Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019669.1 Corchorus olitorius cultivar O-4 contig19702, 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: 18383
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:1106 original size:22 final size:22

Alignment explanation


    Indices: 1053--1106  Score: 81
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       1043 TACGCCACGA

                     *      *     
       1053 CACGACCCACGTGCCGGCACAG
          1 CACGACCCATGTGCCGACACAG

                              *   
       1075 CACGACCCATGTGCCGACGCAG
          1 CACGACCCATGTGCCGACACAG

                      
       1097 CACGACCCAT
          1 CACGACCCAT

       1107 TTTTAATGTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   29  1.00

ACGTcount: A:0.24, C:0.44, G:0.24, T:0.07


Consensus pattern (22 bp):   
CACGACCCATGTGCCGACACAG

Found at i:5575 original size:1 final size:1

Alignment explanation


    Indices: 5569--5599  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

       5559 TAATCTTGTG

                                           
       5569 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       5600 GGGGTTAGTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:6617 original size:24 final size:24

Alignment explanation


    Indices: 6590--6638  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       6580 ATGGTCATTG

                       **   *       
       6590 GTATTATACTTTTTTTTTTAATAA
          1 GTATTATACTTGATTTCTTAATAA

                                    
       6614 GTATTATACTTGATTTCTTAATAA
          1 GTATTATACTTGATTTCTTAATAA

             
       6638 G
          1 G

       6639 GGTGATAAGT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55


Consensus pattern (24 bp):   
GTATTATACTTGATTTCTTAATAA

Found at i:9955 original size:96 final size:98

Alignment explanation


    Indices: 9765--9959  Score: 306
    Period size: 96  Copynumber: 2.0  Consensus size: 98

       9755 GTGATCAAGG

                        *                                        *           
       9765 TATGTCATTTTATTCTTTTGTCAGCTCCTTCATGTTGCCATGATTTATACATGGGCAGTTATGGG
          1 TATGTCATTTTAGTCTTTTGTCAGCTCCTTCATGTTGCCATGATTTATACATGAGCAGTTATGGG

                         *                   
       9830 AAAATGTTGGTGTTACTTATATGTACCATGAAT
         66 AAAATGTTGGTGTCACTTATATGTACCATGAAT

                                          **                                 
       9863 TATGTCATTTTAGTC-TTTGTCAGCTCCTTTGTGTTGCCATGA-TT-TACATGAGCAGTTTATGG
          1 TATGTCATTTTAGTCTTTTGTCAGCTCCTTCATGTTGCCATGATTTATACATGAGCAG-TTATGG

             *                                
       9925 GGAAATGTTGGTGTCACTTATATGTACCATGAAT
         65 GAAAATGTTGGTGTCACTTATATGTACCATGAAT

             
       9959 T
          1 T

       9960 GCCATTCTTG


Statistics
Matches: 90,  Mismatches: 6, Indels: 4
        0.90            0.06        0.04

Matches are distributed among these distances:
  95   10  0.11
  96   41  0.46
  97   25  0.28
  98   14  0.16

ACGTcount: A:0.23, C:0.14, G:0.21, T:0.43


Consensus pattern (98 bp):   
TATGTCATTTTAGTCTTTTGTCAGCTCCTTCATGTTGCCATGATTTATACATGAGCAGTTATGGG
AAAATGTTGGTGTCACTTATATGTACCATGAAT
Done.