Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001584.1 Corchorus capsularis cultivar CVL-1 contig01584, 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: 2819
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Found at i:57 original size:40 final size:40

Alignment explanation


    Indices: 11--150  Score: 136
    Period size: 40  Copynumber: 3.4  Consensus size: 40

          1 CTTCCCTATT

                                          *         
         11 GGAAGGTGTTGTTTTTATTCCCAATTTGCCATTCCCCACC
          1 GGAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACC

                                         *           *  **
         51 GGAAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCCTCATT
          1 GGAAGGTGTTG--T--TT--TTATTCCCAATTTGCCCTTCCCCACC

                          **                  *     
         97 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCGCCACC
          1 GGAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACC

             *      *     
        137 GAAAGGTGCTGTTT
          1 GGAAGGTGTTGTTT

        151 AGTTTCCAGT


Statistics
Matches: 80,  Mismatches: 14, Indels: 12
        0.75            0.13        0.11

Matches are distributed among these distances:
  40   42  0.52
  42    3  0.04
  44    3  0.04
  46   32  0.40

ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38


Consensus pattern (40 bp):   
GGAAGGTGTTGTTTTTATTCCCAATTTGCCCTTCCCCACC

Found at i:183 original size:40 final size:39

Alignment explanation


    Indices: 66--194  Score: 136
    Period size: 40  Copynumber: 3.3  Consensus size: 39

         56 GTGTTGTTTA

                *                                  
         66 GTTGCTTA-TTCCCAGTTTGCCCTTCCTCATTGGAAGGT
          1 GTTGTTTAGTTCCCAGTTTGCCCTTCCTCATTGGAAGGT

                     *      *               ** *     
        104 GTTGTTTAAATTCCCAATTTGCCCTTCGC-CACCGAAAGGT
          1 GTTGTTT-AGTTCCCAGTTTGCCCTTC-CTCATTGGAAGGT

             *         *                            
        144 GCTGTTTAGTTTCCAGTCTTGCCCTTCCTCATTGGAAGGT
          1 GTTGTTTAGTTCCCAGT-TTGCCCTTCCTCATTGGAAGGT

                *      
        184 GTTGCTTAGTT
          1 GTTGTTTAGTT

        195 GTCTAATTAC


Statistics
Matches: 72,  Mismatches: 14, Indels: 8
        0.77            0.15        0.09

Matches are distributed among these distances:
  38    6  0.08
  39    9  0.12
  40   56  0.78
  41    1  0.01

ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39


Consensus pattern (39 bp):   
GTTGTTTAGTTCCCAGTTTGCCCTTCCTCATTGGAAGGT

Found at i:233 original size:47 final size:46

Alignment explanation


    Indices: 154--288  Score: 148
    Period size: 48  Copynumber: 2.9  Consensus size: 46

        144 GCTGTTTAGT

                              *   *                   *    
        154 TTCCAGTCTTGCCCTTCCTCATTGGAAGGTGTTGCTTAGTTGTCTAA
          1 TTCCAGT-TTGCCCTTCCCCATCGGAAGGTGTTGCTTAGTTGCCTAA

                *                                 *        * 
        201 TTACTAGTTCTGCCCTTCCCCA-CGGAAGGTGTTGTCTAAGTTGCCTTA
          1 TT-CCAGTT-TGCCCTTCCCCATCGGAAGGTGTTG-CTTAGTTGCCTAA

                *                                    
        249 TTCCCGTTTCGCCCTTCCCCATCGGAAGGTGTTG-TTAGTT
          1 TTCCAGTTT-GCCCTTCCCCATCGGAAGGTGTTGCTTAGTT

        289 TTAGCGGTTT


Statistics
Matches: 74,  Mismatches: 9, Indels: 11
        0.79            0.10        0.12

Matches are distributed among these distances:
  46    6  0.08
  47   29  0.39
  48   39  0.53

ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38


Consensus pattern (46 bp):   
TTCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGCTTAGTTGCCTAA

Found at i:1868 original size:2 final size:2

Alignment explanation


    Indices: 1863--1911  Score: 52
    Period size: 2  Copynumber: 26.5  Consensus size: 2

       1853 GGATAATCTG

                               *                    *                     
       1863 TA TA TA TA T- TA TC T- TA TA -A TA -A TG TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                            
       1901 TA TA TA TA TA T
          1 TA TA TA TA TA T

       1912 CAGTAACTTC


Statistics
Matches: 40,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
   1    4  0.10
   2   36  0.90

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51


Consensus pattern (2 bp):   
TA

Done.