Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015936.1 Corchorus capsularis cultivar CVL-1 contig15957, 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: 16624
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31


Found at i:1505 original size:60 final size:62

Alignment explanation


    Indices: 1412--1563  Score: 220
    Period size: 60  Copynumber: 2.5  Consensus size: 62

       1402 CTGAAAACTA

                                *     *                                    
       1412 AGAAAGACCTGTCTGAGGTCCGGAACAGAAGAAGAT-CAGTTTGTGGTCGA-ATTGAA-ATCG
          1 AGAAAGACCTGTCTGAGGTCTGGAACTGAAGAAG-TCCAGTTTGTGGTCGATATTGAAGATCG

                                                               *        * 
       1472 AGAAAGACCTGTCTGAGGTCTGGAACTGAAGAAGTCCAGTTTGTGGTCGATTTTGAAGATTG
          1 AGAAAGACCTGTCTGAGGTCTGGAACTGAAGAAGTCCAGTTTGTGGTCGATATTGAAGATCG

                      *  *                
       1534 AGAAAGACCTATCCGAGGTCTGGAACTGAA
          1 AGAAAGACCTGTCTGAGGTCTGGAACTGAA

       1564 TATCTGTATG


Statistics
Matches: 83,  Mismatches: 6, Indels: 4
        0.89            0.06        0.04

Matches are distributed among these distances:
  59    1  0.01
  60   46  0.55
  61    5  0.06
  62   31  0.37

ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24


Consensus pattern (62 bp):   
AGAAAGACCTGTCTGAGGTCTGGAACTGAAGAAGTCCAGTTTGTGGTCGATATTGAAGATCG

Found at i:1589 original size:87 final size:87

Alignment explanation


    Indices: 1480--1640  Score: 216
    Period size: 87  Copynumber: 1.9  Consensus size: 87

       1470 CGAGAAAGAC

                *                     *     *           *     * * *          
       1480 CTGTCTGAGGTCTGGAACTGAAGAAGTCCAGTTTGTGGTCGATTTTG-AAGATTGAGAAAGACCT
          1 CTGTATGAGGTCTGGAACTGAAGAAGACCAGTCTGTGGTCGA-TATGAAAAACTAAGAAAGACCT

                                   
       1544 ATCCGAGGTCTGGAACTGAATAT
         65 ATCCGAGGTCTGGAACTGAATAT

                             *      *                                       *
       1567 CTGTATGAGGTCTGGAATTGAAGAGGACCAGTCTGTGGTCGATATGAAAAACTAAGAAAGACCTG
          1 CTGTATGAGGTCTGGAACTGAAGAAGACCAGTCTGTGGTCGATATGAAAAACTAAGAAAGACCTA

                     
       1632 TCCGAGGTC
         66 TCCGAGGTC

       1641 AACTTTGATA


Statistics
Matches: 63,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  86    3  0.05
  87   60  0.95

ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26


Consensus pattern (87 bp):   
CTGTATGAGGTCTGGAACTGAAGAAGACCAGTCTGTGGTCGATATGAAAAACTAAGAAAGACCTA
TCCGAGGTCTGGAACTGAATAT

Found at i:1695 original size:28 final size:27

Alignment explanation


    Indices: 1653--1709  Score: 71
    Period size: 28  Copynumber: 2.1  Consensus size: 27

       1643 CTTTGATAAA

                             *          
       1653 TGAAATTGAGAAAGACCCGTCTGAGGTC
          1 TGAAATTGAGAAAGACCAGTCTGA-GTC

                             *          
       1681 TGAAATTGA-ATAAGACTAGTCTGAGTC
          1 TGAAATTGAGA-AAGACCAGTCTGAGTC

              
       1708 TG
          1 TG

       1710 TATTGATACT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  27    6  0.23
  28   20  0.77

ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26


Consensus pattern (27 bp):   
TGAAATTGAGAAAGACCAGTCTGAGTC

Found at i:14615 original size:48 final size:48

Alignment explanation


    Indices: 14235--14603  Score: 459
    Period size: 48  Copynumber: 7.6  Consensus size: 48

      14225 AAAAGCGAGT

                    * *                                **     
      14235 AAAATTAGCGTCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAGAGTGAGTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAA-ACAG-GTA

                  *                                      *   
      14285 AAAATTGGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAA-CAGGTA

                           **   **            *       *  **  
      14334 AAAATTAGTGCCTTCAATCCAAGAAGGGCGTTTTGGGAAAATGCAATTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAA-ACAGGTA

              *    *                                        
      14383 AAGATTAATGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA

                 *               *        *   *            *
      14431 AAAATCAGTGCCTTCCGTCCGAGAAGGGCGGTTTGGGAAAAACAGGTG
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA

              *                                             
      14479 AAGATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA

                 *                          * *             
      14527 AAAATCAGTGCCTTCCGTCCGGGAAGGGCGTTCTGGGAAAAACAGGTA
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA

                 * *                     
      14575 AAAATCAATGCCTTCCGTCCGGGAAGGGC
          1 AAAATTAGTGCCTTCCGTCCGGGAAGGGC

      14604 ATTATGGGAA


Statistics
Matches: 275,  Mismatches: 42, Indels: 6
        0.85            0.13        0.02

Matches are distributed among these distances:
  48  159  0.58
  49   78  0.28
  50   38  0.14

ACGTcount: A:0.31, C:0.18, G:0.30, T:0.22


Consensus pattern (48 bp):   
AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA

Found at i:15628 original size:18 final size:18

Alignment explanation


    Indices: 15605--15670  Score: 114
    Period size: 18  Copynumber: 3.7  Consensus size: 18

      15595 CTGCAATAAC

                     *        
      15605 ACTATGAACTCTTAAGAA
          1 ACTATGAACCCTTAAGAA

                              
      15623 ACTATGAACCCTTAAGAA
          1 ACTATGAACCCTTAAGAA

                        *     
      15641 ACTATGAACCCTAAAGAA
          1 ACTATGAACCCTTAAGAA

                        
      15659 ACTATGAACCCT
          1 ACTATGAACCCT

      15671 CAAGTTTTTT


Statistics
Matches: 46,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   46  1.00

ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23


Consensus pattern (18 bp):   
ACTATGAACCCTTAAGAA
Done.