Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015471.1 Corchorus olitorius cultivar O-4 contig15504, 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: 9589
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Found at i:330 original size:60 final size:61

Alignment explanation


    Indices: 237--397  Score: 236
    Period size: 60  Copynumber: 2.7  Consensus size: 61

        227 GCTAATTGCT

                            *   **                                       
        237 CAAATAAGGGCCTAATGTTTATCAAAATGTTCAAATAAGAGAC-CGATCTTTTAATTTGAC
          1 CAAATAAGGGCCTAATATTTGCCAAAATGTTCAAATAAGAGACTCGATCTTTTAATTTGAC

                      *                              *                 * 
        297 CAAATAAGGGTCTAATATTTGCCAAAATGTTCAAATAAG-GGCTCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAATATTTGCCAAAATGTTCAAATAAGAGACTCGATCTTTTAATTTGAC

                           *             *           
        357 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGAG
          1 CAAATAAGGGCCTAATATTTGCCAAAATGTTCAAATAAGAG

        398 CCTGACATCA


Statistics
Matches: 90,  Mismatches: 9, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  59    2  0.02
  60   87  0.97
  61    1  0.01

ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29


Consensus pattern (61 bp):   
CAAATAAGGGCCTAATATTTGCCAAAATGTTCAAATAAGAGACTCGATCTTTTAATTTGAC

Found at i:395 original size:31 final size:31

Alignment explanation


    Indices: 297--405  Score: 82
    Period size: 31  Copynumber: 3.6  Consensus size: 31

        287 TTAATTTGAC

                      *    *             * 
        297 CAAATAAGGGTCTAATATTTGCCAAAATGTT
          1 CAAATAAGGGCCTAACATTTGCCAAAATGCT

                         * *       *  **     
        328 CAAATAAGGGCTCGATC-TTT--TAATTTGGC-
          1 CAAATAAGGGC-CTAACATTTGCCAAAAT-GCT

                                           
        357 CAAATAAGGGCCTAACATTTGCCAAAATGCT
          1 CAAATAAGGGCCTAACATTTGCCAAAATGCT

                    *    *    
        388 CAAATAAGAGCCTGACAT
          1 CAAATAAGGGCCTAACAT

        406 CAAAAATTCT


Statistics
Matches: 57,  Mismatches: 15, Indels: 12
        0.68            0.18        0.14

Matches are distributed among these distances:
  28    3  0.05
  29   17  0.30
  30    3  0.05
  31   32  0.56
  32    2  0.04

ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28


Consensus pattern (31 bp):   
CAAATAAGGGCCTAACATTTGCCAAAATGCT

Found at i:482 original size:31 final size:31

Alignment explanation


    Indices: 439--542  Score: 97
    Period size: 31  Copynumber: 3.4  Consensus size: 31

        429 AACTGATGTC

                *                          
        439 AGGCTCTTATTTGACCATTTTCGATAACGTT
          1 AGGCCCTTATTTGACCATTTTCGATAACGTT

                         *   **        *   *
        470 AGGCCCTTATTTGGCCAAATT--A-AAAGATC
          1 AGGCCCTTATTTGACCATTTTCGATAACG-TT

            *             **               
        499 GGGCCCTTATTTGAGTATTTTCGATAACGTT
          1 AGGCCCTTATTTGACCATTTTCGATAACGTT

                         
        530 AGGCCCTTATTTG
          1 AGGCCCTTATTTG

        543 GCCAAATTAA


Statistics
Matches: 54,  Mismatches: 15, Indels: 8
        0.70            0.19        0.10

Matches are distributed among these distances:
  28    3  0.06
  29   17  0.31
  31   31  0.57
  32    3  0.06

ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38


Consensus pattern (31 bp):   
AGGCCCTTATTTGACCATTTTCGATAACGTT

Found at i:591 original size:60 final size:60

Alignment explanation


    Indices: 444--579  Score: 227
    Period size: 60  Copynumber: 2.3  Consensus size: 60

        434 ATGTCAGGCT

                     *                                             * *  
        444 CTTATTTGACCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCC
          1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC

                      *                                                 
        504 CTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC
          1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC

            *               
        564 TTTATTTGAGCATTTT
          1 CTTATTTGAGCATTTT

        580 GTCAAACGTT


Statistics
Matches: 70,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  60   70  1.00

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Consensus pattern (60 bp):   
CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC
Done.