Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010424.1 Corchorus olitorius cultivar O-4 contig10456, 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: 2943
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40


Found at i:1114 original size:5 final size:5

Alignment explanation


    Indices: 1104--1166  Score: 54
    Period size: 5  Copynumber: 14.4  Consensus size: 5

       1094 TATATAGTAG

                                                                       
       1104 TAAGA TAAGA TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA T-AG- TAAGA
          1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA

                           *          
       1148 T-AG- TAA-A TAAAA TAAGA TA
          1 TAAGA TAAGA TAAGA TAAGA TA

       1167 TATCTATACT


Statistics
Matches: 48,  Mismatches: 1, Indels: 18
        0.72            0.01        0.27

Matches are distributed among these distances:
   3    4  0.08
   4   18  0.38
   5   26  0.54

ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24


Consensus pattern (5 bp):   
TAAGA

Found at i:1123 original size:21 final size:20

Alignment explanation


    Indices: 1109--1157  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       1099 AGTAGTAAGA

                                 
       1109 TAAGATAAGATAGTAAGATAG
          1 TAAGATAAGATAGT-AGATAG

                                 
       1130 TAAGATAAGATAGTAAGATAG
          1 TAAGATAAGATAGT-AGATAG

                    
       1151 TAA-ATAA
          1 TAAGATAA

       1158 AATAAGATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  20    4  0.14
  21   24  0.86

ACGTcount: A:0.55, C:0.00, G:0.20, T:0.24


Consensus pattern (20 bp):   
TAAGATAAGATAGTAGATAG

Found at i:1127 original size:8 final size:8

Alignment explanation


    Indices: 1101--1153  Score: 67
    Period size: 8  Copynumber: 6.8  Consensus size: 8

       1091 TTTTATATAG

                    
       1101 TAGTAAGA
          1 TAGTAAGA

                      
       1109 TAAGATAAGA
          1 T-AG-TAAGA

                    
       1119 TAGTAAGA
          1 TAGTAAGA

                    
       1127 TAGTAAG-
          1 TAGTAAGA

                    
       1134 -A-TAAGA
          1 TAGTAAGA

                    
       1140 TAGTAAGA
          1 TAGTAAGA

                  
       1148 TAGTAA
          1 TAGTAA

       1154 ATAAAATAAG


Statistics
Matches: 40,  Mismatches: 0, Indels: 10
        0.80            0.00        0.20

Matches are distributed among these distances:
   5    4  0.10
   6    1  0.03
   7    1  0.03
   8   24  0.60
   9    4  0.10
  10    6  0.15

ACGTcount: A:0.53, C:0.00, G:0.23, T:0.25


Consensus pattern (8 bp):   
TAGTAAGA

Found at i:1127 original size:13 final size:13

Alignment explanation


    Indices: 1101--1149  Score: 66
    Period size: 13  Copynumber: 3.8  Consensus size: 13

       1091 TTTTATATAG

                         
       1101 TAGTAAGATAAGA
          1 TAGTAAGATAAGA

                           
       1114 TAAG-ATAG-TAAGA
          1 T-AGTA-AGATAAGA

                         
       1127 TAGTAAGATAAGA
          1 TAGTAAGATAAGA

                      
       1140 TAGTAAGATA
          1 TAGTAAGATA

       1150 GTAAATAAAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
  12    4  0.12
  13   24  0.75
  14    4  0.12

ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24


Consensus pattern (13 bp):   
TAGTAAGATAAGA
Done.