Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019256.1 Corchorus olitorius cultivar O-4 contig19289, 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: 22723
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5123 original size:15 final size:15

Alignment explanation


    Indices: 5093--5134  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5083 TTACTTTGTT

                            
       5093 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       5109 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       5124 TTGTTTTCTGT
          1 TTGTTTTCTGT

       5135 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:6172 original size:13 final size:13

Alignment explanation


    Indices: 6154--6179  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6144 CTTGGCATGA

                         
       6154 GTGATGATTTTTG
          1 GTGATGATTTTTG

                         
       6167 GTGATGATTTTTG
          1 GTGATGATTTTTG

       6180 TTGTTACCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54


Consensus pattern (13 bp):   
GTGATGATTTTTG

Found at i:7981 original size:18 final size:19

Alignment explanation


    Indices: 7932--7983  Score: 52
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       7922 CCGAGAAATC

                               *
       7932 AAAAACCAGCTCCTGCAGCT
          1 AAAAACCAGCTCC-GCAGCA

             *    **           
       7952 ACAAACTTGCTCCGC-GCA
          1 AAAAACCAGCTCCGCAGCA

                          
       7970 AAAAACCAGCTCCG
          1 AAAAACCAGCTCCG

       7984 TGCTTATTTT


Statistics
Matches: 25,  Mismatches: 7, Indels: 2
        0.74            0.21        0.06

Matches are distributed among these distances:
  18   13  0.52
  19    2  0.08
  20   10  0.40

ACGTcount: A:0.35, C:0.37, G:0.15, T:0.13


Consensus pattern (19 bp):   
AAAAACCAGCTCCGCAGCA

Found at i:8156 original size:51 final size:51

Alignment explanation


    Indices: 8060--8156  Score: 117
    Period size: 51  Copynumber: 1.9  Consensus size: 51

       8050 TCAAATTATC

                                                * **           
       8060 CTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTTTTCT
          1 CTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTTTTCT

                                *     *                     
       8111 CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT

       8157 CTTCATTTAG


Statistics
Matches: 39,  Mismatches: 5, Indels: 4
        0.81            0.10        0.08

Matches are distributed among these distances:
  50    2  0.05
  51   36  0.92
  52    1  0.03

ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39


Consensus pattern (51 bp):   
CTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTTTTCT

Found at i:9899 original size:22 final size:22

Alignment explanation


    Indices: 9873--9917  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9863 AATGATTACA

                                  
       9873 TATGCCTTCTATTTTACTAAGG
          1 TATGCCTTCTATTTTACTAAGG

                              *   
       9895 TATGCCTTCTATTTTACTCAGG
          1 TATGCCTTCTATTTTACTAAGG

             
       9917 T
          1 T

       9918 TACATAATCC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47


Consensus pattern (22 bp):   
TATGCCTTCTATTTTACTAAGG
Done.