Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023968.1 Corchorus olitorius cultivar O-4 contig24001, 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: 6564
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26


Found at i:1250 original size:21 final size:20

Alignment explanation


    Indices: 1226--1271  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 20

       1216 GGCGCCCACA

                         *     * 
       1226 TGGTTGCCTTGAGCACCCATG
          1 TGGTTG-CTTGAGAACCCAGG

                                 
       1247 TGGTTTGCTTGAGAACCCAGG
          1 TGG-TTGCTTGAGAACCCAGG

                
       1268 TGGT
          1 TGGT

       1272 CAGTGTCACG


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.82
  22    3  0.14

ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30


Consensus pattern (20 bp):   
TGGTTGCTTGAGAACCCAGG

Found at i:1354 original size:76 final size:76

Alignment explanation


    Indices: 1204--1355  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1194 ACAAGGACCC

                                                               *           * 
       1204 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

              *        
       1269 GGTCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       1280 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       1342 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

       1356 TAGCTCATCA


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:2053 original size:155 final size:155

Alignment explanation


    Indices: 1771--2073  Score: 543
    Period size: 155  Copynumber: 2.0  Consensus size: 155

       1761 CTATGGCGGC

                                             *               *               
       1771 AGTGTATAAGGCCTTCGTGAAAGCCGATATGATTCAATCAGGACAATATTATAGGGAGGTTAGTG
          1 AGTGTATAAGGCCTTCGTGAAAGCCGATATGATGCAATCAGGACAATATGATAGGGAGGTTAGTG

                                     *                                       
       1836 GTGAAGAATGCCCTATGCATAAAGGGCACACCATCCAACATTGCAAAGAGTTCAGGACCTTTGTT
         66 GTGAAGAATGCCCTATGCATAAAGGACACACCATCCAACATTGCAAAGAGTTCAGGACCTTTGTT

                                     
       1901 CAGAAGATGATGAATGAAAGCTGGT
        131 CAGAAGATGATGAATGAAAGCTGGT

                                   *  *                                  *   
       1926 AGTGTATAAGGCCTTCGTGAAAGTCGGTATGATGCAATCAGGACAATATGATAGGGAGGTTTGTG
          1 AGTGTATAAGGCCTTCGTGAAAGCCGATATGATGCAATCAGGACAATATGATAGGGAGGTTAGTG

                        *                                                    
       1991 GTGAAGAATGCCTTATGCATAAAGGACACACCATCCAACATTGCAAAGAGTTCAGGACCTTTGTT
         66 GTGAAGAATGCCCTATGCATAAAGGACACACCATCCAACATTGCAAAGAGTTCAGGACCTTTGTT

                              
       2056 CAGAAGATGATGAATGAA
        131 CAGAAGATGATGAATGAA

       2074 TCTAGGATTC


Statistics
Matches: 141,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 155  141  1.00

ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25


Consensus pattern (155 bp):   
AGTGTATAAGGCCTTCGTGAAAGCCGATATGATGCAATCAGGACAATATGATAGGGAGGTTAGTG
GTGAAGAATGCCCTATGCATAAAGGACACACCATCCAACATTGCAAAGAGTTCAGGACCTTTGTT
CAGAAGATGATGAATGAAAGCTGGT
Done.