Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004827.1 Corchorus capsularis cultivar CVL-1 contig04845, 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, 634

Length: 1057
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31


Found at i:284 original size:33 final size:30

Alignment explanation


    Indices: 247--326  Score: 81
    Period size: 30  Copynumber: 2.6  Consensus size: 30

        237 TTGTATAGTA

                  *                           
        247 TTTGGACGTTTTGCCCCATGAACTTAATTCAA-T
          1 TTTGGATGTTTTGCCCCAT-AA---AATTCAATT

                   *    *         *       
        280 TTTGGATATTTTACCCCATAAATTTCAATT
          1 TTTGGATGTTTTGCCCCATAAAATTCAATT

                             
        310 TTTGGATGTTTTGCCCC
          1 TTTGGATGTTTTGCCCC

        327 TTCAGATTTA


Statistics
Matches: 40,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  29    6  0.15
  30   16  0.40
  32    2  0.05
  33   16  0.40

ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44


Consensus pattern (30 bp):   
TTTGGATGTTTTGCCCCATAAAATTCAATT

Found at i:575 original size:29 final size:30

Alignment explanation


    Indices: 543--609  Score: 109
    Period size: 31  Copynumber: 2.2  Consensus size: 30

        533 ATGCAATTTG

                                          
        543 GGATATAACGTTAC-AAAACAAGCAATTAA
          1 GGATATAACGTTACAAAAACAAGCAATTAA

                                 *         
        572 GGATATAACGTTACGAAAAACGAGCAATTAA
          1 GGATATAACGTTAC-AAAAACAAGCAATTAA

                   
        603 GGATATA
          1 GGATATA

        610 GCCCGTTAGA


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  31   21  0.60

ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21


Consensus pattern (30 bp):   
GGATATAACGTTACAAAAACAAGCAATTAA

Found at i:774 original size:31 final size:31

Alignment explanation


    Indices: 739--819  Score: 126
    Period size: 31  Copynumber: 2.6  Consensus size: 31

        729 CCCTAACTGA

                                    *    * 
        739 TTATATCCTTAATTGCTTGAAATCGAAAATG
          1 TTATATCCTTAATTGCTTGAAATCAAAAACG

                             *             
        770 TTATATCCTTAATTGCTCGAAATCAAAAACG
          1 TTATATCCTTAATTGCTTGAAATCAAAAACG

                  *            
        801 TTATATTCTTAATTGCTTG
          1 TTATATCCTTAATTGCTTG

        820 TTTTGTAACG


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   45  1.00

ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41


Consensus pattern (31 bp):   
TTATATCCTTAATTGCTTGAAATCAAAAACG

Found at i:916 original size:3 final size:3

Alignment explanation


    Indices: 908--966  Score: 118
    Period size: 3  Copynumber: 19.7  Consensus size: 3

        898 AAAGCAACCC

                                                                           
        908 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                          
        956 ATA ATA ATA AT
          1 ATA ATA ATA AT

        967 CCTAATTTCA


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   56  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Done.