Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007040.1 Corchorus capsularis cultivar CVL-1 contig07061, 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: 32367
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:4802 original size:21 final size:21

Alignment explanation


    Indices: 4777--4844  Score: 64
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       4767 TCATCATCAC

                                 
       4777 CACCACCTATATTCTCTTCCT
          1 CACCACCTATATTCTCTTCCT

                 * * *   *  ** * 
       4798 CACCAACAACATTTTCAACTT
          1 CACCACCTATATTCTCTTCCT

            *                    
       4819 TACCACCTATATTCTCTTCCT
          1 CACCACCTATATTCTCTTCCT

                 
       4840 CACCA
          1 CACCA

       4845 TCTTCATTAT


Statistics
Matches: 31,  Mismatches: 16, Indels: 0
        0.66            0.34        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.26, C:0.40, G:0.00, T:0.34


Consensus pattern (21 bp):   
CACCACCTATATTCTCTTCCT

Found at i:8010 original size:50 final size:51

Alignment explanation


    Indices: 7950--8090  Score: 126
    Period size: 50  Copynumber: 2.8  Consensus size: 51

       7940 TTCTCTAAAT

                                     *           *              
       7950 TAAAGATCCAATTTCTAATATCA-ACTTACCAAGACTTAACCG-TTACTATG
          1 TAAAGATCCAATTTCTAATATCACAATTACCAAGACTCAA-CGTTTACTATG

                 *        *  * *                              *
       8000 TAAAGGTCCAATTTTTATTGTCACAATTACCAAGACTCAACGTTTACTATC
          1 TAAAGATCCAATTTCTAATATCACAATTACCAAGACTCAACGTTTACTATG

            *       *       **     *   * *           
       8051 CAAAGATCTAATTT-TGTTATCAAAATCATCAAGACTCAAC
          1 TAAAGATCCAATTTCTAATATCACAATTACCAAGACTCAAC

       8091 CTATGCTATC


Statistics
Matches: 74,  Mismatches: 15, Indels: 4
        0.80            0.16        0.04

Matches are distributed among these distances:
  50   42  0.57
  51   32  0.43

ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33


Consensus pattern (51 bp):   
TAAAGATCCAATTTCTAATATCACAATTACCAAGACTCAACGTTTACTATG

Found at i:11243 original size:44 final size:44

Alignment explanation


    Indices: 11172--11303  Score: 176
    Period size: 44  Copynumber: 3.0  Consensus size: 44

      11162 AGTCATCACA

                       *                          *      
      11172 AAATAATAACAGCTTAATG-TTAGACAAAATATTCTAACCAAACC
          1 AAATAATAACACCTTAATGTTTA-ACAAAATATTCTAAACAAACC

                *                                *     *
      11216 AAATCATAACACCTTAATGTTTAACAAAATATTCTAAGCAAACA
          1 AAATAATAACACCTTAATGTTTAACAAAATATTCTAAACAAACC

                          *   *   *                     
      11260 AAATAATAACACCTCAATATTTGACAAAATATTCTAAACAAACC
          1 AAATAATAACACCTTAATGTTTAACAAAATATTCTAAACAAACC

      11304 TAGTAAAAGA


Statistics
Matches: 77,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  44   74  0.96
  45    3  0.04

ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26


Consensus pattern (44 bp):   
AAATAATAACACCTTAATGTTTAACAAAATATTCTAAACAAACC

Found at i:12489 original size:27 final size:27

Alignment explanation


    Indices: 12458--12519  Score: 81
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      12448 TGAGGTTGTA

                  * *                *  
      12458 TTCAGGTTTTGGTT-GAGTTGGTTGGGG
          1 TTCAGGGTCTGGTTGGA-TTGGTTGCGG

                                       
      12485 TTCAGGGTCTGGTTGGATTGGTTGCGG
          1 TTCAGGGTCTGGTTGGATTGGTTGCGG

                    
      12512 TTCAGGGT
          1 TTCAGGGT

      12520 AATGTAAGGT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  27   29  0.94
  28    2  0.06

ACGTcount: A:0.08, C:0.08, G:0.44, T:0.40


Consensus pattern (27 bp):   
TTCAGGGTCTGGTTGGATTGGTTGCGG

Found at i:17738 original size:15 final size:15

Alignment explanation


    Indices: 17718--17754  Score: 74
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      17708 ATCCATTAGA

                           
      17718 GAAGGCATAAGAGTC
          1 GAAGGCATAAGAGTC

                           
      17733 GAAGGCATAAGAGTC
          1 GAAGGCATAAGAGTC

                   
      17748 GAAGGCA
          1 GAAGGCA

      17755 GAAAGGGTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.41, C:0.14, G:0.35, T:0.11


Consensus pattern (15 bp):   
GAAGGCATAAGAGTC

Found at i:29767 original size:33 final size:32

Alignment explanation


    Indices: 29730--29836  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 32

      29720 CGCCTAGCGA

                                  *           
      29730 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG

                             *            *  
      29763 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                               *            *
      29796 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG

                    
      29829 TGGCCGGT
          1 TGGCCGGT

      29837 CACTAGTGCT


Statistics
Matches: 64,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  33   62  0.97
  34    2  0.03

ACGTcount: A:0.09, C:0.29, G:0.38, T:0.23


Consensus pattern (32 bp):   
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.