Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015593.1 Corchorus capsularis cultivar CVL-1 contig15614, 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: 3870
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34


Found at i:1856 original size:55 final size:54

Alignment explanation


    Indices: 1768--1893  Score: 189
    Period size: 55  Copynumber: 2.3  Consensus size: 54

       1758 TTTTCTTCCC

                 *            *      *        *                   
       1768 TTTTATTATTGGTATTTTTGTAAACCCAAATGCATTAGTGTACTTATGAAGGAT
          1 TTTTACTATTGGTATTTTGGTAAACACAAATGCAATAGTGTACTTATGAAGGAT

                                   *                        *      
       1822 TTTTACTATTGAGTATTTTGGTATACACAAATGCAATAGTGTACTTATTAAGGAT
          1 TTTTACTATTG-GTATTTTGGTAAACACAAATGCAATAGTGTACTTATGAAGGAT

                             
       1877 TTTTACTATTGGTATTT
          1 TTTTACTATTGGTATTT

       1894 AATCTTTTTT


Statistics
Matches: 65,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  54   16  0.25
  55   49  0.75

ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46


Consensus pattern (54 bp):   
TTTTACTATTGGTATTTTGGTAAACACAAATGCAATAGTGTACTTATGAAGGAT

Found at i:2369 original size:27 final size:27

Alignment explanation


    Indices: 2309--2415  Score: 133
    Period size: 27  Copynumber: 3.9  Consensus size: 27

       2299 TGATCTTTAA

                     *      *       *    
       2309 AAAAATGACTAAAATGCCCTCCTGAGTGC
          1 AAAAATGACCAAAAT-ACC-CCTGGGTGC

                      *                
       2338 AAAAATGACCGAAATACCCCTGGGTGC
          1 AAAAATGACCAAAATACCCCTGGGTGC

            *              *           
       2365 GAAAATGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATACCCCTGGGTGC

                               *    
       2392 AAAAATGACCAAAATACCCTTGGG
          1 AAAAATGACCAAAATACCCCTGGG

       2416 CGACTCTAAT


Statistics
Matches: 68,  Mismatches: 10, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  27   53  0.78
  28    2  0.03
  29   13  0.19

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


Consensus pattern (27 bp):   
AAAAATGACCAAAATACCCCTGGGTGC

Found at i:2407 original size:54 final size:56

Alignment explanation


    Indices: 2310--2415  Score: 162
    Period size: 54  Copynumber: 1.9  Consensus size: 56

       2300 GATCTTTAAA

                    *                             *                 
       2310 AAAATGACTAAAATGCCCTCCTGAGTGCAAAAATGACCGAAATACCCCTGGGTGCG
          1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG

                                   *                       *    
       2366 AAAATGACCAAAATG-CC-CCTGGGTGCAAAAATGACCAAAATACCCTTGGG
          1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGG

       2416 CGACTCTAAT


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  54   30  0.65
  55    2  0.04
  56   14  0.30

ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17


Consensus pattern (56 bp):   
AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG

Found at i:3430 original size:16 final size:16

Alignment explanation


    Indices: 3408--3453  Score: 58
    Period size: 15  Copynumber: 2.9  Consensus size: 16

       3398 AATAAGTACT

                           *
       3408 ATAACCCGAAACCGAT
          1 ATAACCCGAAACCGAG

            *          *    
       3424 TTAACCCG-AATCGAG
          1 ATAACCCGAAACCGAG

                           
       3439 ATAACCCGAAACCGA
          1 ATAACCCGAAACCGA

       3454 CAAAATCCGA


Statistics
Matches: 24,  Mismatches: 5, Indels: 2
        0.77            0.16        0.06

Matches are distributed among these distances:
  15   12  0.50
  16   12  0.50

ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13


Consensus pattern (16 bp):   
ATAACCCGAAACCGAG
Done.