Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015660.1 Corchorus capsularis cultivar CVL-1 contig15681, 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: 8617
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38


Found at i:4864 original size:21 final size:21

Alignment explanation


    Indices: 4840--4879  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4830 TTGCTTGCTT

                  *              
       4840 AGATGGCTGGTGCTATTGAAA
          1 AGATGGATGGTGCTATTGAAA

                          *    
       4861 AGATGGATGGTGCTTTTGA
          1 AGATGGATGGTGCTATTGA

       4880 TGTGACGGAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.25, C:0.07, G:0.35, T:0.33


Consensus pattern (21 bp):   
AGATGGATGGTGCTATTGAAA

Found at i:8157 original size:21 final size:21

Alignment explanation


    Indices: 8131--8171  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8121 CGTCATCTCC

                    *            
       8131 ATCTCTCCGATTCTTTCTACT
          1 ATCTCTCCAATTCTTTCTACT

                                
       8152 ATCTCTCCAATTCTTTCTAC
          1 ATCTCTCCAATTCTTTCTAC

       8172 CACCTTCAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.17, C:0.34, G:0.02, T:0.46


Consensus pattern (21 bp):   
ATCTCTCCAATTCTTTCTACT

Found at i:8297 original size:56 final size:56

Alignment explanation


    Indices: 8234--8352  Score: 193
    Period size: 56  Copynumber: 2.1  Consensus size: 56

       8224 TATATATTCA

                                     *             *                
       8234 TTCTTCAAAATTAATCACTTTATATTGGTAAAAAAGACATAATAACTAATCAATTT
          1 TTCTTCAAAATTAATCACTTTATATCGGTAAAAAAGACAGAATAACTAATCAATTT

                                                 *       *          
       8290 TTCTTCAAAATTAATCACTTTATATCGGTAAAAAAGATAGAATAATTAATCAATTT
          1 TTCTTCAAAATTAATCACTTTATATCGGTAAAAAAGACAGAATAACTAATCAATTT

              *    
       8346 TTATTCA
          1 TTCTTCA

       8353 CCAAATTTTT


Statistics
Matches: 58,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  56   58  1.00

ACGTcount: A:0.44, C:0.12, G:0.06, T:0.39


Consensus pattern (56 bp):   
TTCTTCAAAATTAATCACTTTATATCGGTAAAAAAGACAGAATAACTAATCAATTT

Found at i:8599 original size:1 final size:1

Alignment explanation


    Indices: 8593--8617  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       8583 ATGATTGATG

                                     
       8593 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

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


Consensus pattern (1 bp):   
A

Done.