Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000301.1 Corchorus capsularis cultivar CVL-1 contig00301, 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, 822

Length: 1370
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42

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


Found at i:1189 original size:23 final size:23

Alignment explanation


    Indices: 1157--1200  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1147 ATTTAGGTTT

                                   
       1157 TTATAGTTTTACTCAATTAAAAA
          1 TTATAGTTTTACTCAATTAAAAA

                 *     * *       
       1180 TTATATTTTTATTTAATTAAA
          1 TTATAGTTTTACTCAATTAAA

       1201 TATAATATCT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52


Consensus pattern (23 bp):   
TTATAGTTTTACTCAATTAAAAA

Found at i:1208 original size:23 final size:23

Alignment explanation


    Indices: 1171--1214  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1161 AGTTTTACTC

                      *    *       
       1171 AATTAAAAATTATATTTTTATTT
          1 AATTAAAAATAATATCTTTATTT

                   *             
       1194 AATTAAATATAATATCTTTAT
          1 AATTAAAAATAATATCTTTAT

       1215 AATTATTTTA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52


Consensus pattern (23 bp):   
AATTAAAAATAATATCTTTATTT

Found at i:1306 original size:78 final size:69

Alignment explanation


    Indices: 1155--1369  Score: 259
    Period size: 78  Copynumber: 3.0  Consensus size: 69

       1145 TTATTTAGGT

                              *        *         *         *                 
       1155 TTTTATAGTTTTACTCAATTAAAAATTATATTTTTATTTAATTAAATATAATATCTTTATAATTA
          1 TTTTATA-TTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA

                 
       1220 TTTTA
         65 TTTTA

                                     *                                       
       1225 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAGTTA
          1 TTTTA-TATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCTTTATA---A

                         
       1290 TTATATTTTACCA
         62 -T-TATTTT---A

                                        *                          *      *  
       1303 TTTTAGTATTTTACTCAACTAAAAATTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
          1 TTTTA-TATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA

              
       1368 TT
         65 TT

       1370 A


Statistics
Matches: 126,  Mismatches: 10, Indels: 15
        0.83            0.07        0.10

Matches are distributed among these distances:
  70   53  0.42
  71    2  0.02
  73    5  0.04
  74    1  0.01
  75    7  0.06
  78   58  0.46

ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51


Consensus pattern (69 bp):   
TTTTATATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCTTTATAATTAT
TTTA

Done.