Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005742.1 Corchorus capsularis cultivar CVL-1 contig05760, 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: 4476
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32


Found at i:148 original size:31 final size:31

Alignment explanation


    Indices: 80--178  Score: 139
    Period size: 31  Copynumber: 3.2  Consensus size: 31

         70 GGCGGCGGGT

                                             
         80 ACGCCACTATTTAGCGGCG-CTTAGGACCTCAG
          1 ACGCCACTATTTAGCGGCGTCTT-GGACCT-AG

                         *                 
        112 ACGCCACTATTTATCGGCGTCTTGGACCTAG
          1 ACGCCACTATTTAGCGGCGTCTTGGACCTAG

                                         *  
        143 ACGCCACTATTTAGCGGCGTC-TGGAACCCAG
          1 ACGCCACTATTTAGCGGCGTCTTGG-ACCTAG

                 
        174 ACGCC
          1 ACGCC

        179 GCGCTGCTAT


Statistics
Matches: 62,  Mismatches: 3, Indels: 5
        0.89            0.04        0.07

Matches are distributed among these distances:
  30    3  0.05
  31   32  0.52
  32   24  0.39
  33    3  0.05

ACGTcount: A:0.21, C:0.32, G:0.24, T:0.22


Consensus pattern (31 bp):   
ACGCCACTATTTAGCGGCGTCTTGGACCTAG

Found at i:291 original size:31 final size:31

Alignment explanation


    Indices: 253--324  Score: 108
    Period size: 31  Copynumber: 2.3  Consensus size: 31

        243 AGGACCTCAT

                                    *      
        253 ACGCCACTATTTAGCAGCGTCTTGGACACAG
          1 ACGCCACTATTTAGCAGCGTCTTGAACACAG

                           *           *   
        284 ACGCCACTATTTAGCGGCGTCTTGAACCCAG
          1 ACGCCACTATTTAGCAGCGTCTTGAACACAG

                 *    
        315 ACGCCGCTAT
          1 ACGCCACTAT

        325 CTTTTAGCCT


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   37  1.00

ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22


Consensus pattern (31 bp):   
ACGCCACTATTTAGCAGCGTCTTGAACACAG

Found at i:420 original size:144 final size:138

Alignment explanation


    Indices: 100--432  Score: 447
    Period size: 141  Copynumber: 2.3  Consensus size: 138

         90 TTAGCGGCGC

                       *             *                                       
        100 TTAGGACCTCAGACGCCACTATTTATCGGCGTCTTGGACCTAGACGCCACTATTTAGCGGCGTCT
          1 TTAGGACCTCATACGCCACTATTTAGCGGCGTCTTGGACC-AGACGCCACTATTTAGCGGCGTCT

                                                                             
        165 GGAACCCAGACGCCGCGCTGCTATCTTTTAGCCTTCTTTTTTACCCAATTCGCCTTCCTTAGAAA
         65 GGAACCCAGA--CCGCGCTGCTATCTTTTAGCCTTCTTTTTTACCCAATTCGCCTTCCTTAGAAA

                   *   
        230 GAGGGCGGCGT
        128 GAGGGCGACGT

                                       *                                     
        241 TTAGGACCTCATACGCCACTATTTAGCAGCGTCTTGGACACAGACGCCACTATTTAGCGGCGTCT
          1 TTAGGACCTCATACGCCACTATTTAGCGGCGTCTTGGAC-CAGACGCCACTATTTAGCGGCGTCT

            *                                               *                
        306 TGAACCCAGA-CGC-C-GCTATCTTTTAGCCTTCTTTTTTACCCAATTTGCCTTCCTCATAGAAA
         65 GGAACCCAGACCGCGCTGCTATCTTTTAGCCTTCTTTTTTACCCAATTCGCCTTCCT--TAG---

                    *        
        368 ATTAAAGATGGCGACGT
        125 ---AAAGAGGGCGACGT

                                          *     *           
        385 TTAGGACCTCATACGCCACTATTTAGCGGCATCTTGAACTCAGACGCC
          1 TTAGGACCTCATACGCCACTATTTAGCGGCGTCTTGGAC-CAGACGCC

        433 GCTAAATTTT


Statistics
Matches: 172,  Mismatches: 11, Indels: 15
        0.87            0.06        0.08

Matches are distributed among these distances:
 136   39  0.23
 137    1  0.01
 138    6  0.03
 141   69  0.40
 142    1  0.01
 144   56  0.33

ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29


Consensus pattern (138 bp):   
TTAGGACCTCATACGCCACTATTTAGCGGCGTCTTGGACCAGACGCCACTATTTAGCGGCGTCTG
GAACCCAGACCGCGCTGCTATCTTTTAGCCTTCTTTTTTACCCAATTCGCCTTCCTTAGAAAGAG
GGCGACGT

Found at i:3664 original size:29 final size:29

Alignment explanation


    Indices: 3632--3694  Score: 92
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       3622 GTCTTTTGAC

                  *                       
       3632 TGGATCTGACTCCTCTCCAGTCTATA-AGA
          1 TGGATCCGACTCCTCTCCAGTCTATACA-A

                    *                    
       3661 TGGATCCGGCTCCTCTCCAGTCTATACAA
          1 TGGATCCGACTCCTCTCCAGTCTATACAA

                 
       3690 TGGAT
          1 TGGAT

       3695 TGGAGAGGTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  29   30  0.97
  30    1  0.03

ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30


Consensus pattern (29 bp):   
TGGATCCGACTCCTCTCCAGTCTATACAA
Done.