Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012638.1 Corchorus olitorius cultivar O-4 contig12671, 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: 10080
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:2811 original size:90 final size:90

Alignment explanation


    Indices: 2652--2816  Score: 267
    Period size: 90  Copynumber: 1.8  Consensus size: 90

       2642 AATGTAGGCT

                *                                      *               *     
       2652 CTGCGAGAAGATGGGGCATACCAAGGACCGATGTTATGAAATCCTTGGATATCCTGCGGTGTGGC
          1 CTGCCAGAAGATGGGGCATACCAAGGACCGATGTTATGAAATCATTGGATATCCTGCGGGGTGGC

                                     
       2717 GTAAAAACCTGTCAAGATATGGCCA
         66 GTAAAAACCTGTCAAGATATGGCCA

                                **     *                                    *
       2742 CTGCCAGAAGATGGGGCATATTAAGGATCGATGTTATGAAATCATTGGATATCCTGCGGGGTGGT
          1 CTGCCAGAAGATGGGGCATACCAAGGACCGATGTTATGAAATCATTGGATATCCTGCGGGGTGGC

                      
       2807 GTAAAAACCT
         66 GTAAAAACCT

       2817 ACGGAATAAG


Statistics
Matches: 68,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  90   68  1.00

ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24


Consensus pattern (90 bp):   
CTGCCAGAAGATGGGGCATACCAAGGACCGATGTTATGAAATCATTGGATATCCTGCGGGGTGGC
GTAAAAACCTGTCAAGATATGGCCA

Found at i:2969 original size:15 final size:15

Alignment explanation


    Indices: 2948--2998  Score: 57
    Period size: 15  Copynumber: 3.4  Consensus size: 15

       2938 ATCAAATCAA

                           
       2948 CAAATATTACCGCAG
          1 CAAATATTACCGCAG

            *       ** *   
       2963 GAAATATTGTCACAG
          1 CAAATATTACCGCAG

            *              
       2978 TAAATATTACCGCAG
          1 CAAATATTACCGCAG

                  
       2993 CAAATA
          1 CAAATA

       2999 CTGCTGCAGA


Statistics
Matches: 27,  Mismatches: 9, Indels: 0
        0.75            0.25        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.43, C:0.20, G:0.14, T:0.24


Consensus pattern (15 bp):   
CAAATATTACCGCAG

Found at i:6535 original size:17 final size:15

Alignment explanation


    Indices: 6513--6546  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 15

       6503 CTTCGTCTTC

                             
       6513 TTCTTCTTCTACCACAA
          1 TTCTTCTTC-ACCA-AA

                           
       6530 TTCTTCTTCACCAAA
          1 TTCTTCTTCACCAAA

              
       6545 TT
          1 TT

       6547 TTACATAAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    4  0.24
  16    4  0.24
  17    9  0.53

ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44


Consensus pattern (15 bp):   
TTCTTCTTCACCAAA
Done.