Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000253.1 Corchorus capsularis cultivar CVL-1 contig00253, 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: 5671
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Found at i:136 original size:21 final size:21

Alignment explanation


    Indices: 97--136  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

         87 AGGGGGTTGT

                        *        
         97 TAAATACCGCCCTAGTTTTAC
          1 TAAATACCGCCCCAGTTTTAC

                          *    
        118 TAAATACCGCCCCATTTTT
          1 TAAATACCGCCCCAGTTTT

        137 TACACTTTTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35


Consensus pattern (21 bp):   
TAAATACCGCCCCAGTTTTAC

Found at i:269 original size:22 final size:23

Alignment explanation


    Indices: 228--270  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        218 CCTCCCCACT

                           *       
        228 GGGCGGCTTCACCATGGGCAGTG
          1 GGGCGGCTTCACCATCGGCAGTG

                      *          
        251 GGGCGGCTTCGCCA-CGGCAG
          1 GGGCGGCTTCACCATCGGCAG

        271 CCCGCCTTCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  22    5  0.28
  23   13  0.72

ACGTcount: A:0.12, C:0.30, G:0.44, T:0.14


Consensus pattern (23 bp):   
GGGCGGCTTCACCATCGGCAGTG

Found at i:411 original size:32 final size:32

Alignment explanation


    Indices: 340--414  Score: 96
    Period size: 32  Copynumber: 2.3  Consensus size: 32

        330 AAAAATAGCC

                                            
        340 GAGCCGCCCCACCGAGGCGACCTGCCGTGGCA
          1 GAGCCGCCCCACCGAGGCGACCTGCCGTGGCA

            * *           *    *      *    *
        372 AAACCGCCCCACCGGGGCGGCCTGCCTTGGCG
          1 GAGCCGCCCCACCGAGGCGACCTGCCGTGGCA

                       
        404 GAGCCGCCCCA
          1 GAGCCGCCCCA

        415 GTGGGGCGTC


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.15, C:0.45, G:0.33, T:0.07


Consensus pattern (32 bp):   
GAGCCGCCCCACCGAGGCGACCTGCCGTGGCA

Found at i:1776 original size:2 final size:2

Alignment explanation


    Indices: 1769--1794  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1759 TTATTATTTA

                                                  
       1769 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1795 TTCTATGTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1907 original size:63 final size:61

Alignment explanation


    Indices: 1770--1923  Score: 245
    Period size: 63  Copynumber: 2.4  Consensus size: 61

       1760 TATTATTTAA

                                                                         
       1770 TATATATATATATATATATATATATTTCTATGTTTATTTTGTTTATAGAGTAAATTAAGAT
          1 TATATATATATATATATATATATATTTCTATGTTTATTTTGTTTATAGAGTAAATTAAGAT

                  *                                                        
       1831 TATTATTTAATATATATATATATATATTTCTATGTTTATTTTGTTTATAGAGTAAATTAAGAT
          1 TA-TATAT-ATATATATATATATATATTTCTATGTTTATTTTGTTTATAGAGTAAATTAAGAT

                                          
       1894 TGATATGATATATATATCATAGTATATATT
          1 T-ATAT-ATATATATAT-ATA-TATATATT

       1924 AATGAGTTAA


Statistics
Matches: 85,  Mismatches: 2, Indels: 8
        0.89            0.02        0.08

Matches are distributed among these distances:
  61    2  0.02
  62    4  0.05
  63   66  0.78
  64    5  0.06
  65    8  0.09

ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52


Consensus pattern (61 bp):   
TATATATATATATATATATATATATTTCTATGTTTATTTTGTTTATAGAGTAAATTAAGAT
Done.