCTCCAA

                                             
       8337 GTCGCGTGGCCGGTGTTGCGCGGGCATCTCCAA
          1 GTCGCGTGGCCGGTGTTGCGCGGGCATCTCCAA

                          
       8370 GTCGCGTGGCCGGT
          1 GTCGCGTGGCCGGT

       8384 CACAAGTGCT


Statistics
Matches: 73,  Mismatches: 6, Indels: 2
        0.90            0.07        0.02

Matches are distributed among these distances:
  33   72  0.99
  34    1  0.01

ACGTcount: A:0.10, C:0.29, G:0.39, T:0.22


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTGTTGCGCGGGCATCTCCAA

Found at i:12687 original size:33 final size:32

Alignment explanation


    Indices: 12620--12693  Score: 87
    Period size: 33  Copynumber: 2.2  Consensus size: 32

      12610 CTTGGAGATT

                *                *       *   
      12620 CCCGACCATCACCGGCCACGCTACTCGGAGATG
          1 CCCGGCCATCACCGGCCACGCGACTC-GACATG

                                              
      12653 CCCGGCCATCACCGGCCACGCGACAT-GACCATG
          1 CCCGGCCATCACCGGCCACGCGAC-TCGA-CATG

                    
      12686 CCCGGCCA
          1 CCCGGCCA

      12694 CAACCAGCCA


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  32    2  0.06
  33   33  0.92
  34    1  0.03

ACGTcount: A:0.20, C:0.46, G:0.24, T:0.09


Consensus pattern (32 bp):   
CCCGGCCATCACCGGCCACGCGACTCGACATG

Found at i:21671 original size:8 final size:8

Alignment explanation


    Indices: 21643--21676  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

      21633 GAATCGGCTA

                    
      21643 TGAATTTT
          1 TGAATTTT

                    *
      21651 TGAAGTTTC
          1 TGAA-TTTT

                    
      21660 TGAATTTT
          1 TGAATTTT

                    
      21668 TGAATTTT
          1 TGAATTTT

             
      21676 T
          1 T

      21677 CAAGAAGGTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:22649 original size:33 final size:32

Alignment explanation


    Indices: 22612--22718  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 32

      22602 GCCCTAGCGA

                                  *           
      22612 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG

                             *               
      22645 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCGCG
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                             * *            *
      22678 TGGCCGGTGTTGGCCGGTCTTCTCCAAGTCGCA
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                    
      22711 TGGCCGGT
          1 TGGCCGGT

      22719 CACTCGCACC


Statistics
Matches: 66,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  33   64  0.97
  34    2  0.03

ACGTcount: A:0.07, C:0.29, G:0.39, T:0.24


Consensus pattern (32 bp):   
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG

Found at i:24496 original size:33 final size:33

Alignment explanation


    Indices: 24425--24499  Score: 82
    Period size: 33  Copynumber: 2.3  Consensus size: 33

      24415 AAAGGATCGT

                        *                   *
      24425 GTGGCCGGTTGTGGCCGAGCATGACCGAGTCGT
          1 GTGGCCGGTTGTAGCCGAGCATGACCGAGTCGC

            *                       *          
      24458 TTGGCCGGTTGTAGCCG-GCCATGTCC-ATGTCGC
          1 GTGGCCGGTTGTAGCCGAG-CATGACCGA-GTCGC

                     
      24491 GTGGCCGGT
          1 GTGGCCGGT

      24500 CTTGTGGCCG


Statistics
Matches: 35,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  32    2  0.06
  33   33  0.94

ACGTcount: A:0.09, C:0.27, G:0.40, T:0.24


Consensus pattern (33 bp):   
GTGGCCGGTTGTAGCCGAGCATGACCGAGTCGC
Done.