Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005957.1 Corchorus capsularis cultivar CVL-1 contig05975, 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: 5751
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Found at i:2759 original size:10 final size:10

Alignment explanation


    Indices: 2740--2789  Score: 57
    Period size: 10  Copynumber: 4.9  Consensus size: 10

       2730 CCTTGCAAAA

                 *    
       2740 TTTTGGTTTT
          1 TTTTGTTTTT

                      
       2750 TTTTGTTTTT
          1 TTTTGTTTTT

                       
       2760 TGTTT-TTTTT
          1 T-TTTGTTTTT

             *         
       2770 TGTTGTTTTTT
          1 TTTTG-TTTTT

                     
       2781 TTTTGTTTT
          1 TTTTGTTTT

       2790 GCGACTCGGC


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
   9    2  0.06
  10   20  0.59
  11   12  0.35

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (10 bp):   
TTTTGTTTTT

Found at i:2766 original size:17 final size:18

Alignment explanation


    Indices: 2740--2790  Score: 68
    Period size: 17  Copynumber: 2.8  Consensus size: 18

       2730 CCTTGCAAAA

                 *            
       2740 TTTTGGTTTTTTTTGTT-
          1 TTTTGTTTTTTTTTGTTG

                              
       2757 TTTTGTTTTTTTTTGTTG
          1 TTTTGTTTTTTTTTGTTG

                *           
       2775 TTTTTTTTTTGTTTTG
          1 TTTTGTTTTT-TTTTG

       2791 CGACTCGGCT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   16  0.53
  18    9  0.30
  19    5  0.17

ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84


Consensus pattern (18 bp):   
TTTTGTTTTTTTTTGTTG

Found at i:2775 original size:13 final size:13

Alignment explanation


    Indices: 2748--2783  Score: 54
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       2738 AATTTTGGTT

                      *   
       2748 TTTTTTGTTTTTTG
          1 TTTTTT-TTTGTTG

                         
       2762 TTTTTTTTTGTTG
          1 TTTTTTTTTGTTG

                     
       2775 TTTTTTTTT
          1 TTTTTTTTT

       2784 TGTTTTGCGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  13   15  0.71
  14    6  0.29

ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89


Consensus pattern (13 bp):   
TTTTTTTTTGTTG

Found at i:2775 original size:20 final size:19

Alignment explanation


    Indices: 2746--2790  Score: 65
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       2736 AAAATTTTGG

                                
       2746 TTTTTT-TTGTTTTTTGTTT
          1 TTTTTTGTTGTTTTTT-TTT

                               
       2765 TTTTTTGTTGTTTTTTTTT
          1 TTTTTTGTTGTTTTTTTTT

             *     
       2784 TGTTTTG
          1 TTTTTTG

       2791 CGACTCGGCT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  19   15  0.62
  20    9  0.38

ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87


Consensus pattern (19 bp):   
TTTTTTGTTGTTTTTTTTT

Found at i:2785 original size:14 final size:14

Alignment explanation


    Indices: 2747--2787  Score: 57
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       2737 AAATTTTGGT

                       *   
       2747 TTTTTTTGTTTTTTG
          1 TTTTTTT-TTTGTTG

                          
       2762 -TTTTTTTTTGTTG
          1 TTTTTTTTTTGTTG

                         
       2775 TTTTTTTTTTGTT
          1 TTTTTTTTTTGTT

       2788 TTGCGACTCG


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  13    6  0.25
  14   18  0.75

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (14 bp):   
TTTTTTTTTTGTTG

Found at i:5666 original size:129 final size:130

Alignment explanation


    Indices: 5428--5684  Score: 444
    Period size: 129  Copynumber: 2.0  Consensus size: 130

       5418 AAGGTGTGGA

                                      *             *                        
       5428 GTCCCTCCACAATTTGGTAAGAACTTGCACAAGCCAAAAGTCGTGACCATTTACAAATTCCGTGA
          1 GTCCCTCCACAATTTGGTAAGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAAATTCCGTGA

                                     *                                       
       5493 ATAATCAGGGTTCTTGCCTTTATGCTATTGATGCAAATGAATGTTATGACAAGTTATAACATGGG
         66 ATAATCAGGGTTCTTGCCTTTATGCAATTGATGCAAATGAATGTTATGACAAGTTATAACATGGG

                               *             *                          *    
       5558 GTCCCTCCACAATTTGGTAGGAACTTCCACAAGTCAAAAGCCGTGACCATTTAC-AATTCTGTGA
          1 GTCCCTCCACAATTTGGTAAGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAAATTCCGTGA

                                              *                            
       5622 ATAATCAGGGTTCTTGCCTTTATGCAATTGATGCGAATGAATGTTATGACAAGTTATAACATG
         66 ATAATCAGGGTTCTTGCCTTTATGCAATTGATGCAAATGAATGTTATGACAAGTTATAACATG

       5685 AGCTATCCTT


Statistics
Matches: 120,  Mismatches: 7, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
 129   70  0.58
 130   50  0.42

ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30


Consensus pattern (130 bp):   
GTCCCTCCACAATTTGGTAAGAACTTCCACAAGCCAAAAGCCGTGACCATTTACAAATTCCGTGA
ATAATCAGGGTTCTTGCCTTTATGCAATTGATGCAAATGAATGTTATGACAAGTTATAACATGGG
Done.