Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019561.1 Corchorus olitorius cultivar O-4 contig19594, 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: 6327
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:853 original size:27 final size:27

Alignment explanation


    Indices: 778--860  Score: 112
    Period size: 30  Copynumber: 3.0  Consensus size: 27

        768 ATACCACTAA

                         *           * 
        778 TAATAATTATTATTATAATAATAAGCT
          1 TAATAATTATTATAATAATAATAAGTT

                      *                   
        805 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATA--A-TAATAATAAGTT

                                      
        835 TAATAATTATTATAATAATAATAAGT
          1 TAATAATTATTATAATAATAATAAGT

        861 CTAAATTAAC


Statistics
Matches: 49,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
  27   23  0.47
  28    1  0.02
  29    1  0.02
  30   24  0.49

ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41


Consensus pattern (27 bp):   
TAATAATTATTATAATAATAATAAGTT

Found at i:1157 original size:6 final size:6

Alignment explanation


    Indices: 1139--1191  Score: 65
    Period size: 6  Copynumber: 8.8  Consensus size: 6

       1129 GTTTAGACTT

                                                            *        
       1139 ATATAG TATATAG ATATAG ATATAG ATATAG --ATAG TATATGG ATATAG
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG -ATATAG ATATAG

                 
       1187 ATATA
          1 ATATA

       1192 TAAAATTTAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
   4    4  0.10
   6   28  0.68
   7    9  0.22

ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36


Consensus pattern (6 bp):   
ATATAG

Found at i:1178 original size:23 final size:22

Alignment explanation


    Indices: 1148--1191  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       1138 TATATAGTAT

                                  
       1148 ATAGATATAGATATAGATATAG
          1 ATAGATATAGATATAGATATAG

                     *            
       1170 ATAGTATATGGATATAGATATA
          1 ATAG-ATATAGATATAGATATA

       1192 TAAAATTTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34


Consensus pattern (22 bp):   
ATAGATATAGATATAGATATAG

Found at i:1183 original size:17 final size:17

Alignment explanation


    Indices: 1138--1193  Score: 62
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       1128 AGTTTAGACT

                              
       1138 TATATAGTATATAGATA-
          1 TATATAG-ATATAGATAG

                               
       1155 TAGATATAGATATAGATAG
          1 T--ATATAGATATAGATAG

                 *           
       1174 TATATGGATATAGATA-
          1 TATATAGATATAGATAG

                
       1190 TATA
          1 TATA

       1194 AAATTTATTT


Statistics
Matches: 35,  Mismatches: 1, Indels: 7
        0.81            0.02        0.16

Matches are distributed among these distances:
  16    4  0.11
  17   15  0.43
  18    9  0.26
  19    7  0.20

ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38


Consensus pattern (17 bp):   
TATATAGATATAGATAG

Found at i:4208 original size:14 final size:15

Alignment explanation


    Indices: 4165--4215  Score: 50
    Period size: 14  Copynumber: 3.3  Consensus size: 15

       4155 CTCCCTAAAA

                         * 
       4165 TTCTCCTTCAAATGT
          1 TTCTCCTTCAAATCT

                *     *      
       4180 TCCTTTCCTTGAAAT-T
          1 T--TCTCCTTCAAATCT

                           
       4196 TTCTCCTTCAAATCT
          1 TTCTCCTTCAAATCT

                 
       4211 TTCTC
          1 TTCTC

       4216 AACATTTTCC


Statistics
Matches: 29,  Mismatches: 4, Indels: 6
        0.74            0.10        0.15

Matches are distributed among these distances:
  14   10  0.34
  15    7  0.24
  16    2  0.07
  17   10  0.34

ACGTcount: A:0.18, C:0.29, G:0.04, T:0.49


Consensus pattern (15 bp):   
TTCTCCTTCAAATCT
Done.