Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001395.1 Corchorus capsularis cultivar CVL-1 contig01395, 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: 7854
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:154 original size:56 final size:56

Alignment explanation


    Indices: 82--259  Score: 324
    Period size: 56  Copynumber: 3.2  Consensus size: 56

         72 TGAATCTGCT

                *                                  *                
         82 TTTACATGAATACAAAATCTTAACATTCCATCTAAAAAAAATATAAATATGAAGAG
          1 TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG

                                                                    
        138 TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG
          1 TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG

                                                                    
        194 TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG
          1 TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG

                        
        250 TTT-GA-GAATA
          1 TTTAGATGAATA

        260 AATCCCTTGA


Statistics
Matches: 120,  Mismatches: 2, Indels: 2
        0.97            0.02        0.02

Matches are distributed among these distances:
  54    5  0.04
  55    2  0.02
  56  113  0.94

ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30


Consensus pattern (56 bp):   
TTTAGATGAATACAAAATCTTAACATTCCATCTAAAAAATATATAAATATGAAGAG

Found at i:3389 original size:23 final size:23

Alignment explanation


    Indices: 3345--3391  Score: 69
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3335 TTTGATTATG

                    *              
       3345 GAAATCCATGCAAGGTTGCCGTT
          1 GAAATCCAAGCAAGGTTGCCGTT

                                    
       3368 GAAATCTCAAGCAAGGTT-CCGTT
          1 GAAATC-CAAGCAAGGTTGCCGTT

             
       3391 G
          1 G

       3392 TGTTTGCAAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23   12  0.55
  24   10  0.45

ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26


Consensus pattern (23 bp):   
GAAATCCAAGCAAGGTTGCCGTT

Found at i:4426 original size:54 final size:54

Alignment explanation


    Indices: 4362--4471  Score: 150
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       4352 TGAAACTCCA

                 *          *                    *                 
       4362 GTACCCCTCGAGGAACGTTTATCTT-GGCTTCGGGCTGGAGGATATGAAGGGATG
          1 GTACCACTCGAGGAACATTT-TCTTCGGCTTCGGGCTAGAGGATATGAAGGGATG

                                 *         *               *      
       4416 GTACCACTCGAGGAACATTTTTTTCGGCTTCTGGCTAGAGGATATGAGGGGATG
          1 GTACCACTCGAGGAACATTTTCTTCGGCTTCGGGCTAGAGGATATGAAGGGATG

              
       4470 GT
          1 GT

       4472 GACTTCGTAT


Statistics
Matches: 49,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  53    3  0.06
  54   46  0.94

ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28


Consensus pattern (54 bp):   
GTACCACTCGAGGAACATTTTCTTCGGCTTCGGGCTAGAGGATATGAAGGGATG
Done.