Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001002.1 Corchorus capsularis cultivar CVL-1 contig01002, 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: 3346
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39


Found at i:104 original size:2 final size:2

Alignment explanation


    Indices: 97--125  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

         87 CATTATCTTT

                                                        
         97 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        126 AGTCTAAACT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

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


Consensus pattern (2 bp):   
TA

Found at i:522 original size:74 final size:74

Alignment explanation


    Indices: 444--595  Score: 270
    Period size: 74  Copynumber: 2.1  Consensus size: 74

        434 TGGTCTTTTC

                                         *                                   
        444 ACACTTTTCGGATGACTAAAAAGTCCC-TTTATGAGCTTCCCCCATTCCTTTTCCTTCTACCCTT
          1 ACACTTTTCGGATGACTAAAAAG-CCCATCTATGAGCTTCCCCCATTCCTTTTCCTTCTACCCTT

                      
        508 TTTCGTAATT
         65 TTTCGTAATT

                                               *                             
        518 ACACTTTTCGGATGACTAAAAAGCCCATCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
          1 ACACTTTTCGGATGACTAAAAAGCCCATCTATGAGCTTCCCCCATTCCTTTTCCTTCTACCCTTT

                     
        583 TTCGTAATT
         66 TTCGTAATT

                
        592 ACAC
          1 ACAC

        596 ATTCCCCTTC


Statistics
Matches: 75,  Mismatches: 2, Indels: 2
        0.95            0.03        0.03

Matches are distributed among these distances:
  73    3  0.04
  74   72  0.96

ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39


Consensus pattern (74 bp):   
ACACTTTTCGGATGACTAAAAAGCCCATCTATGAGCTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT

Found at i:1853 original size:27 final size:27

Alignment explanation


    Indices: 1821--1875  Score: 85
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1811 TGACTATAAA

                      *                 
       1821 TAACGTATATTGATCTAAAAA-AAATAT
          1 TAACGTATATCGA-CTAAAAAGAAATAT

                                       
       1848 TAACGTATATCGACTAAAAAGAAATAT
          1 TAACGTATATCGACTAAAAAGAAATAT

             
       1875 T
          1 T

       1876 GTTTCCTTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  26    7  0.27
  27   19  0.73

ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31


Consensus pattern (27 bp):   
TAACGTATATCGACTAAAAAGAAATAT

Found at i:2716 original size:36 final size:36

Alignment explanation


    Indices: 2669--2738  Score: 115
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       2659 GAGATTTTGG

                                   *             
       2669 AGAAATATGATAA-TCAAAATTATAAAAAATGTAATA
          1 AGAAATATGATAACT-AAAATTACAAAAAATGTAATA

                                              
       2705 AGAAATATGATAACTAAAATTACAAAAAATGTAA
          1 AGAAATATGATAACTAAAATTACAAAAAATGTAA

       2739 GGTTATTGAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  36   31  0.97
  37    1  0.03

ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26


Consensus pattern (36 bp):   
AGAAATATGATAACTAAAATTACAAAAAATGTAATA
Done.