Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005493.1 Corchorus capsularis cultivar CVL-1 contig05511, 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: 8885
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33


Found at i:3195 original size:21 final size:21

Alignment explanation


    Indices: 3171--3449  Score: 264
    Period size: 21  Copynumber: 13.2  Consensus size: 21

       3161 CAAAAATAAC

                                 
       3171 TTGGGGTTTGACTATCAAAAT
          1 TTGGGGTTTGACTATCAAAAT

                                  
       3192 TTGGGGTTTGACTAT-AAAATT
          1 TTGGGGTTTGACTATCAAAA-T

                 *     *       ** 
       3213 TTGGGATTTGAGTAT-AAGCTT
          1 TTGGGGTTTGACTATCAA-AAT

                                 
       3234 TTGGGGTTTGACTATCAAAAT
          1 TTGGGGTTTGACTATCAAAAT

                 *              * 
       3255 TTGGGTTTTGACTA-CATAACT
          1 TTGGGGTTTGACTATCA-AAAT

               *   *              
       3276 TTGTGG-ATGAACTATCAAAAT
          1 TTGGGGTTTG-ACTATCAAAAT

            *    *     *        * 
       3297 GTGGGATTTGAATAT-ATAATT
          1 TTGGGGTTTGACTATCA-AAAT

                               ** 
       3318 TTGGGGTTTGACTAT-AAGCTT
          1 TTGGGGTTTGACTATCAA-AAT

                                 
       3339 TTGGGGTTTGACTATCAAAAT
          1 TTGGGGTTTGACTATCAAAAT

                 *             * 
       3360 TTGGGTTTTGACTATCAAACT
          1 TTGGGGTTTGACTATCAAAAT

                *              * 
       3381 TTGGAGTTTGACTATCAAATT
          1 TTGGGGTTTGACTATCAAAAT

                     *       * * 
       3402 TTGGGGTTTAACTATCAGACT
          1 TTGGGGTTTGACTATCAAAAT

                                 
       3423 TTGGGGTTTGACTATCAAAAT
          1 TTGGGGTTTGACTATCAAAAT

                  
       3444 GTTGGG
          1 -TTGGG

       3450 CTTACATAGA


Statistics
Matches: 209,  Mismatches: 38, Indels: 21
        0.78            0.14        0.08

Matches are distributed among these distances:
  20   10  0.05
  21  186  0.89
  22   13  0.06

ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40


Consensus pattern (21 bp):   
TTGGGGTTTGACTATCAAAAT

Found at i:3567 original size:60 final size:56

Alignment explanation


    Indices: 3500--3651  Score: 154
    Period size: 53  Copynumber: 2.8  Consensus size: 56

       3490 AGGGTTTAGT

                                    *                         *         
       3500 GTCAAACCACAAAAAGTATTAAATTATTGTACATCCATGGTCAAACCCCACAATTCAATA
          1 GTCAAACCACAAAAA--A--AAATCATTGTACATCCATGGTCAAACCCCAAAATTCAATA

                             *         *  *                         
       3560 GTCAAACCAC---AAAACATCATTGTATATGCATGGTCAAACCCCAAAATTCAATA
          1 GTCAAACCACAAAAAAAAATCATTGTACATCCATGGTCAAACCCCAAAATTCAATA

                             *            *   *       
       3613 GTCAAACCAC---AAAATATCATTGTACATGCATAGTCAAAC
          1 GTCAAACCACAAAAAAAAATCATTGTACATCCATGGTCAAAC

       3652 TCAAAAAGAC


Statistics
Matches: 84,  Mismatches: 8, Indels: 7
        0.85            0.08        0.07

Matches are distributed among these distances:
  53   71  0.85
  55    1  0.01
  57    2  0.02
  60   10  0.12

ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24


Consensus pattern (56 bp):   
GTCAAACCACAAAAAAAAATCATTGTACATCCATGGTCAAACCCCAAAATTCAATA

Found at i:3608 original size:53 final size:53

Alignment explanation


    Indices: 3525--3651  Score: 209
    Period size: 53  Copynumber: 2.4  Consensus size: 53

       3515 GTATTAAATT

                     *               *                           
       3525 ATTGTACATCCATGGTCAAACCCCACAATTCAATAGTCAAACCACAAAACATC
          1 ATTGTACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATC

                  *                                          *   
       3578 ATTGTATATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAATATC
          1 ATTGTACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATC

                         *       
       3631 ATTGTACATGCATAGTCAAAC
          1 ATTGTACATGCATGGTCAAAC

       3652 TCAAAAAGAC


Statistics
Matches: 68,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  53   68  1.00

ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24


Consensus pattern (53 bp):   
ATTGTACATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATC

Found at i:3670 original size:53 final size:53

Alignment explanation


    Indices: 3525--3670  Score: 157
    Period size: 53  Copynumber: 2.8  Consensus size: 53

       3515 GTATTAAATT

                     *   *         * *  **                       
       3525 ATTGTACATCCATGGTCAAACCCCACAATTCAATAGTCAAACCACAAAACATC
          1 ATTGTACATGCATAGTCAAACCCAAAAAGACAATAGTCAAACCACAAAACATC

                  *      *         *    **                   *   
       3578 ATTGTATATGCATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAATATC
          1 ATTGTACATGCATAGTCAAACCCAAAAAGACAATAGTCAAACCACAAAACATC

                                 *         *  *     
       3631 ATTGTACATGCATAGTCAAACTCAAAAAGACGATGGTCAA
          1 ATTGTACATGCATAGTCAAACCCAAAAAGACAATAGTCAA

       3671 CCCCCAACGT


Statistics
Matches: 81,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  53   81  1.00

ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23


Consensus pattern (53 bp):   
ATTGTACATGCATAGTCAAACCCAAAAAGACAATAGTCAAACCACAAAACATC
Done.