Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005962.1 Corchorus olitorius cultivar O-4 contig05987, 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, 688

Length: 1147
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40


Found at i:56 original size:22 final size:23

Alignment explanation


    Indices: 6--56  Score: 61
    Period size: 22  Copynumber: 2.3  Consensus size: 23

          1 CCGCA

                        *           
          6 CTATGAAAATTTTGATAACCACAC
          1 CTATG-AAATTTCGATAACCACAC

                               *   
         30 C-ATGAAATTTCGATAACCTC-C
          1 CTATGAAATTTCGATAACCACAC

                  
         51 CTATGA
          1 CTATGA

         57 GAATGAAACG


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  21    2  0.08
  22   18  0.75
  23    3  0.12
  24    1  0.04

ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29


Consensus pattern (23 bp):   
CTATGAAATTTCGATAACCACAC

Found at i:117 original size:22 final size:23

Alignment explanation


    Indices: 85--145  Score: 63
    Period size: 22  Copynumber: 2.7  Consensus size: 23

         75 CTCTCTATGT

                            *       
         85 ATTTTCGATAACCTCTGC-ATAAA
          1 ATTTTC-ATAACCTCTCCTATAAA

                       *           
        108 ATTTTCATAACTTC-CCTATAAA
          1 ATTTTCATAACCTCTCCTATAAA

                 **         
        130 ATTTTGTTAACCTCTC
          1 ATTTTCATAACCTCTC

        146 TAGGAAATTT


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  21    1  0.03
  22   23  0.74
  23    7  0.23

ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41


Consensus pattern (23 bp):   
ATTTTCATAACCTCTCCTATAAA

Found at i:213 original size:22 final size:22

Alignment explanation


    Indices: 188--271  Score: 91
    Period size: 22  Copynumber: 3.8  Consensus size: 22

        178 CCTCCCTCCC

                        *        *
        188 TATGAAATTTTGGTAACCTCTG
          1 TATGAAATTTTGATAACCTCTA

                                   
        210 TATGAAATTTTGATAA-CTAC-A
          1 TATGAAATTTTGATAACCT-CTA

                   *         *     
        231 CTATGAAGTTTTGATAATCTCTA
          1 -TATGAAATTTTGATAACCTCTA

                        *     
        254 TATGAAATTTTGGTAACC
          1 TATGAAATTTTGATAACC

        272 ACACTACAAA


Statistics
Matches: 52,  Mismatches: 6, Indels: 8
        0.79            0.09        0.12

Matches are distributed among these distances:
  21    2  0.04
  22   47  0.90
  23    3  0.06

ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTCTA

Found at i:310 original size:44 final size:44

Alignment explanation


    Indices: 192--311  Score: 141
    Period size: 44  Copynumber: 2.7  Consensus size: 44

        182 CCTCCCTATG

                    *   *    *            *    *      **
        192 AAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACACTATG
          1 AAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTACA

              *                                         
        236 AAGTTTTGATAATCTCTATATGAAATTTTGGTAACCACACTACA
          1 AAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTACA

                           * *    *         
        280 AAATTTTGATAATCTTTCTATGTAATTTTGGT
          1 AAATTTTGATAATCTCTATATGAAATTTTGGT

        312 TTGATTATCA


Statistics
Matches: 64,  Mismatches: 12, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  44   64  1.00

ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42


Consensus pattern (44 bp):   
AAATTTTGATAATCTCTATATGAAATTTTGGTAACCACACTACA

Found at i:759 original size:6 final size:6

Alignment explanation


    Indices: 748--789  Score: 68
    Period size: 6  Copynumber: 7.0  Consensus size: 6

        738 TCAGCTACCA

                                                             
        748 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTTT GTTTTT -TTTTT
          1 GTTTTT GTTTTT GTTTTT GTTTTT G-TTTTT GTTTTT GTTTTT

        790 ACGAAAGCTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
   5    5  0.14
   6   24  0.69
   7    6  0.17

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (6 bp):   
GTTTTT

Done.