Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006985.1 Corchorus capsularis cultivar CVL-1 contig07006, 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: 30232
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:2675 original size:33 final size:33

Alignment explanation


    Indices: 2638--2734  Score: 122
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       2628 AGCACTAGTG

                    *            *           
       2638 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                     **    *       *         
       2671 ACCGGCCACATGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                          *    *           
       2704 ACCGGCCACGCGACATGGACATGTCCGGCCA
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCA

       2735 CAACCGACCA


Statistics
Matches: 52,  Mismatches: 12, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   52  1.00

ACGTcount: A:0.24, C:0.37, G:0.29, T:0.10


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

Found at i:8977 original size:21 final size:21

Alignment explanation


    Indices: 8951--8991  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8941 TCTTGAAGGC

                  *              
       8951 TTGAAGTCCATTGAAGATCAA
          1 TTGAAGACCATTGAAGATCAA

                   **           
       8972 TTGAAGAGTATTGAAGATCA
          1 TTGAAGACCATTGAAGATCA

       8992 TAAGCCAAGG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29


Consensus pattern (21 bp):   
TTGAAGACCATTGAAGATCAA

Found at i:14420 original size:165 final size:165

Alignment explanation


    Indices: 14148--14477  Score: 633
    Period size: 165  Copynumber: 2.0  Consensus size: 165

      14138 GATTGTATAC

                                                                             
      14148 TCCTTTGCATATTCCTCATGAACCATGGAATCATATTAGCATAGATTTTGTGTTAGGTTTACCTC
          1 TCCTTTGCATATTCCTCATGAACCATGGAATCATATTAGCATAGATTTTGTGTTAGGTTTACCTC

                             *                                               
      14213 GTTCTAAGAGAGGTAAAGATTCTATCTTTGTGGTTGTTGATAGGTTTTCTAAGATGGCACACTTC
         66 GTTCTAAGAGAGGTAAACATTCTATCTTTGTGGTTGTTGATAGGTTTTCTAAGATGGCACACTTC

                                               
      14278 ATTGCATGTACTAAAACAGATGATGCCATTAATGT
        131 ATTGCATGTACTAAAACAGATGATGCCATTAATGT

                                         *                                   
      14313 TCCTTTGCATATTCCTCATGAACCATGGACTCATATTAGCATAGATTTTGTGTTAGGTTTACCTC
          1 TCCTTTGCATATTCCTCATGAACCATGGAATCATATTAGCATAGATTTTGTGTTAGGTTTACCTC

                                                                             
      14378 GTTCTAAGAGAGGTAAACATTCTATCTTTGTGGTTGTTGATAGGTTTTCTAAGATGGCACACTTC
         66 GTTCTAAGAGAGGTAAACATTCTATCTTTGTGGTTGTTGATAGGTTTTCTAAGATGGCACACTTC

                             *                 
      14443 ATTGCATGTACTAAAACGGATGATGCCATTAATGT
        131 ATTGCATGTACTAAAACAGATGATGCCATTAATGT

      14478 AGCTAATTTG


Statistics
Matches: 162,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 165  162  1.00

ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38


Consensus pattern (165 bp):   
TCCTTTGCATATTCCTCATGAACCATGGAATCATATTAGCATAGATTTTGTGTTAGGTTTACCTC
GTTCTAAGAGAGGTAAACATTCTATCTTTGTGGTTGTTGATAGGTTTTCTAAGATGGCACACTTC
ATTGCATGTACTAAAACAGATGATGCCATTAATGT

Found at i:15528 original size:21 final size:21

Alignment explanation


    Indices: 15502--15542  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      15492 TCTTGAAGGC

                  *              
      15502 TTGAAGTCCATTGAAGATCAA
          1 TTGAAGACCATTGAAGATCAA

                   **           
      15523 TTGAAGAGTATTGAAGATCA
          1 TTGAAGACCATTGAAGATCA

      15543 TAAGCCAAGG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29


Consensus pattern (21 bp):   
TTGAAGACCATTGAAGATCAA

Found at i:23348 original size:23 final size:23

Alignment explanation


    Indices: 23276--23349  Score: 62
    Period size: 23  Copynumber: 3.2  Consensus size: 23

      23266 AGTTTTTGTT

                  *      *          
      23276 TTTCCGTTTTTTCTAAAAAAAAAG
          1 TTTCCGATTTTT-AAAAAAAAAAG

               *                  ** 
      23300 TTTGCGA--TTTAAAAAAATTACGG
          1 TTTCCGATTTTTAAAAAAA--AAAG

                                   
      23323 TTTCCGATTTTTAAAAAAAAAAG
          1 TTTCCGATTTTTAAAAAAAAAAG

                
      23346 TTTC
          1 TTTC

      23350 TCTTTTCCGT


Statistics
Matches: 38,  Mismatches: 8, Indels: 9
        0.69            0.15        0.16

Matches are distributed among these distances:
  21    6  0.16
  22    3  0.08
  23   14  0.37
  24    5  0.13
  25   10  0.26

ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39


Consensus pattern (23 bp):   
TTTCCGATTTTTAAAAAAAAAAG
Done.