Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023816.1 Corchorus olitorius cultivar O-4 contig23849, 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: 9680
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:377 original size:32 final size:32

Alignment explanation


    Indices: 336--441  Score: 176
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        326 TTTCAAAATA

                                *        *  
        336 GCCGCTATTTAGTGGCGTTTACGTACCGAGAC
          1 GCCGCTATTTAGTGGCGTTTCCGTACCGAAAC

                           *                
        368 GCCGCTATTTAGTGGTGTTTCCGTACCGAAAC
          1 GCCGCTATTTAGTGGCGTTTCCGTACCGAAAC

                                     *      
        400 GCCGCTATTTAGTGGCGTTTCCGTATCGAAAC
          1 GCCGCTATTTAGTGGCGTTTCCGTACCGAAAC

                      
        432 GCCGCTATTT
          1 GCCGCTATTT

        442 GGCTTGTTTA


Statistics
Matches: 69,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   69  1.00

ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31


Consensus pattern (32 bp):   
GCCGCTATTTAGTGGCGTTTCCGTACCGAAAC

Found at i:1226 original size:31 final size:29

Alignment explanation


    Indices: 1190--1256  Score: 80
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1180 TACAGGTCCT

                                           
       1190 TCTACTTTCAAAAAAGGATCAATTTGATCCC
          1 TCTACTTT-AAAAAAGG-TCAATTTGATCCC

                  *      **         *    
       1221 TCTACTATAAAAACTGTCAATTTGGTCCC
          1 TCTACTTTAAAAAAGGTCAATTTGATCCC

                   
       1250 TCTACTT
          1 TCTACTT

       1257 ACAATTTGGT


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  29   18  0.58
  30    6  0.19
  31    7  0.23

ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36


Consensus pattern (29 bp):   
TCTACTTTAAAAAAGGTCAATTTGATCCC

Found at i:1599 original size:29 final size:31

Alignment explanation


    Indices: 1556--1629  Score: 98
    Period size: 29  Copynumber: 2.5  Consensus size: 31

       1546 CACCAAATTA

                              *     *      
       1556 TAAGTAGAGGGACCAAATTGA-CAGTTTTTG
          1 TAAGTAGAGGGACCAAATCGATCACTTTTTG

                   *               *       
       1586 T-AGTAGGGGGACCAAATCGATCCCTTTTTG
          1 TAAGTAGAGGGACCAAATCGATCACTTTTTG

                          
       1616 TAAGTAGAGGGACC
          1 TAAGTAGAGGGACC

       1630 TGTACGGTAT


Statistics
Matches: 37,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  29   17  0.46
  30    9  0.24
  31   11  0.30

ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27


Consensus pattern (31 bp):   
TAAGTAGAGGGACCAAATCGATCACTTTTTG

Found at i:3393 original size:55 final size:55

Alignment explanation


    Indices: 3333--3484  Score: 261
    Period size: 55  Copynumber: 2.8  Consensus size: 55

       3323 GAGCCATATG

                                  **  *                             
       3333 TTGATGAAGGGAT-AAGTAAACAGCAACAAAGAGCTTTTAGAACTGATGTGAATAA
          1 TTGATGAAGGGATCAAGT-AACTCCATCAAAGAGCTTTTAGAACTGATGTGAATAA

                                                                   
       3388 TTGATGAAGGGATCAAGTAACTCCATCAAAGAGCTTTTAGAACTGATGTGAATAA
          1 TTGATGAAGGGATCAAGTAACTCCATCAAAGAGCTTTTAGAACTGATGTGAATAA

                                                      
       3443 TTGATGAAGGGATCAAGTAACTCCATCAAAGAGCTTTTAGAA
          1 TTGATGAAGGGATCAAGTAACTCCATCAAAGAGCTTTTAGAA

       3485 GAGATTGAGA


Statistics
Matches: 93,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
  55   89  0.96
  56    4  0.04

ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26


Consensus pattern (55 bp):   
TTGATGAAGGGATCAAGTAACTCCATCAAAGAGCTTTTAGAACTGATGTGAATAA
Done.