Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016187.1 Corchorus olitorius cultivar O-4 contig16220, 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: 20991
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:6326 original size:70 final size:71

Alignment explanation


    Indices: 6208--6345  Score: 233
    Period size: 70  Copynumber: 2.0  Consensus size: 71

       6198 TGGAAATACA

                                                             **   *          
       6208 GGGAAATGATTCAGTAAAGACGTGTTAAAGATGATTTGTGGTTCAACAATGATTTCTACATGAAA
          1 GGGAAATGATTCAGTAAAGACGTGTTAAAGATGATTTGTGGTTCAACAACAATTCCTACATGAAA

                  
       6273 GCAAGG
         66 GCAAGG

                                                       *                     
       6279 GGGAAATGATTCAGTAAA-ACGTGTTAAAGATGATTTGTGGTTGAACAACAATTCCTACATGAAA
          1 GGGAAATGATTCAGTAAAGACGTGTTAAAGATGATTTGTGGTTCAACAACAATTCCTACATGAAA

               
       6343 GCA
         66 GCA

       6346 TGCCAGACAA


Statistics
Matches: 63,  Mismatches: 4, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  70   45  0.71
  71   18  0.29

ACGTcount: A:0.38, C:0.11, G:0.24, T:0.28


Consensus pattern (71 bp):   
GGGAAATGATTCAGTAAAGACGTGTTAAAGATGATTTGTGGTTCAACAACAATTCCTACATGAAA
GCAAGG

Found at i:16368 original size:19 final size:20

Alignment explanation


    Indices: 16330--16380  Score: 59
    Period size: 19  Copynumber: 2.5  Consensus size: 20

      16320 TAATAATCCC

                                 
      16330 ATATGTACAGTACCTAATCTA
          1 ATATGTACAGTA-CTAATCTA

                        *      *
      16351 ATATGTACAGT-GTAATCTC
          1 ATATGTACAGTACTAATCTA

              *        
      16370 ATCTGTACAGT
          1 ATATGTACAGT

      16381 TGCTAAACAG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  19   16  0.59
  21   11  0.41

ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Consensus pattern (20 bp):   
ATATGTACAGTACTAATCTA

Found at i:19518 original size:31 final size:31

Alignment explanation


    Indices: 19479--19603  Score: 151
    Period size: 31  Copynumber: 4.0  Consensus size: 31

      19469 GCATGTCATA

                                 *    *    
      19479 TGTCACTTTTTGGTACACATGGCGTGACACG
          1 TGTCACTTTTTGGTACACATGACGTGCCACG

               *             **            
      19510 TGTTACTTTTTGGTACATGTGACGTGCCACG
          1 TGTCACTTTTTGGTACACATGACGTGCCACG

                             *    *        
      19541 TGTCACTTTTTGGTACATATGATGTGCCACG
          1 TGTCACTTTTTGGTACACATGACGTGCCACG

                *    *        *    *       
      19572 TGTCGCTTTATGGTACACGTGACATGCCACG
          1 TGTCACTTTTTGGTACACATGACGTGCCACG

             
      19603 T
          1 T

      19604 CGGCTACCGT


Statistics
Matches: 80,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   80  1.00

ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35


Consensus pattern (31 bp):   
TGTCACTTTTTGGTACACATGACGTGCCACG

Found at i:19546 original size:62 final size:62

Alignment explanation


    Indices: 19442--19603  Score: 175
    Period size: 62  Copynumber: 2.6  Consensus size: 62

      19432 AAAATGACAT

                               *       * *    *  **                     * 
      19442 GTGACACGTGTC-CTTT-TTGTACACGAGGCATGTCATATGTCACTTTTTGGTACACATGGC
          1 GTGACACGTGTCACTTTATGGTACACGTGACATGCCACGTGTCACTTTTTGGTACACATGAC

                       *     *       *     *                        *    *
      19502 GTGACACGTGTTACTTTTTGGTACATGTGACGTGCCACGTGTCACTTTTTGGTACATATGAT
          1 GTGACACGTGTCACTTTATGGTACACGTGACATGCCACGTGTCACTTTTTGGTACACATGAC

               *        *                           
      19564 GTGCCACGTGTCGCTTTATGGTACACGTGACATGCCACGT
          1 GTGACACGTGTCACTTTATGGTACACGTGACATGCCACGT

      19604 CGGCTACCGT


Statistics
Matches: 82,  Mismatches: 18, Indels: 2
        0.80            0.18        0.02

Matches are distributed among these distances:
  60   11  0.13
  61    4  0.05
  62   67  0.82

ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35


Consensus pattern (62 bp):   
GTGACACGTGTCACTTTATGGTACACGTGACATGCCACGTGTCACTTTTTGGTACACATGAC

Found at i:20729 original size:2 final size:2

Alignment explanation


    Indices: 20722--20749  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      20712 AATTCCACCA

                                                     
      20722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      20750 TCAGCAAATG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.