Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007348.1 Corchorus capsularis cultivar CVL-1 contig07369, 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: 29331
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:1775 original size:167 final size:167

Alignment explanation


    Indices: 1460--1791  Score: 423
    Period size: 167  Copynumber: 2.0  Consensus size: 167

       1450 TCATTTGTTA

                                * * *           *                    *       
       1460 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCTCTCAAGAATAAAAAAATTAGGACATTTA
          1 ATTGAGAAATGACCAAAAAGATCACTTATTTAATCCCCTCAAGAATAAAAAAATTAGAACATTTA

             *           *    *            ** *           *  ** *   *       *
       1525 AGTAATCTGCCAAGTAGGTAAAGACGAAAAATGTTAGTTCTCTAATTCATCATCAATCCTTGATG
         66 ACTAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTCTCTAATCCAAAAGCAAGCCTTGATA

                       *          *       *      
       1590 GGGATCATTTATTAATTCCACTGCTCTATTTAAGTAC
        131 GGGATCATTTAGTAATTCCACTACTCTATTAAAGTAC

                                                           *    *            
       1627 ATTGAGAAATGACCAAAAAGATCACTTATTTAATCCCCTCAAGAAT-CAAAAGTTAGAACATTTA
          1 ATTGAGAAATGACCAAAAAGATCACTTATTTAATCCCCTCAAGAATAAAAAAATTAGAACATTTA

                                                     *                     * 
       1691 ACTAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTCTTTAACTCCAAAAGCAAGCCTTGGT
         66 ACTAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTCTCTAA-TCCAAAAGCAAGCCTTGAT

                   *                            
       1756 AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGT
        130 AGGGATCATTTAGTAATTCCACTACTCTATTAAAGT

       1792 TTAGGTCATT


Statistics
Matches: 139,  Mismatches: 25, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
 166   53  0.38
 167   86  0.62

ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30


Consensus pattern (167 bp):   
ATTGAGAAATGACCAAAAAGATCACTTATTTAATCCCCTCAAGAATAAAAAAATTAGAACATTTA
ACTAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTCTCTAATCCAAAAGCAAGCCTTGATA
GGGATCATTTAGTAATTCCACTACTCTATTAAAGTAC

Found at i:3661 original size:38 final size:39

Alignment explanation


    Indices: 3609--3690  Score: 148
    Period size: 38  Copynumber: 2.1  Consensus size: 39

       3599 AGCAATTTCT

                                                   
       3609 GATGACTTTGAACATTCAATTTCTCACTTTTATCTTAGA
          1 GATGACTTTGAACATTCAATTTCTCACTTTTATCTTAGA

                                    *              
       3648 -ATGACTTTGAACATTCAATTTCTTACTTTTATCTTAGA
          1 GATGACTTTGAACATTCAATTTCTCACTTTTATCTTAGA

                 
       3686 GATGA
          1 GATGA

       3691 TTGGTTCTAC


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  38   37  0.90
  39    4  0.10

ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44


Consensus pattern (39 bp):   
GATGACTTTGAACATTCAATTTCTCACTTTTATCTTAGA

Found at i:12397 original size:46 final size:49

Alignment explanation


    Indices: 12306--12403  Score: 130
    Period size: 52  Copynumber: 2.0  Consensus size: 49

      12296 TGATGAGTAT

                      *                                         
      12306 AGTGATAAAAGCTTGAGCTTGAGTAATTAGATTACATACAAATACAAATAAA
          1 AGTGATAAAAACTTGAGCTTGAGTAATTAGATT--ATAC-AATACAAATAAA

                             *                               
      12358 AGTGATAAAAACTTGAGTTTGAGTAATTAGA-T-TAC-ATACAAATAAA
          1 AGTGATAAAAACTTGAGCTTGAGTAATTAGATTATACAATACAAATAAA

      12404 TAATTAGATT


Statistics
Matches: 44,  Mismatches: 2, Indels: 6
        0.85            0.04        0.12

Matches are distributed among these distances:
  46   11  0.25
  48    3  0.07
  51    1  0.02
  52   29  0.66

ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29


Consensus pattern (49 bp):   
AGTGATAAAAACTTGAGCTTGAGTAATTAGATTATACAATACAAATAAA

Found at i:13300 original size:21 final size:20

Alignment explanation


    Indices: 13266--13306  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 20

      13256 AACCTAGCTT

                     *     *    
      13266 TCTCTCTCTTTCCCTTTCTC
          1 TCTCTCTCTCTCCCTCTCTC

                                 
      13286 TCTCTTCTCTCTCCCTCTCTC
          1 TCTC-TCTCTCTCCCTCTCTC

      13307 CCCTTTGCCG


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20    4  0.22
  21   14  0.78

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (20 bp):   
TCTCTCTCTCTCCCTCTCTC

Found at i:23863 original size:6 final size:5

Alignment explanation


    Indices: 23835--23860  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

      23825 GTGCTTATCA

                                           
      23835 TCTTT TCTTT TCTTT TCTTT TCTTT T
          1 TCTTT TCTTT TCTTT TCTTT TCTTT T

      23861 TCTCTTTTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (5 bp):   
TCTTT
Done.