Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009840.1 Corchorus capsularis cultivar CVL-1 contig09861, 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: 37759
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:773 original size:12 final size:12

Alignment explanation


    Indices: 758--782  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        748 AAATAATTAC

                        
        758 TAAAAAATATAT
          1 TAAAAAATATAT

                        
        770 TAAAAAATATAT
          1 TAAAAAATATAT

             
        782 T
          1 T

        783 CAATATAGGT


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:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (12 bp):   
TAAAAAATATAT

Found at i:5209 original size:11 final size:11

Alignment explanation


    Indices: 5193--5218  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       5183 AACAATTTTA

                       
       5193 TCGCAAGTATG
          1 TCGCAAGTATG

                       
       5204 TCGCAAGTATG
          1 TCGCAAGTATG

                
       5215 TCGC
          1 TCGC

       5219 TTATGCTGTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27


Consensus pattern (11 bp):   
TCGCAAGTATG

Found at i:12907 original size:13 final size:13

Alignment explanation


    Indices: 12889--12913  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      12879 CTGTAGTTTA

                         
      12889 TTATAATTGATAT
          1 TTATAATTGATAT

                        
      12902 TTATAATTGATA
          1 TTATAATTGATA

      12914 ATGCATGTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52


Consensus pattern (13 bp):   
TTATAATTGATAT

Found at i:24945 original size:3 final size:3

Alignment explanation


    Indices: 24937--24961  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      24927 GATCATTCGG

                                             
      24937 CTC CTC CTC CTC CTC CTC CTC CTC C
          1 CTC CTC CTC CTC CTC CTC CTC CTC C

      24962 GCCTGCGGCG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32


Consensus pattern (3 bp):   
CTC

Found at i:28490 original size:19 final size:20

Alignment explanation


    Indices: 28464--28510  Score: 94
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      28454 AAGCAATATT

                                
      28464 GTTTTTTTTTTTCATAACAA
          1 GTTTTTTTTTTTCATAACAA

                                
      28484 GTTTTTTTTTTTCATAACAA
          1 GTTTTTTTTTTTCATAACAA

                   
      28504 GTTTTTT
          1 GTTTTTT

      28511 ATAATAAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   27  1.00

ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64


Consensus pattern (20 bp):   
GTTTTTTTTTTTCATAACAA

Found at i:34857 original size:13 final size:13

Alignment explanation


    Indices: 34839--34867  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      34829 TGAAACGGGG

                         
      34839 TTTTTTTT-AATT
          1 TTTTTTTTAAATT

                         
      34851 TTTTTTTTAAATT
          1 TTTTTTTTAAATT

                
      34864 TTTT
          1 TTTT

      34868 CCTTGTTCCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    8  0.50
  13    8  0.50

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (13 bp):   
TTTTTTTTAAATT

Found at i:35112 original size:2 final size:2

Alignment explanation


    Indices: 35105--35163  Score: 63
    Period size: 2  Copynumber: 31.5  Consensus size: 2

      35095 ATATTATTAG

                                                                          
      35105 TA TA TA TA TA TA TA TA TA TA -A TA -A TA -A TA -A TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                     *     *        *      
      35143 TA TA TA CA TA CA TA TA CA TA T
          1 TA TA TA TA TA TA TA TA TA TA T

      35164 GTGTGTCTTT


Statistics
Matches: 47,  Mismatches: 6, Indels: 8
        0.77            0.10        0.13

Matches are distributed among these distances:
   1    4  0.09
   2   43  0.91

ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42


Consensus pattern (2 bp):   
TA

Done.