Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007633.1 Corchorus capsularis cultivar CVL-1 contig07654, 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: 4960
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36


Found at i:1296 original size:26 final size:26

Alignment explanation


    Indices: 1267--1318  Score: 95
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1257 CTTTACTTTG

                                      
       1267 GCCTTTTAGATGCAACCAAATGGGGA
          1 GCCTTTTAGATGCAACCAAATGGGGA

                            *         
       1293 GCCTTTTAGATGCAACTAAATGGGGA
          1 GCCTTTTAGATGCAACCAAATGGGGA

       1319 AATGTAACTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25


Consensus pattern (26 bp):   
GCCTTTTAGATGCAACCAAATGGGGA

Found at i:3348 original size:9 final size:9

Alignment explanation


    Indices: 3334--3362  Score: 58
    Period size: 9  Copynumber: 3.2  Consensus size: 9

       3324 TCTATGATGA

                     
       3334 GGGCACTTG
          1 GGGCACTTG

                     
       3343 GGGCACTTG
          1 GGGCACTTG

                     
       3352 GGGCACTTG
          1 GGGCACTTG

              
       3361 GG
          1 GG

       3363 CTTTGATGAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.10, C:0.21, G:0.48, T:0.21


Consensus pattern (9 bp):   
GGGCACTTG

Found at i:4877 original size:21 final size:21

Alignment explanation


    Indices: 4853--4919  Score: 64
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       4843 TTTTACTGAA

                                 
       4853 TTACTGATTACCATTACTATT
          1 TTACTGATTACCATTACTATT

                       * *        
       4874 TTACTGATTATTCTTTACT-TT
          1 TTACTGATTA-CCATTACTATT

            *          *      *   
       4895 GTACTGATTACTAGTTACCATT
          1 TTACTGATTACCA-TTACTATT

               
       4917 TTA
          1 TTA

       4920 TTCTTTGCTG


Statistics
Matches: 35,  Mismatches: 8, Indels: 5
        0.73            0.17        0.10

Matches are distributed among these distances:
  21   25  0.71
  22   10  0.29

ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51


Consensus pattern (21 bp):   
TTACTGATTACCATTACTATT
Done.