Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009968.1 Corchorus capsularis cultivar CVL-1 contig09989, 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: 6759
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:3920 original size:81 final size:81

Alignment explanation


    Indices: 3775--4010  Score: 409
    Period size: 81  Copynumber: 2.9  Consensus size: 81

       3765 GAATGTCGGG

                  *      **                                            *     
       3775 TCTAGTTGAAGGAACTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTGGTAAT
          1 TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAAT

                            
       3840 GAATGAAATCGATACT
         66 GAATGAAATCGATACT

                                                         *        *          
       3856 TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCCTTTTGGTCTTTTTAGTAAT
          1 TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAAT

                            
       3921 GAATGAAATCGATACT
         66 GAATGAAATCGATACT

                                                                   *         
       3937 TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCGTTTAGTAAT
          1 TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAAT

                     
       4002 GAATGAAAT
         66 GAATGAAAT

       4011 TTGTTCTTCC


Statistics
Matches: 146,  Mismatches: 9, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  81  146  1.00

ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37


Consensus pattern (81 bp):   
TCTAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAAT
GAATGAAATCGATACT

Found at i:4139 original size:97 final size:96

Alignment explanation


    Indices: 3939--4195  Score: 343
    Period size: 97  Copynumber: 2.7  Consensus size: 96

       3929 TCGATACTTC

                       **                                        *           
       3939 TAGTGGAAGGATTTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCGTTTAGTAATGA
          1 TAGTGGAAGGAACTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAATGA

              *    *          **        *  
       4004 ATGAAATTTGTTCTTCCTTGAATGTCGGTTA
         66 ATAAAATCTGTTCTTCCTCAAATGTCGGGTA

              *                         *                       *            
       4035 TACTGGAAGGAACTCGAAACCCTTTTAACCAAGGTGTTTATGCATTTTTGGTGCTTTTAGTAATG
          1 TAGTGGAAGGAACTCGAAACCCTTTTAAGCAAGGTGTTTATGCA-TTTTGGTCCTTTTAGTAATG

                                           *
       4100 AATAAAATCTGTTCTTCCTCAAATGTCGGGTC
         65 AATAAAATCTGTTCTTCCTCAAATGTCGGGTA

             *             *        *         **             *              
       4132 TGGTGGAAGGAACTCAAAACCCTTCTAAGCAAGGCATTTATGCATTTTGATCCTTTTAGTAATG
          1 TAGTGGAAGGAACTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAATG

       4196 TTCAACACAA


Statistics
Matches: 139,  Mismatches: 21, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
  96   58  0.42
  97   81  0.58

ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37


Consensus pattern (96 bp):   
TAGTGGAAGGAACTCGAAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTTAGTAATGA
ATAAAATCTGTTCTTCCTCAAATGTCGGGTA

Found at i:6097 original size:5 final size:5

Alignment explanation


    Indices: 6087--6112  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       6077 ATCTGAGAAC

                                           
       6087 TTGAT TTGAT TTGAT TTGAT TTGAT T
          1 TTGAT TTGAT TTGAT TTGAT TTGAT T

       6113 CAAGGGTCGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62


Consensus pattern (5 bp):   
TTGAT

Found at i:6532 original size:16 final size:16

Alignment explanation


    Indices: 6511--6545  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       6501 ATCTGAAATA

                            
       6511 CTTCAGAGCTTTTATG
          1 CTTCAGAGCTTTTATG

                            
       6527 CTTCAGAGCTTTTATG
          1 CTTCAGAGCTTTTATG

               
       6543 CTT
          1 CTT

       6546 TCTGAATTGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46


Consensus pattern (16 bp):   
CTTCAGAGCTTTTATG
Done.