Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024007.1 Corchorus olitorius cultivar O-4 contig24040, 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: 5794
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:101 original size:16 final size:15

Alignment explanation


    Indices: 63--104  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

         53 ACAGAGATTG

                   *       
         63 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
         78 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
         93 ACTAGAAAACAA
          1 AC-AGAAAACAA

        105 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:1460 original size:20 final size:20

Alignment explanation


    Indices: 1435--1504  Score: 131
    Period size: 20  Copynumber: 3.5  Consensus size: 20

       1425 CCATGGCTTG

                     *          
       1435 TCTTCAATTAAAGCTCCAAT
          1 TCTTCAATTCAAGCTCCAAT

                                
       1455 TCTTCAATTCAAGCTCCAAT
          1 TCTTCAATTCAAGCTCCAAT

                                
       1475 TCTTCAATTCAAGCTCCAAT
          1 TCTTCAATTCAAGCTCCAAT

                      
       1495 TCTTCAATTC
          1 TCTTCAATTC

       1505 TTCCCCTTGA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  20   49  1.00

ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37


Consensus pattern (20 bp):   
TCTTCAATTCAAGCTCCAAT

Found at i:2518 original size:15 final size:16

Alignment explanation


    Indices: 2488--2520  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       2478 CTCTTGCATG

                  *         
       2488 AAAACACTTCTTTTTT
          1 AAAACAATTCTTTTTT

                            
       2504 AAAACAATT-TTTTTT
          1 AAAACAATTCTTTTTT

              
       2519 AA
          1 AA

       2521 CTACCCTTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48


Consensus pattern (16 bp):   
AAAACAATTCTTTTTT

Found at i:3044 original size:14 final size:15

Alignment explanation


    Indices: 3025--3054  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3015 CAATCAAAGC

                           
       3025 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       3039 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       3054 A
          1 A

       3055 TTAAAAAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:3433 original size:21 final size:21

Alignment explanation


    Indices: 3409--3460  Score: 77
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       3399 GGCACTGAAT

                *             *  
       3409 GGTGATGGCACGGGCATAGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
       3430 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                      
       3451 GGTGGTGGCA
          1 GGTGGTGGCA

       3461 TGGTGAATGG


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Done.