Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002284.1 Corchorus capsularis cultivar CVL-1 contig02290, 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, 766

Length: 1277
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41


Found at i:1125 original size:18 final size:18

Alignment explanation


    Indices: 1102--1136  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1092 ATCATTATTG

                              
       1102 ATTATTATATGATAATTA
          1 ATTATTATATGATAATTA

                             
       1120 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

       1137 CATTTTTTGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51


Consensus pattern (18 bp):   
ATTATTATATGATAATTA

Found at i:1212 original size:49 final size:49

Alignment explanation


    Indices: 1120--1245  Score: 243
    Period size: 49  Copynumber: 2.6  Consensus size: 49

       1110 ATGATAATTA

                                                              
       1120 ATTATTATATGATAATTCATTTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCA-TTTTTGAAATTTAGAATTTCATCATTATTG

                                                             
       1170 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                       
       1219 ATTATTATATGATAATTCATTTTTGAA
          1 ATTATTATATGATAATTCATTTTTGAA

       1246 TGATGATTTT


Statistics
Matches: 76,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  49   57  0.75
  50   19  0.25

ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52


Consensus pattern (49 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

Found at i:1219 original size:24 final size:24

Alignment explanation


    Indices: 1143--1219  Score: 79
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       1133 AATTCATTTT

                                    
       1143 TTGAAATTTAGAATTTCATCATTA
          1 TTGAAATTTAGAATTTCATCATTA

                 *           *          
       1167 TTGATTATTATATGATAATTCAT--TT-
          1 TTGA-AATT-TA-GA-ATTTCATCATTA

                                    
       1192 TTGAAATTTAGAATTTCATCATTA
          1 TTGAAATTTAGAATTTCATCATTA

                
       1216 TTGA
          1 TTGA

       1220 TTATTATATG


Statistics
Matches: 42,  Mismatches: 4, Indels: 14
        0.70            0.07        0.23

Matches are distributed among these distances:
  21    6  0.14
  22    2  0.05
  23    4  0.10
  24   11  0.26
  25    7  0.17
  26    4  0.10
  27    2  0.05
  28    6  0.14

ACGTcount: A:0.35, C:0.06, G:0.09, T:0.49


Consensus pattern (24 bp):   
TTGAAATTTAGAATTTCATCATTA

Found at i:1238 original size:25 final size:25

Alignment explanation


    Indices: 1161--1244  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       1151 TAGAATTTCA

                                     
       1161 TCATTATTGATTATTATATGATAAT
          1 TCATTATTGATTATTATATGATAAT

                 *     *            * 
       1186 TCATTTTTGA-AATT-TA-GA-ATTT
          1 TCATTATTGATTATTATATGATA-AT

                                       
       1208 CATCATTATTGATTATTATATGATAAT
          1 --TCATTATTGATTATTATATGATAAT

                 *    
       1235 TCATTTTTGA
          1 TCATTATTGA

       1245 ATGATGATTT


Statistics
Matches: 45,  Mismatches: 7, Indels: 14
        0.68            0.11        0.21

Matches are distributed among these distances:
  21    1  0.02
  22    3  0.07
  23    2  0.04
  24   12  0.27
  25   21  0.47
  26    2  0.04
  27    3  0.07
  28    1  0.02

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52


Consensus pattern (25 bp):   
TCATTATTGATTATTATATGATAAT
Done.