Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006819.1 Corchorus capsularis cultivar CVL-1 contig06840, 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: 11752
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35


Found at i:1247 original size:31 final size:31

Alignment explanation


    Indices: 1206--1313  Score: 90
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       1196 AATGGCTAAT

                                *          
       1206 TGCTCAAATAAGGGCCCAACGTTTGTGAAAA
          1 TGCTCAAATAAGGGCCCAACATTTGTGAAAA

              *           ***  *         * 
       1237 TGTTCAAATAAGGGTTTAATATTTGTGAATA
          1 TGCTCAAATAAGGGCCCAACATTTGTGAAAA

                     *          *   ****    
       1268 TGCTCAAATTAGGGCCCAAAGATTAAAAAAAA
          1 TGCTCAAATAAGGGCCC-AACATTTGTGAAAA

                          
       1300 TGCTCAAATAAGGG
          1 TGCTCAAATAAGGG

       1314 TCTATTGTTG


Statistics
Matches: 57,  Mismatches: 19, Indels: 1
        0.74            0.25        0.01

Matches are distributed among these distances:
  31   36  0.63
  32   21  0.37

ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27


Consensus pattern (31 bp):   
TGCTCAAATAAGGGCCCAACATTTGTGAAAA

Found at i:5443 original size:31 final size:31

Alignment explanation


    Indices: 5408--5578  Score: 173
    Period size: 31  Copynumber: 5.5  Consensus size: 31

       5398 GGTGTTCGAA

                  *                   *   *
       5408 GTGGCATGCCACGTGGATCAAAAAGTAACAT
          1 GTGGCACGCCACGTGGATCAAAAAGTGACAC

                   *   *                   
       5439 GTGGCACACCATGTGGATCAAAAAGTGACAC
          1 GTGGCACGCCACGTGGATCAAAAAGTGACAC

              *               *              
       5470 GTTGCACGCCACGTGTG-CCAAAAAAGTGACAC
          1 GTGGCACGCCACGTG-GATC-AAAAAGTGACAC

                    *   *  **           *  
       5502 GTGGCACGTCACATGTTTCAAAAAGTGATAC
          1 GTGGCACGCCACGTGGATCAAAAAGTGACAC

                           * *             
       5533 GTGGCACGCCACGTGTACCAAAAAGTGACAC
          1 GTGGCACGCCACGTGGATCAAAAAGTGACAC

            *     *        
       5564 ATGGCATGCCACGTG
          1 GTGGCACGCCACGTG

       5579 CACTAAAGGA


Statistics
Matches: 115,  Mismatches: 22, Indels: 6
        0.80            0.15        0.04

Matches are distributed among these distances:
  31   89  0.77
  32   26  0.23

ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18


Consensus pattern (31 bp):   
GTGGCACGCCACGTGGATCAAAAAGTGACAC

Found at i:5508 original size:63 final size:62

Alignment explanation


    Indices: 5408--5569  Score: 184
    Period size: 63  Copynumber: 2.6  Consensus size: 62

       5398 GGTGTTCGAA

                  *        * *        *   *                                 
       5408 GTGGCATGCCACGTGGATCAAAAAGTAACATGTGGCAC-AC-CATGTGGATCAAAAAGTGACAC
          1 GTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGACACATGT--ATCAAAAAGTGACAC

              *             *                       *       *           *  
       5470 GTTGCACGCCACGTGTGCCAAAAAAGTGACACGTGGCACGTCACATGTTTCAAAAAGTGATAC
          1 GTGGCACGCCACGTGTACC-AAAAAGTGACACGTGGCACGACACATGTATCAAAAAGTGACAC

                                           *     
       5533 GTGGCACGCCACGTGTACCAAAAAGTGACACATGGCA
          1 GTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCA

       5570 TGCCACGTGC


Statistics
Matches: 84,  Mismatches: 13, Indels: 6
        0.82            0.13        0.06

Matches are distributed among these distances:
  62   31  0.37
  63   47  0.56
  64    1  0.01
  65    5  0.06

ACGTcount: A:0.33, C:0.23, G:0.25, T:0.18


Consensus pattern (62 bp):   
GTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGACACATGTATCAAAAAGTGACAC

Found at i:9464 original size:45 final size:45

Alignment explanation


    Indices: 9400--9489  Score: 180
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       9390 ATCTGAATCT

                                                         
       9400 GAAACTGGAGATACTTTGGCAGTGGAGGATGGCTGAGGCTGAGGG
          1 GAAACTGGAGATACTTTGGCAGTGGAGGATGGCTGAGGCTGAGGG

                                                         
       9445 GAAACTGGAGATACTTTGGCAGTGGAGGATGGCTGAGGCTGAGGG
          1 GAAACTGGAGATACTTTGGCAGTGGAGGATGGCTGAGGCTGAGGG

       9490 TCATCGTCGT


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   45  1.00

ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20


Consensus pattern (45 bp):   
GAAACTGGAGATACTTTGGCAGTGGAGGATGGCTGAGGCTGAGGG

Found at i:10910 original size:16 final size:16

Alignment explanation


    Indices: 10891--10924  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 16

      10881 TTAATTTTGG

                             
      10891 AAAA-AAAATTTGACAA
          1 AAAATAAAATTTGA-AA

                            
      10907 AAAATAAAATTTGAAA
          1 AAAATAAAATTTGAAA

              
      10923 AA
          1 AA

      10925 TAAGAACAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    8  0.47
  17    9  0.53

ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21


Consensus pattern (16 bp):   
AAAATAAAATTTGAAA

Done.