Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021402.1 Corchorus olitorius cultivar O-4 contig21435, 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: 7523
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:1679 original size:13 final size:13

Alignment explanation


    Indices: 1663--1716  Score: 58
    Period size: 13  Copynumber: 4.3  Consensus size: 13

       1653 GAATTCAATA

                         
       1663 TCTGAAATCAGAT
          1 TCTGAAATCAGAT

                         
       1676 TCTGAAATCAG-T
          1 TCTGAAATCAGAT

                 ** *    
       1688 T-TGATTTTAGAT
          1 TCTGAAATCAGAT

                       * 
       1700 TCTGAAATCAGTT
          1 TCTGAAATCAGAT

                
       1713 TCTG
          1 TCTG

       1717 TTTTCAGTTC


Statistics
Matches: 32,  Mismatches: 7, Indels: 4
        0.74            0.16        0.09

Matches are distributed among these distances:
  11    6  0.19
  12    4  0.12
  13   22  0.69

ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41


Consensus pattern (13 bp):   
TCTGAAATCAGAT

Found at i:3320 original size:11 final size:11

Alignment explanation


    Indices: 3304--3351  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       3294 GAAGTTCGTG

                       
       3304 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       3315 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       3326 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       3335 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       3345 -TTGAAGA
          1 TTTGAAGA

       3352 TTTATTTCAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA

Found at i:4763 original size:15 final size:15

Alignment explanation


    Indices: 4733--4774  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4723 TTACTTTGTT

                            
       4733 TTGTTTTCTGGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       4749 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       4764 TTGTTTTCTGT
          1 TTGTTTTCTGT

       4775 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA
Done.