Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016853.1 Corchorus olitorius cultivar O-4 contig16886, 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: 5980
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:4080 original size:51 final size:54

Alignment explanation


    Indices: 4004--4156  Score: 197
    Period size: 60  Copynumber: 2.8  Consensus size: 54

       3994 GCAACTAATA

                 *          *                                      
       4004 AAAACTTTTCTGCAAACGAC-AACTAATGTTAAATTGATGGAGTTC-T-A-AATG
          1 AAAACATTT-TGCAAATGACAAACTAATGTTAAATTGATGGAGTTCATAACAATG

                                                                        
       4055 AAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTCTAAATGCAACTAATG
          1 AAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTC---AT--AAC-AATG

                                                      
       4115 AAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
          1 AAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

       4157 AATTGCTAAA


Statistics
Matches: 90,  Mismatches: 2, Indels: 11
        0.87            0.02        0.11

Matches are distributed among these distances:
  50    9  0.10
  51   33  0.37
  55    1  0.01
  58    1  0.01
  60   46  0.51

ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30


Consensus pattern (54 bp):   
AAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTCATAACAATG

Found at i:4387 original size:29 final size:28

Alignment explanation


    Indices: 4355--4518  Score: 116
    Period size: 29  Copynumber: 5.7  Consensus size: 28

       4345 AAATGAACTT

                   *        *            
       4355 AAAATGATCAAAATGCTCCTGAATATGCA
          1 AAAATGACCAAAATGCCCCTGAATATG-A

                      *             *   
       4384 AAAATGACCATAATGCCCCTGAATGTGA
          1 AAAATGACCAAAATGCCCCTGAATATGA

                         *          ** * * 
       4412 AAAATGACCAAAAAGCCCCCTGGGTTTTTAA
          1 AAAATGACCAAAATG-CCCCT--GAATATGA

                    *               *   
       4443 AAAATGACTAAAATGCCCCTGAATGTG-
          1 AAAATGACCAAAATGCCCCTGAATATGA

            *       *               * *   
       4470 CAAATGACTAAAATGCCCCCTAGATTTTG-
          1 AAAATGACCAAAATG-CCCCT-GAATATGA

                     *          
       4499 AAAATGACCGAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       4519 AGTTGATCCC


Statistics
Matches: 108,  Mismatches: 22, Indels: 11
        0.77            0.16        0.08

Matches are distributed among these distances:
  27   14  0.13
  28   27  0.25
  29   45  0.42
  30    5  0.05
  31   17  0.16

ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGAATATGA

Found at i:4501 original size:88 final size:86

Alignment explanation


    Indices: 4355--4517  Score: 195
    Period size: 88  Copynumber: 1.9  Consensus size: 86

       4345 AAATGAACTT

                            *                      *                         
       4355 AAAATGATCAAAATGCTCCTGAATATGCAAAAATGACCATAATGCCCCTGAATGTGAAAAATGAC
          1 AAAATGATCAAAATGCCCCTGAATATGC-AAAATGACCAAAATGCCCCTGAATGTG-AAAATGAC

                                   
       4420 CAAAAAGCCCCCTGGGTTTTTAA
         64 CAAAAAGCCCCCTGGGTTTTTAA

                                     *           *               * *         
       4443 AAAATGA-CTAAAATGCCCCTGAATGTGC-AAATGACTAAAATGCCCCCTAGATTTTGAAAATGA
          1 AAAATGATC-AAAATGCCCCTGAATATGCAAAATGACCAAAATG-CCCCT-GAATGTGAAAATGA

              *   *     
       4506 CCGAAATGCCCC
         63 CCAAAAAGCCCC

       4518 TAGTTGATCC


Statistics
Matches: 64,  Mismatches: 8, Indels: 7
        0.81            0.10        0.09

Matches are distributed among these distances:
  86   12  0.19
  87   23  0.36
  88   29  0.45

ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22


Consensus pattern (86 bp):   
AAAATGATCAAAATGCCCCTGAATATGCAAAATGACCAAAATGCCCCTGAATGTGAAAATGACCA
AAAAGCCCCCTGGGTTTTTAA
Done.