Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011643.1 Corchorus capsularis cultivar CVL-1 contig11664, 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: 20020
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:6368 original size:14 final size:14

Alignment explanation


    Indices: 6349--6382  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       6339 TACTATTTAT

                          
       6349 TAATTATTATAATA
          1 TAATTATTATAATA

                      *   
       6363 TAATTATTATTATA
          1 TAATTATTATAATA

            *     
       6377 GAATTA
          1 TAATTA

       6383 AATAAAGAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (14 bp):   
TAATTATTATAATA

Found at i:9392 original size:3 final size:3

Alignment explanation


    Indices: 9386--9417  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       9376 AAAACCTTTA

                                                      
       9386 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       9418 AGACTGTCGC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:9466 original size:24 final size:23

Alignment explanation


    Indices: 9426--9478  Score: 72
    Period size: 24  Copynumber: 2.3  Consensus size: 23

       9416 AAAGACTGTC

                                *  
       9426 GCGCGA-CCGGCGCCATGGCTAG
          1 GCGCGACCCGGCGCCATGGCCAG

                       *            
       9448 GTCGCGACCCGTCGCCATGGCCAG
          1 G-CGCGACCCGGCGCCATGGCCAG

                   
       9472 GCGCGAC
          1 GCGCGAC

       9479 GTGGGTCGAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  22    1  0.04
  23   11  0.41
  24   15  0.56

ACGTcount: A:0.13, C:0.40, G:0.38, T:0.09


Consensus pattern (23 bp):   
GCGCGACCCGGCGCCATGGCCAG

Found at i:10086 original size:44 final size:44

Alignment explanation


    Indices: 10028--10113  Score: 172
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      10018 CTACAATGTT

                                                        
      10028 AAGAAGACACTAATTCAAGTACGTAAAGAATGTCTCAACCAATG
          1 AAGAAGACACTAATTCAAGTACGTAAAGAATGTCTCAACCAATG

                                                      
      10072 AAGAAGACACTAATTCAAGTACGTAAAGAATGTCTCAACCAA
          1 AAGAAGACACTAATTCAAGTACGTAAAGAATGTCTCAACCAA

      10114 ACGAGGATTG


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   42  1.00

ACGTcount: A:0.47, C:0.19, G:0.15, T:0.20


Consensus pattern (44 bp):   
AAGAAGACACTAATTCAAGTACGTAAAGAATGTCTCAACCAATG

Found at i:11362 original size:2 final size:2

Alignment explanation


    Indices: 11357--11435  Score: 61
    Period size: 2  Copynumber: 43.5  Consensus size: 2

      11347 ACTATTAAAC

                                                          *                 
      11357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC A- ACT GAT A- AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT

                                                                          
      11398 AT -T A- AT AT AT AT A- AT -T AT -T AT -T AT AT AT A- AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
      11433 AT A
          1 AT A

      11436 AATTTTTTAT


Statistics
Matches: 65,  Mismatches: 0, Indels: 24
        0.73            0.00        0.27

Matches are distributed among these distances:
   1   10  0.15
   2   53  0.82
   3    1  0.02
   4    1  0.02

ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:11428 original size:25 final size:26

Alignment explanation


    Indices: 11368--11436  Score: 79
    Period size: 25  Copynumber: 2.7  Consensus size: 26

      11358 TATATATATA

                                       
      11368 TATATATATATATATATAACAACTGAT
          1 TATATATA-ATATATATAACAACTGAT

            *                 **   *  
      11395 AATAT-TAATATATATAATTA-TTAT
          1 TATATATAATATATATAACAACTGAT

                              
      11419 TATATATAATATATATAA
          1 TATATATAATATATATAA

      11437 ATTTTTTATT


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  24    7  0.19
  25   23  0.64
  26    2  0.06
  27    4  0.11

ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45


Consensus pattern (26 bp):   
TATATATAATATATATAACAACTGAT

Found at i:12291 original size:21 final size:21

Alignment explanation


    Indices: 12266--12307  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      12256 AATCTAAAAG

                     *           
      12266 TTACATTAATCTACTCCTAAA
          1 TTACATTAAACTACTCCTAAA

                                 
      12287 TTACATTAAACTACTCCTAAA
          1 TTACATTAAACTACTCCTAAA

      12308 AGATAAACAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36


Consensus pattern (21 bp):   
TTACATTAAACTACTCCTAAA
Done.