Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014306.1 Corchorus capsularis cultivar CVL-1 contig14327, 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: 8588
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:2343 original size:145 final size:145

Alignment explanation


    Indices: 2080--2368  Score: 578
    Period size: 145  Copynumber: 2.0  Consensus size: 145

       2070 CTAATTGCTA

                                                                             
       2080 AATTGAGGGTTAATTAGTCAATGAACTAATTGAGCTTAAACTATATGATTAAAATGCAACAATAC
          1 AATTGAGGGTTAATTAGTCAATGAACTAATTGAGCTTAAACTATATGATTAAAATGCAACAATAC

                                                                             
       2145 TAAGCTAAATGAAGATGCAACTAAATTACTAAATGAAAATATGCAAAAATGCCAAGGTGCATATT
         66 TAAGCTAAATGAAGATGCAACTAAATTACTAAATGAAAATATGCAAAAATGCCAAGGTGCATATT

                           
       2210 GAGATTTTTTCCAAC
        131 GAGATTTTTTCCAAC

                                                                             
       2225 AATTGAGGGTTAATTAGTCAATGAACTAATTGAGCTTAAACTATATGATTAAAATGCAACAATAC
          1 AATTGAGGGTTAATTAGTCAATGAACTAATTGAGCTTAAACTATATGATTAAAATGCAACAATAC

                                                                             
       2290 TAAGCTAAATGAAGATGCAACTAAATTACTAAATGAAAATATGCAAAAATGCCAAGGTGCATATT
         66 TAAGCTAAATGAAGATGCAACTAAATTACTAAATGAAAATATGCAAAAATGCCAAGGTGCATATT

                          
       2355 GAGATTTTTTCCAA
        131 GAGATTTTTTCCAA

       2369 TGCCATCTAT


Statistics
Matches: 144,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 145  144  1.00

ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29


Consensus pattern (145 bp):   
AATTGAGGGTTAATTAGTCAATGAACTAATTGAGCTTAAACTATATGATTAAAATGCAACAATAC
TAAGCTAAATGAAGATGCAACTAAATTACTAAATGAAAATATGCAAAAATGCCAAGGTGCATATT
GAGATTTTTTCCAAC

Found at i:2496 original size:28 final size:28

Alignment explanation


    Indices: 2423--2494  Score: 92
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       2413 GTAGATTAAG

                                        
       2423 AATGACCAAAATACCCCTAAAATGCAAA
          1 AATGACCAAAATACCCCTAAAATGCAAA

                       *       *    **  
       2451 AATGACCAAAAAACCCCT-GAATGTGAA
          1 AATGACCAAAATACCCCTAAAATGCAAA

                        *    
       2478 AATGACCAAAATGCCCC
          1 AATGACCAAAATACCCC

       2495 CTAGATGACC


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  27   21  0.55
  28   17  0.45

ACGTcount: A:0.49, C:0.26, G:0.11, T:0.14


Consensus pattern (28 bp):   
AATGACCAAAATACCCCTAAAATGCAAA

Found at i:6941 original size:28 final size:28

Alignment explanation


    Indices: 6904--6958  Score: 110
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6894 TCTTTTGAAA

                                        
       6904 AATAAACTCATTTTCAACAAAGCCCTTG
          1 AATAAACTCATTTTCAACAAAGCCCTTG

                                       
       6932 AATAAACTCATTTTCAACAAAGCCCTT
          1 AATAAACTCATTTTCAACAAAGCCCTT

       6959 CAACCATTCA


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

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.40, C:0.25, G:0.05, T:0.29


Consensus pattern (28 bp):   
AATAAACTCATTTTCAACAAAGCCCTTG
Done.