Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023466.1 Corchorus olitorius cultivar O-4 contig23499, 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: 3003
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33


Found at i:126 original size:11 final size:11

Alignment explanation


    Indices: 112--145  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

        102 TAAAGGAAAA

                       
        112 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        123 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
        134 AGCTAGGAAGG
          1 AGCTAGGAAGG

             
        145 A
          1 A

        146 CCCTACTCCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09


Consensus pattern (11 bp):   
AGCTAGGAAGG

Found at i:553 original size:21 final size:21

Alignment explanation


    Indices: 515--673  Score: 223
    Period size: 21  Copynumber: 7.6  Consensus size: 21

        505 CTTAGGCAAT

                    *    *       
        515 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAACTTGGAACCTTC

             *  *   *            
        536 TTCAGTGATCTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
        557 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
        578 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
        599 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *             
        620 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                    *             
        641 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                        
        662 TCCAATGAACTT
          1 TCCAATGAACTT

        674 CTAGCTTCTT


Statistics
Matches: 128,  Mismatches: 9, Indels: 2
        0.92            0.06        0.01

Matches are distributed among these distances:
  20    3  0.02
  21  125  0.98

ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30


Consensus pattern (21 bp):   
TCCAATGAACTTGGAACCTTC

Found at i:1359 original size:66 final size:66

Alignment explanation


    Indices: 1250--1376  Score: 166
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1240 AGTAATTCTG

                 *    *                                                      
       1250 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTATTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTATTTTAGATGTTGTTAGTGATGATACT

             
       1315 A
         66 A

                                  **             * *      *       *       
       1316 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTATTTTAGATGTTGTTAGTGATGA

       1377 AACAAATTTT


Statistics
Matches: 52,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  66   51  0.98
  67    1  0.02

ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTATTTTAGATGTTGTTAGTGATGATACT
A

Found at i:1365 original size:33 final size:33

Alignment explanation


    Indices: 1262--1376  Score: 124
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       1252 CCTGATTTGA

                      **                      
       1262 GTGTTGTTTGCAATGACA-TGAAATCTATTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATCTATTTTAG

            *       *       *      *   *    *
       1295 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAATCTATTTTAG

                                    * *      
       1328 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
          1 GTGTTGTTTGTGATGACACTAAATCTATTTTAG

                            
       1361 GTGTTGTTTGTGATGA
          1 GTGTTGTTTGTGATGA

       1377 AACAAATTTT


Statistics
Matches: 65,  Mismatches: 16, Indels: 2
        0.78            0.19        0.02

Matches are distributed among these distances:
  33   64  0.98
  34    1  0.02

ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44


Consensus pattern (33 bp):   
GTGTTGTTTGTGATGACACTAAATCTATTTTAG

Found at i:1388 original size:33 final size:33

Alignment explanation


    Indices: 1323--1417  Score: 104
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       1313 CTAAACCTAA

                *                *            
       1323 TTTAAGTGTTGTTTGTGATGACACTAAA-TTTGT
          1 TTTAGGTGTTGTTTGTGATGAAAC-AAATTTTGT

                                             
       1356 TTTAGGTGTTGTTTGTGATGAAACAAATTTTGT
          1 TTTAGGTGTTGTTTGTGATGAAACAAATTTTGT

                     * **                 
       1389 TTT-GGATGCTAATTGTGATGAAAACAAAT
          1 TTTAGG-TGTTGTTTGTGATG-AAACAAAT

       1418 CTGTTTTGGT


Statistics
Matches: 54,  Mismatches: 5, Indels: 5
        0.84            0.08        0.08

Matches are distributed among these distances:
  32    5  0.09
  33   41  0.76
  34    8  0.15

ACGTcount: A:0.28, C:0.05, G:0.22, T:0.44


Consensus pattern (33 bp):   
TTTAGGTGTTGTTTGTGATGAAACAAATTTTGT
Done.