Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011244.1 Corchorus capsularis cultivar CVL-1 contig11265, 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: 13381
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2612 original size:28 final size:28

Alignment explanation


    Indices: 2577--2645  Score: 129
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       2567 GCTAGATTTG

                                        
       2577 GGGCCAAACGTTTCAATTACGCCAAAAA
          1 GGGCCAAACGTTTCAATTACGCCAAAAA

                                        
       2605 GGGCCAAACGTTTCAATTACGCCAAAAA
          1 GGGCCAAACGTTTCAATTACGCCAAAAA

               *         
       2633 GGGTCAAACGTTT
          1 GGGCCAAACGTTT

       2646 TCGGGGTTGC


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  28   40  1.00

ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20


Consensus pattern (28 bp):   
GGGCCAAACGTTTCAATTACGCCAAAAA

Found at i:2872 original size:6 final size:7

Alignment explanation


    Indices: 2854--2878  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       2844 CTTCTTCATT

                   
       2854 CTTTTTC
          1 CTTTTTC

                   
       2861 CTTTTTC
          1 CTTTTTC

                   
       2868 CTTTTTC
          1 CTTTTTC

                
       2875 CTTT
          1 CTTT

       2879 CTTTCTTCCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72


Consensus pattern (7 bp):   
CTTTTTC

Found at i:4989 original size:45 final size:45

Alignment explanation


    Indices: 4925--5014  Score: 180
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       4915 AAAATTCCAC

                                                         
       4925 TTAGATGTATTGAAGTTCAAAATAATCAATAATTGGTGGCATAAG
          1 TTAGATGTATTGAAGTTCAAAATAATCAATAATTGGTGGCATAAG

                                                         
       4970 TTAGATGTATTGAAGTTCAAAATAATCAATAATTGGTGGCATAAG
          1 TTAGATGTATTGAAGTTCAAAATAATCAATAATTGGTGGCATAAG

       5015 GGAAAGTGAT


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   45  1.00

ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33


Consensus pattern (45 bp):   
TTAGATGTATTGAAGTTCAAAATAATCAATAATTGGTGGCATAAG

Found at i:8313 original size:26 final size:25

Alignment explanation


    Indices: 8269--8318  Score: 64
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       8259 CAGGCATTTT

                 *                    
       8269 TTTTTTAAATTAATAATTAGTTATTC
          1 TTTTTAAAATTAATAATTA-TTATTC

                        * *         
       8295 TTTTTAAAATTAGTTATTATTATT
          1 TTTTTAAAATTAATAATTATTATT

       8319 TTATATGATT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  25    5  0.24
  26   16  0.76

ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60


Consensus pattern (25 bp):   
TTTTTAAAATTAATAATTATTATTC

Found at i:9358 original size:3 final size:3

Alignment explanation


    Indices: 9352--9445  Score: 188
    Period size: 3  Copynumber: 31.3  Consensus size: 3

       9342 TTTGGTCCAG

                                                                           
       9352 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
          1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA

                                                                         
       9400 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
          1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A

       9446 TAATAATAAT


Statistics
Matches: 91,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   91  1.00

ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00


Consensus pattern (3 bp):   
ACA

Done.