Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013581.1 Corchorus capsularis cultivar CVL-1 contig13602, 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: 13598
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30


Found at i:137 original size:2 final size:2

Alignment explanation


    Indices: 124--157  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

        114 TATCCAATAC

                   *                                          
        124 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        158 TTGAACTTGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2964 original size:16 final size:17

Alignment explanation


    Indices: 2945--2979  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2935 AGAACTCCAA

                      *      
       2945 CATT-AAAAAGAAATGG
          1 CATTCAAAAAAAAATGG

                             
       2961 CATTCAAAAAAAAATGG
          1 CATTCAAAAAAAAATGG

              
       2978 CA
          1 CA

       2980 AACTTCAACC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16    4  0.24
  17   13  0.76

ACGTcount: A:0.57, C:0.11, G:0.14, T:0.17


Consensus pattern (17 bp):   
CATTCAAAAAAAAATGG

Found at i:3033 original size:13 final size:13

Alignment explanation


    Indices: 3015--3040  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3005 ATGGCAAACT

                         
       3015 TCAACCAGATATA
          1 TCAACCAGATATA

                         
       3028 TCAACCAGATATA
          1 TCAACCAGATATA

       3041 CAGCCTAATT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23


Consensus pattern (13 bp):   
TCAACCAGATATA

Found at i:4829 original size:33 final size:34

Alignment explanation


    Indices: 4763--4839  Score: 93
    Period size: 33  Copynumber: 2.3  Consensus size: 34

       4753 AAATGGAGAT

                                 ***          
       4763 TTTGTTTGCATTTTCTATTTTTTTGGTAGAAAGA
          1 TTTGTTTGCATTTTCTATTTTGGGGGTAGAAAGA

                            *                 
       4797 TTTGTTTGCATTTT-TCTTTTGGGGGTAGAAAGA
          1 TTTGTTTGCATTTTCTATTTTGGGGGTAGAAAGA

            *   *     
       4830 GTTGATTGCA
          1 TTTGTTTGCA

       4840 CGTTGGGCAT


Statistics
Matches: 37,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  33   23  0.62
  34   14  0.38

ACGTcount: A:0.19, C:0.06, G:0.23, T:0.51


Consensus pattern (34 bp):   
TTTGTTTGCATTTTCTATTTTGGGGGTAGAAAGA

Found at i:6375 original size:19 final size:19

Alignment explanation


    Indices: 6351--6397  Score: 94
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       6341 CAGTCGACTC

                               
       6351 ACAACCAATACATCTAACA
          1 ACAACCAATACATCTAACA

                               
       6370 ACAACCAATACATCTAACA
          1 ACAACCAATACATCTAACA

                     
       6389 ACAACCAAT
          1 ACAACCAAT

       6398 CAACCAATTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   28  1.00

ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15


Consensus pattern (19 bp):   
ACAACCAATACATCTAACA

Found at i:10085 original size:80 final size:80

Alignment explanation


    Indices: 9953--10106  Score: 238
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       9943 CCAACACAGG

                        **       *                                *          
       9953 AACCTAGCACATTGAACAGGATAACTTACAAGCATCCAACAACAGAAACAAAA-CTGAGAACAGG
          1 AACCTAGCACATCAAACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATATGAGAACAGG

                           
      10017 ACAGAAACAGAGCCT
         66 ACAGAAACAGAGCCT

                                                          *           *      
      10032 AACCTAGCACATCAAACAGGAAAACTTTACAAGCATCCAACAACAGGAACAAAATATGCGAACAG
          1 AACCTAGCACATCAAACAGGAAAAC-TTACAAGCATCCAACAACAGAAACAAAATATGAGAACAG

                      
      10097 GACAGAAACA
         65 GACAGAAACA

      10107 TAAACCAAGA


Statistics
Matches: 67,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  79   22  0.33
  80   27  0.40
  81   18  0.27

ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11


Consensus pattern (80 bp):   
AACCTAGCACATCAAACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATATGAGAACAGG
ACAGAAACAGAGCCT
Done.