Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000984.1 Corchorus olitorius cultivar O-4 contig00984, 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, 628

Length: 1047
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34


Found at i:198 original size:10 final size:10

Alignment explanation


    Indices: 178--208  Score: 53
    Period size: 10  Copynumber: 3.0  Consensus size: 10

        168 GCAAAATGAA

                       
        178 CCCGAAACCCG
          1 CCCG-AACCCG

                      
        189 CCCGAACCCG
          1 CCCGAACCCG

                      
        199 CCCGAACCCG
          1 CCCGAACCCG

        209 AAATTACCCG


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   16  0.80
  11    4  0.20

ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00


Consensus pattern (10 bp):   
CCCGAACCCG

Found at i:236 original size:17 final size:17

Alignment explanation


    Indices: 188--260  Score: 78
    Period size: 17  Copynumber: 4.4  Consensus size: 17

        178 CCCGAAACCC

                             
        188 GCCCGAACCCG-CCCGA
          1 GCCCGAACCCGACCCGA

            *       ***      
        204 ACCCGAA-ATTACCCGA
          1 GCCCGAACCCGACCCGA

                             
        220 GCCCGAACCCGACCCGA
          1 GCCCGAACCCGACCCGA

                  * *        
        237 GCCCGAGCTCGACCCGA
          1 GCCCGAACCCGACCCGA

                   
        254 GCCCGAA
          1 GCCCGAA

        261 TCTGAAATAA


Statistics
Matches: 44,  Mismatches: 11, Indels: 3
        0.76            0.19        0.05

Matches are distributed among these distances:
  16   17  0.39
  17   27  0.61

ACGTcount: A:0.25, C:0.48, G:0.23, T:0.04


Consensus pattern (17 bp):   
GCCCGAACCCGACCCGA

Found at i:241 original size:11 final size:11

Alignment explanation


    Indices: 214--259  Score: 58
    Period size: 11  Copynumber: 4.1  Consensus size: 11

        204 ACCCGAAATT

                       
        214 ACCCGAGCCCG
          1 ACCCGAGCCCG

                        
        225 AACCCGA-CCCG
          1 -ACCCGAGCCCG

                     *  
        236 AGCCCGAGCTCG
          1 A-CCCGAGCCCG

                       
        248 ACCCGAGCCCG
          1 ACCCGAGCCCG

             
        259 A
          1 A

        260 ATCTGAAATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  10    1  0.03
  11   19  0.63
  12   10  0.33

ACGTcount: A:0.22, C:0.50, G:0.26, T:0.02


Consensus pattern (11 bp):   
ACCCGAGCCCG

Found at i:485 original size:12 final size:12

Alignment explanation


    Indices: 468--492  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        458 TTTAAAACTA

                        
        468 AAAAGTACCCTT
          1 AAAAGTACCCTT

                        
        480 AAAAGTACCCTT
          1 AAAAGTACCCTT

             
        492 A
          1 A

        493 TAACTAATTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24


Consensus pattern (12 bp):   
AAAAGTACCCTT

Found at i:762 original size:31 final size:32

Alignment explanation


    Indices: 690--762  Score: 80
    Period size: 31  Copynumber: 2.3  Consensus size: 32

        680 GTCTATCAGC

                                       *     
        690 TTTTAATTTTGTTTAATTTAAGACTTTCATTTT
          1 TTTTAA-TTTGTTTAATTTAAGACTTTAATTTT

            **                               
        723 AATT-ATTTGTTTAATTTAATG-C-TTAATTTT
          1 TTTTAATTTGTTTAATTTAA-GACTTTAATTTT

                      
        753 TTTTAATTTG
          1 TTTTAATTTG

        763 CAATAATTTA


Statistics
Matches: 33,  Mismatches: 5, Indels: 6
        0.75            0.11        0.14

Matches are distributed among these distances:
  30    9  0.27
  31   20  0.61
  32    2  0.06
  33    2  0.06

ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63


Consensus pattern (32 bp):   
TTTTAATTTGTTTAATTTAAGACTTTAATTTT
Done.