Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007093.1 Corchorus olitorius cultivar O-4 contig07118, 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, 918

Length: 1531
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37


Found at i:717 original size:15 final size:15

Alignment explanation


    Indices: 697--737  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        687 GTTCTTTCCT

                           
        697 TTTTTTCTTTTTTCA
          1 TTTTTTCTTTTTTCA

                           
        712 TTTTTTCTTTTTTCA
          1 TTTTTTCTTTTTTCA

                        
        727 TCTTTTT-TTTT
          1 T-TTTTTCTTTT

        738 GTGCACTTGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   20  0.80
  16    5  0.20

ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83


Consensus pattern (15 bp):   
TTTTTTCTTTTTTCA

Found at i:1078 original size:17 final size:16

Alignment explanation


    Indices: 1058--1113  Score: 53
    Period size: 17  Copynumber: 3.4  Consensus size: 16

       1048 GTGATTGATT

                             
       1058 TTTTATTTGATTTTTTG
          1 TTTT-TTTGATTTTTTG

                   *        
       1075 TTTTTTTTA-TTTTTG
          1 TTTTTTTGATTTTTTG

                         *    
       1090 ATTTTTTTTG-TTCTTTG
          1 --TTTTTTTGATTTTTTG

                   
       1107 TTTTTTT
          1 TTTTTTT

       1114 TTTTGGAATT


Statistics
Matches: 33,  Mismatches: 3, Indels: 8
        0.75            0.07        0.18

Matches are distributed among these distances:
  15   13  0.39
  16    4  0.12
  17   16  0.48

ACGTcount: A:0.07, C:0.02, G:0.09, T:0.82


Consensus pattern (16 bp):   
TTTTTTTGATTTTTTG

Found at i:1086 original size:16 final size:16

Alignment explanation


    Indices: 1057--1114  Score: 64
    Period size: 16  Copynumber: 3.5  Consensus size: 16

       1047 TGTGATTGAT

                              
       1057 TTTTTATTTGATTTTTTG
          1 TTTTT-TTT-ATTTTTTG

                            
       1075 TTTTTTTTA-TTTTTG
          1 TTTTTTTTATTTTTTG

                     *  *    
       1090 ATTTTTTTTGTTCTTTG
          1 -TTTTTTTTATTTTTTG

                    
       1107 TTTTTTTT
          1 TTTTTTTT

       1115 TTTGGAATTT


Statistics
Matches: 36,  Mismatches: 2, Indels: 6
        0.82            0.05        0.14

Matches are distributed among these distances:
  15    6  0.17
  16   17  0.47
  17    8  0.22
  18    5  0.14

ACGTcount: A:0.07, C:0.02, G:0.09, T:0.83


Consensus pattern (16 bp):   
TTTTTTTTATTTTTTG

Found at i:1110 original size:23 final size:23

Alignment explanation


    Indices: 1063--1118  Score: 64
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       1053 TGATTTTTTA

                            *      
       1063 TTTGATTTTTTGTTTTTTTTATT
          1 TTTGATTTTTTGTTTTCTTTATT

                                 *  
       1086 TTTGATTTTTT-TTGTTCTTTGTT
          1 TTTGATTTTTTGTT-TTCTTTATT

                        
       1109 TTT--TTTTTTG
          1 TTTGATTTTTTG

       1119 GAATTTCTTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 5
        0.81            0.06        0.14

Matches are distributed among these distances:
  21    6  0.21
  22    2  0.07
  23   21  0.72

ACGTcount: A:0.05, C:0.02, G:0.11, T:0.82


Consensus pattern (23 bp):   
TTTGATTTTTTGTTTTCTTTATT

Found at i:1510 original size:9 final size:8

Alignment explanation


    Indices: 1495--1531  Score: 56
    Period size: 8  Copynumber: 4.5  Consensus size: 8

       1485 AAGTGCCTTA

                    
       1495 ATTTTTTC
          1 ATTTTTTC

                     
       1503 ATTTTTTTC
          1 A-TTTTTTC

                    
       1512 ATTTTTTC
          1 ATTTTTTC

             *      
       1520 AGTTTTTC
          1 ATTTTTTC

                
       1528 ATTT
          1 ATTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
   8   18  0.69
   9    8  0.31

ACGTcount: A:0.14, C:0.11, G:0.03, T:0.73


Consensus pattern (8 bp):   
ATTTTTTC

Done.