Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024533.1 Corchorus olitorius cultivar O-4 contig24566, 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: 2593
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32


Found at i:1290 original size:25 final size:24

Alignment explanation


    Indices: 1253--1299  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1243 CTAGAAAATT

                                      
       1253 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1279 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1300 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:2571 original size:154 final size:154

Alignment explanation


    Indices: 2291--2593  Score: 527
    Period size: 154  Copynumber: 2.0  Consensus size: 154

       2281 TGGCGCATCA

                                  *                   *                      
       2291 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
          1 ATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGATCCGTTTTGAATCGTCTTCGAT

              *                           *                                  
       2356 TTGGCAAACCTCAAAGCTTTTCTTTCCATTTTTTATGGACTAATGATAATCATTTTGGTGAGATT
         66 TTAGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAATGATAATCATTTTGGTGAGATT

                                    
       2421 AGTCCACTGTGAAGTTTTTAGCTC
        131 AGTCCACTGTGAAGTTTTTAGCTC

                                                                             
       2445 ATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGATCCGTTTTGAATCGTCTTCGAT
          1 ATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGATCCGTTTTGAATCGTCTTCGAT

                          *                       *                          
       2510 TTAGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT-ATAATCATTTTGGTGAGAT
         66 TTAGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAA-TGATAATCATTTTGGTGAGAT

                 *              
       2574 TAGTCTACTGTGAAGTTTTT
        130 TAGTCCACTGTGAAGTTTTT


Statistics
Matches: 141,  Mismatches: 7, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
 154  140  0.99
 155    1  0.01

ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41


Consensus pattern (154 bp):   
ATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAGATCCGTTTTGAATCGTCTTCGAT
TTAGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGACTAATGATAATCATTTTGGTGAGATT
AGTCCACTGTGAAGTTTTTAGCTC
Done.