Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014569.1 Corchorus capsularis cultivar CVL-1 contig14590, 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: 34677
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--31  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         32 CCAGGGGCAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2536 original size:4 final size:4

Alignment explanation


    Indices: 2527--2553  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       2517 TTGGAAGTTG

                                             
       2527 AAGA AAGA AAGA AAGA AAGA AAGA AAG
          1 AAGA AAGA AAGA AAGA AAGA AAGA AAG

       2554 GAACAGTGCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (4 bp):   
AAGA

Found at i:6198 original size:21 final size:22

Alignment explanation


    Indices: 6150--6200  Score: 59
    Period size: 21  Copynumber: 2.4  Consensus size: 22

       6140 GTTTAGTGTG

                  *              *
       6150 AGAGAGTGTGGCGAAGAGAGAG
          1 AGAGAGAGTGGCGAAGAGAGAC

             *                    
       6172 AAAGAGAGTGGCG-AGAGAGAC
          1 AGAGAGAGTGGCGAAGAGAGAC

            *       
       6193 TGAGAGAG
          1 AGAGAGAG

       6201 GGAAGAGATG


Statistics
Matches: 24,  Mismatches: 5, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  21   13  0.54
  22   11  0.46

ACGTcount: A:0.39, C:0.06, G:0.47, T:0.08


Consensus pattern (22 bp):   
AGAGAGAGTGGCGAAGAGAGAC

Found at i:7785 original size:2 final size:2

Alignment explanation


    Indices: 7778--7834  Score: 70
    Period size: 2  Copynumber: 30.5  Consensus size: 2

       7768 ATTCATATTC

                                                                           
       7778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AGT A- AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT

                                        
       7819 A- AT A- AT -T AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT A

       7835 CTTCAATATC


Statistics
Matches: 49,  Mismatches: 0, Indels: 12
        0.80            0.00        0.20

Matches are distributed among these distances:
   1    5  0.10
   2   42  0.86
   3    2  0.04

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:11697 original size:3 final size:3

Alignment explanation


    Indices: 11691--11717  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      11681 TTTTTGGAGG

                                               
      11691 AGA AGA AGA AGA AGA AGA AGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA

      11718 GCGGCGAAGC


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

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AGA

Found at i:18753 original size:46 final size:45

Alignment explanation


    Indices: 18687--18779  Score: 161
    Period size: 46  Copynumber: 2.0  Consensus size: 45

      18677 TTACCTTTAG

                                                          
      18687 GCTCATGAATTTTCTTGAAAAGTTACTTTCCCTTTG-CCATCATTT
          1 GCTCATGAATTTTCTTGAAAAGTTACTTTCCC-TTGACCATCATTT

                                                          
      18732 GCTCATGAAATTTTCTTGAAAAGTTACTTTCCCTTGACCATCATTT
          1 GCTCATG-AATTTTCTTGAAAAGTTACTTTCCCTTGACCATCATTT

              
      18778 GC
          1 GC

      18780 ATTAAAATAT


Statistics
Matches: 46,  Mismatches: 0, Indels: 3
        0.94            0.00        0.06

Matches are distributed among these distances:
  45   10  0.22
  46   36  0.78

ACGTcount: A:0.24, C:0.23, G:0.12, T:0.42


Consensus pattern (45 bp):   
GCTCATGAATTTTCTTGAAAAGTTACTTTCCCTTGACCATCATTT

Found at i:29051 original size:31 final size:31

Alignment explanation


    Indices: 28936--29043  Score: 126
    Period size: 31  Copynumber: 3.5  Consensus size: 31

      28926 GTGTTCGACG

                  *    *  *              * 
      28936 TGGCACACCACGTGCACCAAAAAGTGACATA
          1 TGGCACGCCACATGTACCAAAAAGTGACACA

                                           
      28967 TGGCACGCCACATGTACCAAAAAGTGACACA
          1 TGGCACGCCACATGTACCAAAAAGTGACACA

             **       **                  *
      28998 TATCACGCCATGTGTACCAAAAAGTGACACG
          1 TGGCACGCCACATGTACCAAAAAGTGACACA

                 *         
      29029 TGGCATGCCACATGT
          1 TGGCACGCCACATGT

      29044 TTCAAAAAAT


Statistics
Matches: 63,  Mismatches: 14, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   63  1.00

ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17


Consensus pattern (31 bp):   
TGGCACGCCACATGTACCAAAAAGTGACACA
Done.