Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024639.1 Corchorus olitorius cultivar O-4 contig24672, 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: 6096
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30


Found at i:614 original size:81 final size:80

Alignment explanation


    Indices: 476--637  Score: 272
    Period size: 81  Copynumber: 2.0  Consensus size: 80

        466 AACCCAACAA

                                                                *            
        476 GGAATTTGTACACAAAAAAATGGTTGGTATGATGTTTTTTCTTATTAGTTGTGTAATTGGGTTTT
          1 GGAATTTGTACACAAAAAAATGGTTGGTATGATGTTTTTTCTTATTAG-TGTCTAATTGGGTTTT

                            
        541 GTCTGATACTGTTGTT
         65 GTCTGATACTGTTGTT

                        *                                                    
        557 GGAATTTGTACATAAAAAAATTGGTTGGTATGATGTTTTTTCTTAGTTA-TGTCTAATTGGGTTT
          1 GGAATTTGTACACAAAAAAA-TGGTTGGTATGATGTTTTTTCTTA-TTAGTGTCTAATTGGGTTT

                             
        621 TGTCTGATACTGTTGTT
         64 TGTCTGATACTGTTGTT

        638 TAAGGTAAAC


Statistics
Matches: 77,  Mismatches: 2, Indels: 4
        0.93            0.02        0.05

Matches are distributed among these distances:
  81   50  0.65
  82   24  0.31
  83    3  0.04

ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48


Consensus pattern (80 bp):   
GGAATTTGTACACAAAAAAATGGTTGGTATGATGTTTTTTCTTATTAGTGTCTAATTGGGTTTTG
TCTGATACTGTTGTT

Found at i:2864 original size:6 final size:6

Alignment explanation


    Indices: 2845--2876  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       2835 CAGACTGCAC

                      *                          
       2845 CACAAT CACCAT CACAAT CACAAT CACAAT CA
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CA

       2877 TCCGTTAACG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16


Consensus pattern (6 bp):   
CACAAT

Found at i:3032 original size:39 final size:38

Alignment explanation


    Indices: 2906--3053  Score: 172
    Period size: 38  Copynumber: 3.9  Consensus size: 38

       2896 TCGAGTCTAG

                                                  
       2906 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                      *         *     *  *        
       2943 CCAACAGTTTCACCCCCTGAAGCACGAGTACACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                  *            *  * *              
       2981 CCAACAATTTAACCCCCTGTGGTATGGGTCCACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA

               *              *   *  *        
       3020 CCATCAGTTTAACCCCCTTAGGTACAGGTCCACT
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT

       3054 ATGCACAGCC


Statistics
Matches: 91,  Mismatches: 18, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
  37    7  0.08
  38   53  0.58
  39   31  0.34

ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

Found at i:5304 original size:6 final size:6

Alignment explanation


    Indices: 5293--5324  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       5283 CAGGCTGCAC

                                                 
       5293 CACAAT CACAAT CACAAT CACAAT CACAAT CA
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CA

       5325 TCCGTTAACG


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

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16


Consensus pattern (6 bp):   
CACAAT

Found at i:5453 original size:76 final size:75

Alignment explanation


    Indices: 5354--5500  Score: 215
    Period size: 76  Copynumber: 1.9  Consensus size: 75

       5344 TCGAGTCTAG

                                    *                              *         
       5354 CCAACAGTTAACCCCCTGAGGTATGGGTCCACTC-TTACCAACAGTTTAACACCCTGAGGCACGG
          1 CCAACAGTTAACCCCCTGAGGTATAGGTCCACTCTTTACCAACAGTTTAAC-CCCAGAGGCACGG

                       
       5418 GTCCACTCTTA
         65 GTCCACTCTTA

                               *          *           *                 *    
       5429 CCAACAGTTTAACCCCCTGTGGTATAGGTCTACTCTTTACCATCAGTTTAACCCCAGAGGTACGG
          1 CCAACAG-TTAACCCCCTGAGGTATAGGTCCACTCTTTACCAACAGTTTAACCCCAGAGGCACGG

                   
       5494 GTCCACT
         65 GTCCACT

       5501 ATGCTCAGCC


Statistics
Matches: 64,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  75    7  0.11
  76   42  0.66
  77   15  0.23

ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25


Consensus pattern (75 bp):   
CCAACAGTTAACCCCCTGAGGTATAGGTCCACTCTTTACCAACAGTTTAACCCCAGAGGCACGGG
TCCACTCTTA

Found at i:5479 original size:39 final size:38

Alignment explanation


    Indices: 5354--5500  Score: 190
    Period size: 38  Copynumber: 3.9  Consensus size: 38

       5344 TCGAGTCTAG

                                                  
       5354 CCAACAG-TTAACCCCCTGAGGTATGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGTATGGGTCCACTCTTA

                         *        * *             
       5391 CCAACAGTTTAACACCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGTATGGGTCCACTCTTA

                               *     *    *        
       5429 CCAACAGTTTAACCCCCTGTGGTATAGGTCTACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGTATGGGTCCACTC-TTA

               *             *      *         
       5468 CCATCAGTTTAA-CCCCAGAGGTACGGGTCCACT
          1 CCAACAGTTTAACCCCCTGAGGTATGGGTCCACT

       5501 ATGCTCAGCC


Statistics
Matches: 93,  Mismatches: 15, Indels: 3
        0.84            0.14        0.03

Matches are distributed among these distances:
  37    7  0.08
  38   72  0.77
  39   14  0.15

ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGTATGGGTCCACTCTTA
Done.