Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005158.1 Corchorus capsularis cultivar CVL-1 contig05176, 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: 10277
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:1325 original size:31 final size:29

Alignment explanation


    Indices: 1261--1325  Score: 69
    Period size: 31  Copynumber: 2.2  Consensus size: 29

       1251 TATGGGATTT

                                        *
       1261 ATTTGTCCCCAAAAAAAGTAAAGGGGCCG
          1 ATTTGTCCCCAAAAAAAGTAAAGGGGCCA

                                  *       * 
       1290 ATTTGT-CCCAAAATGAATAGTTAAGGGGCTA
          1 ATTTGTCCCCAAAA--AA-AGTAAAGGGGCCA

                 
       1321 ATTTG
          1 ATTTG

       1326 GGTATTAAGC


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  28    7  0.23
  29    6  0.20
  30    2  0.07
  31   15  0.50

ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26


Consensus pattern (29 bp):   
ATTTGTCCCCAAAAAAAGTAAAGGGGCCA

Found at i:3186 original size:15 final size:15

Alignment explanation


    Indices: 3130--3192  Score: 51
    Period size: 15  Copynumber: 4.3  Consensus size: 15

       3120 AAATAATATT

                           
       3130 TTAATTATTACATTA
          1 TTAATTATTACATTA

                  *      * 
       3145 TT--TTTTTA-ATCA
          1 TTAATTATTACATTA

             *       *     
       3157 TAAATTATTCCATTA
          1 TTAATTATTACATTA

                      *    
       3172 TTAATTATTAGATTA
          1 TTAATTATTACATTA

                  
       3187 TATAAT
          1 T-TAAT

       3193 ACGTACGAAT


Statistics
Matches: 35,  Mismatches: 9, Indels: 7
        0.69            0.18        0.14

Matches are distributed among these distances:
  12    4  0.11
  13    5  0.14
  14    4  0.11
  15   18  0.51
  16    4  0.11

ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54


Consensus pattern (15 bp):   
TTAATTATTACATTA

Found at i:3255 original size:31 final size:31

Alignment explanation


    Indices: 3220--3285  Score: 98
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       3210 AACTTTATGT

                     *             *        
       3220 TTTCCAATTGTACCCTTATTTT-TAAAATATA
          1 TTTCCAATTATACCCTT-TTTTAAAAAATATA

                                           
       3251 TTTCCAATTATACCCTTTTTTAAAAAATATA
          1 TTTCCAATTATACCCTTTTTTAAAAAATATA

                
       3282 TTTC
          1 TTTC

       3286 TAAATTGCCA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  30    4  0.12
  31   28  0.88

ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48


Consensus pattern (31 bp):   
TTTCCAATTATACCCTTTTTTAAAAAATATA

Found at i:3318 original size:181 final size:181

Alignment explanation


    Indices: 3005--3385  Score: 683
    Period size: 181  Copynumber: 2.1  Consensus size: 181

       2995 ATCTATACTA

                     *                              *                      * 
       3005 TATATAA-AAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCATTATTTTTAAAATCT
          1 TATATAATACGTACGAATAAGGGGAAACTTTATGTTTTCCAATTGTACCATTATTTTTAAAATAT

                *                              *                             
       3069 ATTTTCAATTATACCCTTTTTTAAAAAATATATTTTTAAATTACCATTACTAAATAATATTTTAA
         66 ATTTCCAATTATACCCTTTTTTAAAAAATATATTTCTAAATTACCATTACTAAATAATATTTTAA

                                                               
       3134 TTATTACATTATTTTTTTAATCATAAATTATTCCATTATTAATTATTAGAT
        131 TTATTACATTATTTTTTTAATCATAAATTATTCCATTATTAATTATTAGAT

                                                             *               
       3185 TATATAATACGTACGAATAAGGGGAAACTTTATGTTTTCCAATTGTACCCTTATTTTTAAAATAT
          1 TATATAATACGTACGAATAAGGGGAAACTTTATGTTTTCCAATTGTACCATTATTTTTAAAATAT

                                                      *                      
       3250 ATTTCCAATTATACCCTTTTTTAAAAAATATATTTCTAAATTGCCATTACTAAATAATATTTTAA
         66 ATTTCCAATTATACCCTTTTTTAAAAAATATATTTCTAAATTACCATTACTAAATAATATTTTAA

                 *                                             
       3315 TTATTCCATTATTTTTTTAATCATAAATTATTCCATTATTAATTATTAGAT
        131 TTATTACATTATTTTTTTAATCATAAATTATTCCATTATTAATTATTAGAT

                                
       3366 TATATAATACGTACGAATAA
          1 TATATAATACGTACGAATAA

       3386 ACTATTTAAT


Statistics
Matches: 192,  Mismatches: 8, Indels: 1
        0.96            0.04        0.00

Matches are distributed among these distances:
 180    7  0.04
 181  185  0.96

ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45


Consensus pattern (181 bp):   
TATATAATACGTACGAATAAGGGGAAACTTTATGTTTTCCAATTGTACCATTATTTTTAAAATAT
ATTTCCAATTATACCCTTTTTTAAAAAATATATTTCTAAATTACCATTACTAAATAATATTTTAA
TTATTACATTATTTTTTTAATCATAAATTATTCCATTATTAATTATTAGAT
Done.