Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015919.1 Corchorus capsularis cultivar CVL-1 contig15940, 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: 17804
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:421 original size:33 final size:33

Alignment explanation


    Indices: 324--428  Score: 113
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        314 TTGAAAAGAG

                    *               *      * 
        324 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

             **                 *    * *      
        357 TAATTT-GAGTGTTGTTTGCAATGACATTAAATC
          1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC

                              *              
        390 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

                  
        423 TGTTTT
          1 TGTTTT

        429 GGATGCTAAT


Statistics
Matches: 57,  Mismatches: 13, Indels: 4
        0.77            0.18        0.05

Matches are distributed among these distances:
  32    1  0.02
  33   55  0.96
  34    1  0.02

ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

Found at i:495 original size:33 final size:32

Alignment explanation


    Indices: 444--565  Score: 115
    Period size: 33  Copynumber: 3.8  Consensus size: 32

        434 CTAATTGTGA

                  *   *  *                   
        444 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
          1 TGAAAATAATCCTATTTTGGTTG-ACATAGCAT

             *        **                     
        477 TAAAAATAATTTTATTTTGGTTGATCATAGCAT
          1 TGAAAATAATCCTATTTTGGTTGA-CATAGCAT

              *                             
        510 TGCAAATAATCCTATTTTGGTTG--ATAGCAT
          1 TGAAAATAATCCTATTTTGGTTGACATAGCAT

                          *      *     
        540 TGAAAATAAAT-CTGTTTTGGGTGACA
          1 TGAAAAT-AATCCTATTTTGGTTGACA

        566 AGAAAGAGAT


Statistics
Matches: 74,  Mismatches: 11, Indels: 9
        0.79            0.12        0.10

Matches are distributed among these distances:
  30   23  0.31
  31    3  0.04
  32    2  0.03
  33   46  0.62

ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39


Consensus pattern (32 bp):   
TGAAAATAATCCTATTTTGGTTGACATAGCAT

Found at i:2393 original size:33 final size:33

Alignment explanation


    Indices: 2343--2429  Score: 97
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       2333 CCGCGCAACA

                                *          *    
       2343 CCGGCCACAAGACCGGCCACGCGAC-TCGGAGATGC
          1 CCGGCCAC-A-ACCGGCCACACGACAT-GGACATGC

                                        *     
       2378 CCGGCCATC-ACCGGCCACACGACATGGCCATGC
          1 CCGGCCA-CAACCGGCCACACGACATGGACATGC

                               
       2411 CCGGCCACAACCGGCCACA
          1 CCGGCCACAACCGGCCACA

       2430 TGATCCTTTA


Statistics
Matches: 46,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  32    1  0.02
  33   36  0.78
  34    1  0.02
  35    7  0.15
  36    1  0.02

ACGTcount: A:0.23, C:0.45, G:0.26, T:0.06


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACACGACATGGACATGC

Found at i:14073 original size:34 final size:34

Alignment explanation


    Indices: 14030--14097  Score: 118
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      14020 CTCAACTTGT

                                 * *          
      14030 AAAGGCGTGATGAAGGCCCGTTTTACTTCATTGG
          1 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG

                                              
      14064 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
          1 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG

      14098 TTGTAAGAGC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   32  1.00

ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26


Consensus pattern (34 bp):   
AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG

Found at i:14777 original size:23 final size:23

Alignment explanation


    Indices: 14751--14796  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      14741 AAGATAAAGT

                                   
      14751 AAATTAGACTAGAATAATAATAA
          1 AAATTAGACTAGAATAATAATAA

                                   
      14774 AAATTAGACTAGAATAATAATAA
          1 AAATTAGACTAGAATAATAATAA

      14797 TAATAATAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26


Consensus pattern (23 bp):   
AAATTAGACTAGAATAATAATAA

Found at i:14792 original size:3 final size:3

Alignment explanation


    Indices: 14786--14834  Score: 91
    Period size: 3  Copynumber: 16.7  Consensus size: 3

      14776 ATTAGACTAG

                                                                           
      14786 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

              
      14833 AA
          1 AA

      14835 CAATTATTTA


Statistics
Matches: 45,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2    2  0.04
   3   43  0.96

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


Consensus pattern (3 bp):   
AAT

Done.