Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007733.1 Corchorus capsularis cultivar CVL-1 contig07754, 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: 14641
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:906 original size:20 final size:21

Alignment explanation


    Indices: 881--919  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        871 ACTAGCGCTG

                                 
        881 GGCG-CCCATGTGGTTTGCTT
          1 GGCGCCCCATGTGGTTTGCTT

                        *      
        901 GGCGCCCCATGTTGTTTGC
          1 GGCGCCCCATGTGGTTTGC

        920 CTCGCAACCC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    4  0.24
  21   13  0.76

ACGTcount: A:0.05, C:0.28, G:0.33, T:0.33


Consensus pattern (21 bp):   
GGCGCCCCATGTGGTTTGCTT

Found at i:4556 original size:27 final size:27

Alignment explanation


    Indices: 4499--4566  Score: 77
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       4489 ATCCTAGGGA

                                   *   
       4499 ACTAACTTTGAATGGGAAACTGTTCTT
          1 ACTAACTTTGAATGGGAAACTGTACTT

                *                       
       4526 ACTAGCTTTGAAT-GGAGAACTG-ACTT
          1 ACTAACTTTGAATGGGA-AACTGTACTT

                     *     
       4552 GACTAACTTGGAATG
          1 -ACTAACTTTGAATG

       4567 AGAGTCTGAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 5
        0.79            0.09        0.12

Matches are distributed among these distances:
  26    6  0.18
  27   28  0.82

ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32


Consensus pattern (27 bp):   
ACTAACTTTGAATGGGAAACTGTACTT

Found at i:7732 original size:18 final size:18

Alignment explanation


    Indices: 7709--7743  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       7699 TTCTTGAATT

                               
       7709 TCTTC-AATAGTCTTCAAA
          1 TCTTCAAATA-TCTTCAAA

                             
       7727 TCTTCAAATATCTTCAA
          1 TCTTCAAATATCTTCAA

       7744 TCACGAACTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   12  0.75
  19    4  0.25

ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40


Consensus pattern (18 bp):   
TCTTCAAATATCTTCAAA

Found at i:7924 original size:22 final size:23

Alignment explanation


    Indices: 7898--7951  Score: 58
    Period size: 22  Copynumber: 2.4  Consensus size: 23

       7888 CAAAATAGGG

                             *      
       7898 TAAAAACATATATAAAAGTAG-TA
          1 TAAAAACATATA-AAAAATAGCTA

                 **                
       7921 -AAAAGTATATAAAAAATAGCTA
          1 TAAAAACATATAAAAAATAGCTA

                     
       7943 TAAAAACAT
          1 TAAAAACAT

       7952 GCCTAATTTG


Statistics
Matches: 24,  Mismatches: 5, Indels: 4
        0.73            0.15        0.12

Matches are distributed among these distances:
  21    7  0.29
  22   11  0.46
  23    6  0.25

ACGTcount: A:0.63, C:0.06, G:0.07, T:0.24


Consensus pattern (23 bp):   
TAAAAACATATAAAAAATAGCTA
Done.