Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006125.1 Corchorus capsularis cultivar CVL-1 contig06143, 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: 20739
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:5773 original size:6 final size:6

Alignment explanation


    Indices: 5764--5859  Score: 75
    Period size: 6  Copynumber: 16.0  Consensus size: 6

       5754 CGTGACCGCA

                                            *          *     **    
       5764 ATAGGG ATAGGG ATAGGG ATAGGG ATAGCG ATAGGG ACAGGG GCAGGG
          1 ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG

              *      * *     *    *   *  *      *      *           
       5812 ATTGGG ATCGTG ATAAGG AAAGGC AGAGGG AGAGGG AGAGGG ATAGGG
          1 ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG ATAGGG

       5860 GCAGGGACCG


Statistics
Matches: 72,  Mismatches: 18, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   6   72  1.00

ACGTcount: A:0.32, C:0.05, G:0.50, T:0.12


Consensus pattern (6 bp):   
ATAGGG

Found at i:7769 original size:50 final size:50

Alignment explanation


    Indices: 7700--7802  Score: 179
    Period size: 50  Copynumber: 2.1  Consensus size: 50

       7690 CCCCCCTAAG

                                                            * 
       7700 TTTTTTCTTTCTCTAATTTATCCTCATGACAATATTTATAAGTTAGTTTT
          1 TTTTTTCTTTCTCTAATTTATCCTCATGACAATATTTATAAGTTAGTTCT

                                  * *                         
       7750 TTTTTTCTTTCTCTAATTTATCTTGATGACAATATTTATAAGTTAGTTCT
          1 TTTTTTCTTTCTCTAATTTATCCTCATGACAATATTTATAAGTTAGTTCT

               
       7800 TTT
          1 TTT

       7803 ATATAAACAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50   50  1.00

ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57


Consensus pattern (50 bp):   
TTTTTTCTTTCTCTAATTTATCCTCATGACAATATTTATAAGTTAGTTCT

Found at i:11866 original size:179 final size:179

Alignment explanation


    Indices: 11528--11881  Score: 444
    Period size: 179  Copynumber: 2.0  Consensus size: 179

      11518 CCCTAAACGG

                              **    **        *                             *
      11528 ACACATGTCAACCCTTTATTCCCGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGTATTAAATG
          1 ACACATGTCAACCCTTTAAACCCGAACGTGCAGTATGCTAAACTCCACTGACGGTGTATTAAATA

                                            *   *                  *         
      11593 ATTTTTCTTATAGAATTATTATACAATACATTGTCATTGTAAATTTTAAACTCCATAAGCAGGTT
         66 ATTTTTCTTATAGAATTATTATACAATACA-TCTCACTGTAAATTTTAAACTCCAGAAGCAGGTT

              *                   *                            
      11658 AAGAAGCTGACACATACAATTTTATAATTAATTAAACA-TTTAATATTCCT
        130 AAAAAGCTGACACATACAATTTCATAATTAATTAAA-ATTTTAATATTCCT

                                                        *               **   
      11708 ACACATGTCAACCC-TTAAACCCGAACGTGCAGTATGCTAAACTTCACTGACGGTGTATTGTATA
          1 ACACATGTCAACCCTTTAAACCCGAACGTGCAGTATGCTAAACTCCACTGACGGTGTATTAAATA

                     * * *                                **          **     
      11772 ATTTTTCTTGTGGGATTATTATACAATACA-CTCACTGTAAATTTTGGACTCCAGAAGTGGGTTA
         66 ATTTTTCTTATAGAATTATTATACAATACATCTCACTGTAAATTTTAAACTCCAGAAGCAGGTTA

                 *     *                                  
      11836 AAAAGTTGACATATACCCAATTTCATAATTAATTAAAATTTTAATA
        131 AAAAGCTGACACATA--CAATTTCATAATTAATTAAAATTTTAATA

      11882 CTAATACATA


Statistics
Matches: 148,  Mismatches: 23, Indels: 7
        0.83            0.13        0.04

Matches are distributed among these distances:
 177   39  0.26
 178    1  0.01
 179   94  0.64
 180   14  0.09

ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35


Consensus pattern (179 bp):   
ACACATGTCAACCCTTTAAACCCGAACGTGCAGTATGCTAAACTCCACTGACGGTGTATTAAATA
ATTTTTCTTATAGAATTATTATACAATACATCTCACTGTAAATTTTAAACTCCAGAAGCAGGTTA
AAAAGCTGACACATACAATTTCATAATTAATTAAAATTTTAATATTCCT

Found at i:16980 original size:80 final size:80

Alignment explanation


    Indices: 16842--17003  Score: 315
    Period size: 80  Copynumber: 2.0  Consensus size: 80

      16832 TCTTGTCCGA

                                                                 *           
      16842 GTGAGTGGCTTGGTGAGAACATCCGCAATTTGATCAATATTGGAGATGTACTTGACGACAACTTC
          1 GTGAGTGGCTTGGTGAGAACATCCGCAATTTGATCAATATTGGAGATGTACTTAACGACAACTTC

                           
      16907 TTGCTTCAATACTTT
         66 TTGCTTCAATACTTT

                                                                             
      16922 GTGAGTGGCTTGGTGAGAACATCCGCAATTTGATCAATATTGGAGATGTACTTAACGACAACTTC
          1 GTGAGTGGCTTGGTGAGAACATCCGCAATTTGATCAATATTGGAGATGTACTTAACGACAACTTC

                           
      16987 TTGCTTCAATACTTT
         66 TTGCTTCAATACTTT

              
      17002 GT
          1 GT

      17004 CCCGAACATA


Statistics
Matches: 81,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  80   81  1.00

ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34


Consensus pattern (80 bp):   
GTGAGTGGCTTGGTGAGAACATCCGCAATTTGATCAATATTGGAGATGTACTTAACGACAACTTC
TTGCTTCAATACTTT

Found at i:18369 original size:2 final size:2

Alignment explanation


    Indices: 18358--18389  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      18348 ATCATCTTTT

                                                             
      18358 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      18390 TTGCAAATTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
TA

Done.