Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006547.1 Corchorus capsularis cultivar CVL-1 contig06568, 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: 9835
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34


Found at i:98 original size:33 final size:33

Alignment explanation


    Indices: 56--149  Score: 125
    Period size: 33  Copynumber: 2.8  Consensus size: 33

         46 GGCCTGCCCA

                *         *                  
         56 TGGTGGAGCCGCCCCAGTGGGGAGGCTCCACCG
          1 TGGTTGAGCCGCCCTAGTGGGGAGGCTCCACCG

                      *                 **   
         89 TGGTTGAGCCTCCCTAGTGGGGAGGCTCTGCCG
          1 TGGTTGAGCCGCCCTAGTGGGGAGGCTCCACCG

                    *  *                
        122 TGGTTGAGTCGTCCTAGTGGGGAGGCTC
          1 TGGTTGAGCCGCCCTAGTGGGGAGGCTC

        150 AGTGTAAAAG


Statistics
Matches: 53,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   53  1.00

ACGTcount: A:0.11, C:0.27, G:0.41, T:0.21


Consensus pattern (33 bp):   
TGGTTGAGCCGCCCTAGTGGGGAGGCTCCACCG

Found at i:984 original size:10 final size:10

Alignment explanation


    Indices: 961--991  Score: 53
    Period size: 10  Copynumber: 3.0  Consensus size: 10

        951 TCAATATTTG

                       
        961 TTCTTTTTTCT
          1 TTCTTTTTT-T

                      
        972 TTCTTTTTTT
          1 TTCTTTTTTT

                      
        982 TTCTTTTTTT
          1 TTCTTTTTTT

        992 GCAGTGGTCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   11  0.55
  11    9  0.45

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


Consensus pattern (10 bp):   
TTCTTTTTTT

Found at i:2686 original size:25 final size:25

Alignment explanation


    Indices: 2655--2704  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2645 AATGTGAATA

                                     
       2655 GTGTCTTTAAATAAAACTGAGCGTT
          1 GTGTCTTTAAATAAAACTGAGCGTT

                                     
       2680 GTGTCTTTAAATAAAACTGAGCGTT
          1 GTGTCTTTAAATAAAACTGAGCGTT

       2705 TTGGTAGTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36


Consensus pattern (25 bp):   
GTGTCTTTAAATAAAACTGAGCGTT

Found at i:8017 original size:21 final size:22

Alignment explanation


    Indices: 7949--8029  Score: 101
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       7939 ATTAAATTTT

                             *  * 
       7949 TATGAAATTTTGATAACAACCC
          1 TATGAAATTTTGATAACTACGC

               *               *  
       7971 TATTAAATTTTGATAACTATGC
          1 TATGAAATTTTGATAACTACGC

                            *     
       7993 TATGAAATTTTGATAATTA-GC
          1 TATGAAATTTTGATAACTACGC

                     *      
       8014 TATGAAATTGTGATAA
          1 TATGAAATTTTGATAA

       8030 ATTCCATATG


Statistics
Matches: 52,  Mismatches: 7, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  21   17  0.33
  22   35  0.67

ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACTACGC

Found at i:8097 original size:44 final size:43

Alignment explanation


    Indices: 7992--8098  Score: 110
    Period size: 44  Copynumber: 2.5  Consensus size: 43

       7982 GATAACTATG

                              *  **           *        
       7992 CTATGAAATTTTGATAA-TTAGCTATGAAATTGTGATAAATTC
          1 CTATGAAATTTTGATAACCTAAATATGAAATTGTAATAAATTC

                    **                       *            
       8034 CATATGAACCTTTGATAACCTAAATATGAAATTTTAATAAACCTTC
          1 C-TATGAAATTTTGATAACCTAAATATGAAATTGTAATAAA--TTC

                                
       8080 CTATGAAATTTTG-TAACCT
          1 CTATGAAATTTTGATAACCT

       8099 TCTTATGATT


Statistics
Matches: 52,  Mismatches: 9, Indels: 6
        0.78            0.13        0.09

Matches are distributed among these distances:
  42    1  0.02
  43   14  0.27
  44   23  0.44
  45   10  0.19
  46    4  0.08

ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38


Consensus pattern (43 bp):   
CTATGAAATTTTGATAACCTAAATATGAAATTGTAATAAATTC
Done.