Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007816.1 Corchorus olitorius cultivar O-4 contig07843, 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, 885

Length: 1475
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:566 original size:20 final size:20

Alignment explanation


    Indices: 541--578  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        531 CTAAACCCTT

                  *             
        541 TTTTTTGTATATTTTTTCAA
          1 TTTTTTCTATATTTTTTCAA

                    *         
        561 TTTTTTCTCTATTTTTTC
          1 TTTTTTCTATATTTTTTC

        579 GGGTTGCTAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74


Consensus pattern (20 bp):   
TTTTTTCTATATTTTTTCAA

Found at i:1219 original size:10 final size:10

Alignment explanation


    Indices: 1197--1240  Score: 52
    Period size: 10  Copynumber: 4.3  Consensus size: 10

       1187 TTTTATATAT

                       
       1197 ATATAGTATAG
          1 ATATAG-ATAG

                      
       1208 ATATAGATAG
          1 ATATAGATAG

               * *    
       1218 ATAGATATAG
          1 ATATAGATAG

                 *    
       1228 ATATAAATAG
          1 ATATAGATAG

               
       1238 ATA
          1 ATA

       1241 GATTATAAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  10   23  0.79
  11    6  0.21

ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32


Consensus pattern (10 bp):   
ATATAGATAG

Found at i:1223 original size:14 final size:15

Alignment explanation


    Indices: 1193--1230  Score: 60
    Period size: 14  Copynumber: 2.6  Consensus size: 15

       1183 GTACTTTTAT

                 *         
       1193 ATATATATAGTATAG
          1 ATATAGATAGTATAG

                           
       1208 ATATAGATAG-ATAG
          1 ATATAGATAGTATAG

                     
       1222 ATATAGATA
          1 ATATAGATA

       1231 TAAATAGATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   13  0.59
  15    9  0.41

ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34


Consensus pattern (15 bp):   
ATATAGATAGTATAG

Found at i:1228 original size:20 final size:20

Alignment explanation


    Indices: 1199--1243  Score: 74
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       1189 TTATATATAT

                           *    
       1199 ATAG-TATAGATATAGATAG
          1 ATAGATATAGATATAAATAG

                                
       1218 ATAGATATAGATATAAATAG
          1 ATAGATATAGATATAAATAG

                  
       1238 ATAGAT
          1 ATAGAT

       1244 TATAAAACAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  19    4  0.17
  20   20  0.83

ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31


Consensus pattern (20 bp):   
ATAGATATAGATATAAATAG
Done.