Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021285.1 Corchorus olitorius cultivar O-4 contig21318, 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: 17005
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30


Found at i:2302 original size:15 final size:16

Alignment explanation


    Indices: 2272--2304  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2262 GCCGAATGAT

                            
       2272 TTGTATTTTAAATTTC
          1 TTGTATTTTAAATTTC

                            
       2288 TTGTATTTT-AATTTC
          1 TTGTATTTTAAATTTC

              
       2303 TT
          1 TT

       2305 CTAATTAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.47
  16    9  0.53

ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67


Consensus pattern (16 bp):   
TTGTATTTTAAATTTC

Found at i:2587 original size:24 final size:24

Alignment explanation


    Indices: 2531--2605  Score: 98
    Period size: 24  Copynumber: 3.1  Consensus size: 24

       2521 ATAATTATAA

                  *               *  
       2531 TTCTTTCAAATATTCTCTCTAAATT
          1 TTCTTTAAAATATTCTCTCT-ATTT

               *                    
       2556 TTCATTAAAATATTCTCTCTATTT
          1 TTCTTTAAAATATTCTCTCTATTT

                                     
       2580 TTCTTTAAAATA-TCTTCTCTATTT
          1 TTCTTTAAAATATTC-TCTCTATTT

              
       2604 TT
          1 TT

       2606 AATTGCTCAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 3
        0.87            0.08        0.06

Matches are distributed among these distances:
  23    2  0.04
  24   25  0.56
  25   18  0.40

ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56


Consensus pattern (24 bp):   
TTCTTTAAAATATTCTCTCTATTT

Found at i:6057 original size:33 final size:33

Alignment explanation


    Indices: 5950--6138  Score: 213
    Period size: 33  Copynumber: 5.7  Consensus size: 33

       5940 AACTGCTCAA

                                      **      
       5950 GGCTAGTCGCGACCGGATCGCGAAC-CACCCGT-
          1 GGCTAGTCGCGACCGGATCGCG-ACTTGCCCGTG

                   *            *     * *    *
       5982 GGCTAAGCCGCGACCGGATCCCGAC-CGGCCGTC
          1 GGCT-AGTCGCGACCGGATCGCGACTTGCCCGTG

                                *  *          
       6015 GGCTAAGTCGCGACCGGATCACGGCTTGCCCGTG
          1 GGCT-AGTCGCGACCGGATCGCGACTTGCCCGTG

                                  *          
       6049 GGCTAGTCGCGACCGGATCGCGTCTTGCCCGTG
          1 GGCTAGTCGCGACCGGATCGCGACTTGCCCGTG

              *      *            *          
       6082 GGATAGTCGTGACCGGATCGCGTCTTGCCCGTG
          1 GGCTAGTCGCGACCGGATCGCGACTTGCCCGTG

                                    
       6115 GGCTAGTCGCGACCGGATCGCGAC
          1 GGCTAGTCGCGACCGGATCGCGAC

       6139 ATCCCCACGG


Statistics
Matches: 137,  Mismatches: 17, Indels: 5
        0.86            0.11        0.03

Matches are distributed among these distances:
  32   11  0.08
  33  117  0.85
  34    9  0.07

ACGTcount: A:0.14, C:0.34, G:0.35, T:0.16


Consensus pattern (33 bp):   
GGCTAGTCGCGACCGGATCGCGACTTGCCCGTG

Found at i:6326 original size:21 final size:21

Alignment explanation


    Indices: 6293--6333  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6283 TTTTACCCCG

                *   *     *      
       6293 TCTGGCGTTGATGGCTCGTTT
          1 TCTGACGTCGATGGATCGTTT

                                
       6314 TCTGACGTCGATGGATCGTT
          1 TCTGACGTCGATGGATCGTT

       6334 ATTGTCCATA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.10, C:0.20, G:0.32, T:0.39


Consensus pattern (21 bp):   
TCTGACGTCGATGGATCGTTT

Found at i:12914 original size:64 final size:64

Alignment explanation


    Indices: 12836--12966  Score: 262
    Period size: 64  Copynumber: 2.0  Consensus size: 64

      12826 TCTTCAAGTC

                                                                            
      12836 ATGAGAAGAGAGGGTTGGATTGGTTATTTTGTAATTTCATATCCTCCTATTATGGTTCTTTATA
          1 ATGAGAAGAGAGGGTTGGATTGGTTATTTTGTAATTTCATATCCTCCTATTATGGTTCTTTATA

                                                                            
      12900 ATGAGAAGAGAGGGTTGGATTGGTTATTTTGTAATTTCATATCCTCCTATTATGGTTCTTTATA
          1 ATGAGAAGAGAGGGTTGGATTGGTTATTTTGTAATTTCATATCCTCCTATTATGGTTCTTTATA

               
      12964 ATG
          1 ATG

      12967 TAAATATTTA


Statistics
Matches: 67,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  64   67  1.00

ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44


Consensus pattern (64 bp):   
ATGAGAAGAGAGGGTTGGATTGGTTATTTTGTAATTTCATATCCTCCTATTATGGTTCTTTATA

Found at i:16801 original size:6 final size:6

Alignment explanation


    Indices: 16790--16835  Score: 58
    Period size: 6  Copynumber: 7.8  Consensus size: 6

      16780 AACTCGAGGC

                           *              *        *              
      16790 AGCCCG AGCCCG AACCCG A-CCCG AGACCG AGCCTG AGCCCG AGCCC
          1 AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCC

      16836 AAACCCGAAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
   5    5  0.15
   6   29  0.85

ACGTcount: A:0.22, C:0.48, G:0.28, T:0.02


Consensus pattern (6 bp):   
AGCCCG

Done.