Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007609.1 Corchorus olitorius cultivar O-4 contig07635, 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: 1943
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39


Found at i:405 original size:31 final size:30

Alignment explanation


    Indices: 386--446  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 30

        376 AAAACAGATT

                                            
        386 AAGCATTAAATTAAACAAA-TAATTAAAATGA
          1 AAGCATTAAATTAAACAAATTAA--AAAATGA

                *                    *    
        417 AAGCCTTAAATTAAACAAATTAAAAGATGA
          1 AAGCATTAAATTAAACAAATTAAAAAATGA

        447 TAGACCCTTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  30    6  0.22
  31   18  0.67
  32    3  0.11

ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25


Consensus pattern (30 bp):   
AAGCATTAAATTAAACAAATTAAAAAATGA

Found at i:1223 original size:15 final size:15

Alignment explanation


    Indices: 1203--1249  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       1193 ATTTTTCTCA

                           
       1203 GGTCATTCGGGTTTC
          1 GGTCATTCGGGTTTC

                           *
       1218 GGTCA-TCAGGGTTTG
          1 GGTCATTC-GGGTTTC

               *        *  
       1233 GGTTATTCGGGTCTC
          1 GGTCATTCGGGTTTC

              
       1248 GG
          1 GG

       1250 GTCTACCAGG


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  14    2  0.08
  15   22  0.85
  16    2  0.08

ACGTcount: A:0.09, C:0.17, G:0.38, T:0.36


Consensus pattern (15 bp):   
GGTCATTCGGGTTTC

Found at i:1241 original size:30 final size:32

Alignment explanation


    Indices: 1207--1268  Score: 83
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1197 TTCTCAGGTC

                    *         *             
       1207 ATTCGGGTTTC-GGTC-ATCAGGGTTTGGGTT
          1 ATTCGGGTCTCGGGTCTACCAGGGTTTGGGTT

                                   *        
       1237 ATTCGGGTCTCGGGTCTACCAGGTTTTGGGTT
          1 ATTCGGGTCTCGGGTCTACCAGGGTTTGGGTT

       1269 GGGCGGGTTC


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  30   10  0.37
  31    4  0.15
  32   13  0.48

ACGTcount: A:0.10, C:0.16, G:0.35, T:0.39


Consensus pattern (32 bp):   
ATTCGGGTCTCGGGTCTACCAGGGTTTGGGTT

Found at i:1539 original size:42 final size:42

Alignment explanation


    Indices: 1493--1577  Score: 134
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1483 TTTGTATTAA

                                              *       
       1493 TTTTGAATATTAAATACATAAATAATTATCAGGTGGGGTATG
          1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG

                                 * *     *            
       1535 TTTTGAATATTAAATACATAATTTATTATTAGGTAGGGTATG
          1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG

             
       1577 T
          1 T

       1578 GTCAACATTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42


Consensus pattern (42 bp):   
TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG
Done.