Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001642.1 Corchorus capsularis cultivar CVL-1 contig01642, 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: 4059
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:768 original size:17 final size:17

Alignment explanation


    Indices: 746--778  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        736 AAAAATCAGA

                   *         
        746 ATATATATTATATATGT
          1 ATATATAATATATATGT

                            
        763 ATATATAATATATATG
          1 ATATATAATATATATG

        779 AAATTAAATT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48


Consensus pattern (17 bp):   
ATATATAATATATATGT

Found at i:1549 original size:17 final size:17

Alignment explanation


    Indices: 1527--1560  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1517 AAACTGTTTC

                             
       1527 TTTTTTGGTACTAATTT
          1 TTTTTTGGTACTAATTT

                             
       1544 TTTTTTGGTACTAATTT
          1 TTTTTTGGTACTAATTT

       1561 AATTTTACCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65


Consensus pattern (17 bp):   
TTTTTTGGTACTAATTT

Found at i:1566 original size:17 final size:17

Alignment explanation


    Indices: 1529--1566  Score: 58
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1519 ACTGTTTCTT

                           **
       1529 TTTTGGTACTAATTTTT
          1 TTTTGGTACTAATTTAA

                             
       1546 TTTTGGTACTAATTTAA
          1 TTTTGGTACTAATTTAA

                
       1563 TTTT
          1 TTTT

       1567 ACCATCAATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63


Consensus pattern (17 bp):   
TTTTGGTACTAATTTAA

Found at i:2103 original size:29 final size:30

Alignment explanation


    Indices: 2071--2128  Score: 100
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2061 TTGTCTTTTA

                                          
       2071 AACTTCAATTTT-GGACATTTTGCCCCATG
          1 AACTTCAATTTTGGGACATTTTGCCCCATG

                             *           
       2100 AACTTCAATTTTGGGACGTTTTGCCCCAT
          1 AACTTCAATTTTGGGACATTTTGCCCCAT

       2129 CAGGCTAACA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  29   12  0.44
  30   15  0.56

ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38


Consensus pattern (30 bp):   
AACTTCAATTTTGGGACATTTTGCCCCATG

Found at i:2250 original size:28 final size:29

Alignment explanation


    Indices: 2191--2250  Score: 86
    Period size: 28  Copynumber: 2.1  Consensus size: 29

       2181 AAATGCCCAT

                     *        *        * 
       2191 AAAATTGAAGTTCATGGGGCAAAACGTTC
          1 AAAATTGAAATTCATGGGACAAAACGTAC

                                         
       2220 AAAATTGAAATTCA-GGGACAAAACGTAC
          1 AAAATTGAAATTCATGGGACAAAACGTAC

               
       2248 AAA
          1 AAA

       2251 CACTACAAGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  28   15  0.54
  29   13  0.46

ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20


Consensus pattern (29 bp):   
AAAATTGAAATTCATGGGACAAAACGTAC
Done.