Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015710.1 Corchorus capsularis cultivar CVL-1 contig15731, 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: 7544
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38


Found at i:322 original size:25 final size:25

Alignment explanation


    Indices: 300--350  Score: 68
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        290 TTCACTTTAG

                                     
        300 ATGACAT-GTTAGGGTTTGGCTTTC
          1 ATGACATGGTTAGGGTTTGGCTTTC

               *              *  *   
        324 ATGTCATGGTTAGGGTTTAGCCTTC
          1 ATGACATGGTTAGGGTTTGGCTTTC

              
        349 AT
          1 AT

        351 CTCACTTAGG


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24    6  0.26
  25   17  0.74

ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41


Consensus pattern (25 bp):   
ATGACATGGTTAGGGTTTGGCTTTC

Found at i:980 original size:67 final size:69

Alignment explanation


    Indices: 907--1039  Score: 225
    Period size: 69  Copynumber: 2.0  Consensus size: 69

        897 CTAGACAAAC

                                               *                 *      *    
        907 TACATATTTGATTATTATAG-A-ATATTGATTATTCTTTTTGTCTCTATATGTGATTGTAGAGTA
          1 TACATATTTGATTATTATAGAATATATTGATTATTATTTTTGTCTCTATATGTAATTGTAAAGTA

                
        970 AAAT
         66 AAAT

                                                                             
        974 TACATATTTGATTATTATAGAATATATTGATTATTATTTTTGTCTCTATATGTAATTGTAAAGTA
          1 TACATATTTGATTATTATAGAATATATTGATTATTATTTTTGTCTCTATATGTAATTGTAAAGTA

             
       1039 A
         66 A

       1040 TTGATTTCAT


Statistics
Matches: 61,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  67   20  0.33
  68    1  0.02
  69   40  0.66

ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50


Consensus pattern (69 bp):   
TACATATTTGATTATTATAGAATATATTGATTATTATTTTTGTCTCTATATGTAATTGTAAAGTA
AAAT

Found at i:1201 original size:16 final size:16

Alignment explanation


    Indices: 1166--1201  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1156 CTTATTGTTG

                        *  *
       1166 ATTTAAATTATAGTAT
          1 ATTTAAATTATAATAC

                            
       1182 ATTTAAATTATAATAC
          1 ATTTAAATTATAATAC

                
       1198 ATTT
          1 ATTT

       1202 GATTTAGGAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50


Consensus pattern (16 bp):   
ATTTAAATTATAATAC

Found at i:1789 original size:27 final size:24

Alignment explanation


    Indices: 1731--1789  Score: 59
    Period size: 27  Copynumber: 2.4  Consensus size: 24

       1721 TTGGCCCGTT

                                    
       1731 TCTTCT-TTGCTTTTCCTTTCCTC
          1 TCTTCTGTTGCTTTTCCTTTCCTC

                              *         
       1754 TCTAT-TGTTGCTCTCTTTCTTTCTCTC
          1 TCT-TCTGTTGCT-T-TTCCTTTC-CTC

                     
       1781 TCTTCTGTT
          1 TCTTCTGTT

       1790 TTTTTCTCAC


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  23    4  0.14
  24    6  0.21
  25    1  0.03
  26    8  0.28
  27   10  0.34

ACGTcount: A:0.02, C:0.31, G:0.07, T:0.61


Consensus pattern (24 bp):   
TCTTCTGTTGCTTTTCCTTTCCTC

Found at i:7386 original size:33 final size:32

Alignment explanation


    Indices: 7286--7390  Score: 131
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       7276 TTGCAAAGAG

                                             
       7286 TGTTTTAGATGTTGTTTGTGATGATACTAAATC
          1 TGTTTTAG-TGTTGTTTGTGATGATACTAAATC

              *   *             *    *        
       7319 TAATTTGAGTGTTGTTT-TCAATGACACTAAATC
          1 T-GTTTTAGTGTTGTTTGT-GATGATACTAAATC

                                             
       7352 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTT-AGTGTTGTTTGTGATGATACTAAATC

                  
       7385 TGTTTT
          1 TGTTTT

       7391 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 8, Indels: 8
        0.79            0.11        0.11

Matches are distributed among these distances:
  32    4  0.07
  33   50  0.83
  34    6  0.10

ACGTcount: A:0.25, C:0.08, G:0.19, T:0.49


Consensus pattern (32 bp):   
TGTTTTAGTGTTGTTTGTGATGATACTAAATC
Done.