Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009448.1 Corchorus capsularis cultivar CVL-1 contig09469, 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: 15893
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:88 original size:24 final size:23

Alignment explanation


    Indices: 31--89  Score: 73
    Period size: 26  Copynumber: 2.4  Consensus size: 23

         21 AGTTTTTGTT

                 *                 
         31 TTTGCGTTTTTTCTAAAAAAAAA
          1 TTTGCTTTTTTTCTAAAAAAAAA

                  *                   
         54 TATTGTGTTTTTTTCTTAAAAAAAAA
          1 T-TTG-CTTTTTTTC-TAAAAAAAAA

                      
         80 TTTGCTTTTT
          1 TTTGCTTTTT

         90 GCGATTTAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  23    1  0.03
  24    8  0.27
  25   10  0.33
  26   11  0.37

ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53


Consensus pattern (23 bp):   
TTTGCTTTTTTTCTAAAAAAAAA

Found at i:1982 original size:20 final size:21

Alignment explanation


    Indices: 1939--1982  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       1929 TTTTCTTTGC

                      *        * 
       1939 ATTGTTTTGCTTTGATTGATT
          1 ATTGTTTTGCATTGATTGACT

                              *  
       1960 ATTGTTTTG-ATTGATTGCCT
          1 ATTGTTTTGCATTGATTGACT

               
       1980 ATT
          1 ATT

       1983 CATTCATTTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20   11  0.55
  21    9  0.45

ACGTcount: A:0.16, C:0.07, G:0.18, T:0.59


Consensus pattern (21 bp):   
ATTGTTTTGCATTGATTGACT

Found at i:2084 original size:21 final size:19

Alignment explanation


    Indices: 2059--2097  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 19

       2049 TATGACTCAT

                                 
       2059 ATGCTATGAATGCTATGATTG
          1 ATGCTATGAAT-CT-TGATTG

                 *            
       2080 ATGCTTTGAATCTTGATT
          1 ATGCTATGAATCTTGATT

       2098 TGCTTGATTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    5  0.29
  20    2  0.12
  21   10  0.59

ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44


Consensus pattern (19 bp):   
ATGCTATGAATCTTGATTG

Found at i:3676 original size:19 final size:18

Alignment explanation


    Indices: 3652--3687  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3642 TGAAGATTTA

                               
       3652 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       3671 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       3688 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:5042 original size:17 final size:18

Alignment explanation


    Indices: 5009--5044  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4999 GGTTACTAAC

                              
       5009 GTTTACCTTTAAAACTAT
          1 GTTTACCTTTAAAACTAT

                              
       5027 GTTTACCTTT-AAACTAT
          1 GTTTACCTTTAAAACTAT

             
       5044 G
          1 G

       5045 CCTAACGTTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    8  0.44
  18   10  0.56

ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44


Consensus pattern (18 bp):   
GTTTACCTTTAAAACTAT

Found at i:6207 original size:87 final size:87

Alignment explanation


    Indices: 6012--6218  Score: 222
    Period size: 87  Copynumber: 2.4  Consensus size: 87

       6002 CAGGCACAAA

                       *                      *   *  *  **                   
       6012 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAATTAAAACTCCATTAGGAAGAT
          1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT

                                  
       6077 CACTAAAATTTGAATTCAAACT
         66 CACTAAAATTTGAATTCAAACT

                 **          *                          *   *                
       6099 ATCCTATACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTAGGAAGA
          1 ATCCTCCACCAT-ATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGA

                                   * 
       6163 TCAC-AATCAA-TTGAATTCAAATT
         65 TCACTAA--AATTTGAATTCAAACT

              *       *            *   *     
       6186 ATTCTCCACCCTATCAGTTTCCACAGAATTTGC
          1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGC

       6219 GCCTAAAAAT


Statistics
Matches: 97,  Mismatches: 19, Indels: 8
        0.78            0.15        0.06

Matches are distributed among these distances:
  86    4  0.04
  87   89  0.92
  88    4  0.04

ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31


Consensus pattern (87 bp):   
ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
CACTAAAATTTGAATTCAAACT
Done.