Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005475.1 Corchorus capsularis cultivar CVL-1 contig05493, 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: 4454
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--28  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

                                                     
          1 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

         29 TGTGCATCCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1043 original size:242 final size:242

Alignment explanation


    Indices: 611--1046  Score: 671
    Period size: 242  Copynumber: 1.8  Consensus size: 242

        601 CATGTTCTCT

                                         *        *              *           
        611 CTTTCATTGCCTTACATAAATCAGTCCATGTCAGATTTGATATCAAATAAAATTAGTTTGTGAAT
          1 CTTTCATTGCCTTACATAAATCAGTCCATCTCAGATTTCATATCAAATAAAATCAGTTTGTGAAT

            *                                     *                          
        676 TAGGGGTTTGCTTTCTCTATGATTCAAACTCTCTAAGCCATGGATCCACATTCAAATATATCAAA
         66 GAGGGGTTTGCTTTCTCTATGATTCAAACTCTCTAAGCAATGGATCCACATTCAAATATATCAAA

                 *  *                *                  *                    
        741 ATTCTGCTTTGTTGGCTAATTTCACTGCAGTGAAGCTTGCAAAATTTCCCCATCTCCTTCATGTG
        131 ATTCTACTCTGTTGGCTAATTTCACCGCAGTGAAGCTTGCAAAAATTCCCCATCTCCTTCATGTG

                                                           
        806 TATGTATAACTATCTTTGCATTGTTGAGAATTATATTTTGTTCTTAA
        196 TATGTATAACTATCTTTGCATTGTTGAGAATTATATTTTGTTCTTAA

                                            *               *                
        853 CTTTCATTGCCTTACATAAATCAGTCCATCTCTGATTTCATATCAAATTAAATCAGTTTGTGAAT
          1 CTTTCATTGCCTTACATAAATCAGTCCATCTCAGATTTCATATCAAATAAAATCAGTTTGTGAAT

                                                                 *       * * 
        918 GAGGGGTTTGCTTTCTCTATGATTCAAACTCT-TGAAGCAATGGATCCACATTGAAAT-TCGTTA
         66 GAGGGGTTTGCTTTCTCTATGATTCAAACTCTCT-AAGCAATGGATCCACATTCAAATAT-ATCA

              *                                      *              *        
        981 AATTTCTACTCTGTTGGCTAATTTCACCGCAGTTG-AGCTTTCAAAAATTCCCCATTTCCTTCAT
        129 AAATTCTACTCTGTTGGCTAATTTCACCGCAG-TGAAGCTTGCAAAAATTCCCCATCTCCTTCAT

              
       1045 GT
        193 GT

       1047 ATATTTTGCA


Statistics
Matches: 174,  Mismatches: 17, Indels: 6
        0.88            0.09        0.03

Matches are distributed among these distances:
 241    2  0.01
 242  170  0.98
 243    2  0.01

ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39


Consensus pattern (242 bp):   
CTTTCATTGCCTTACATAAATCAGTCCATCTCAGATTTCATATCAAATAAAATCAGTTTGTGAAT
GAGGGGTTTGCTTTCTCTATGATTCAAACTCTCTAAGCAATGGATCCACATTCAAATATATCAAA
ATTCTACTCTGTTGGCTAATTTCACCGCAGTGAAGCTTGCAAAAATTCCCCATCTCCTTCATGTG
TATGTATAACTATCTTTGCATTGTTGAGAATTATATTTTGTTCTTAA

Found at i:2448 original size:63 final size:62

Alignment explanation


    Indices: 2324--2449  Score: 234
    Period size: 63  Copynumber: 2.0  Consensus size: 62

       2314 AACTTCTAAT

                                                *                         
       2324 CAAGAGAGTTATTCTGAATTAACAAACAAAGAAACCTGAGTGAAGTGGATGCCAAAACAAAC
          1 CAAGAGAGTTATTCTGAATTAACAAACAAAGAAACCCGAGTGAAGTGGATGCCAAAACAAAC

                                                                           
       2386 CAAGAGAGTTATTCTGAATTAACAAACAAAGGAAACCCGAGTGAAGTGGATGCCAAAACAAAC
          1 CAAGAGAGTTATTCTGAATTAACAAACAAA-GAAACCCGAGTGAAGTGGATGCCAAAACAAAC

             
       2449 C
          1 C

       2450 TGAGTGAGGT


Statistics
Matches: 62,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  62   30  0.48
  63   32  0.52

ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17


Consensus pattern (62 bp):   
CAAGAGAGTTATTCTGAATTAACAAACAAAGAAACCCGAGTGAAGTGGATGCCAAAACAAAC

Found at i:3032 original size:79 final size:79

Alignment explanation


    Indices: 2901--3050  Score: 264
    Period size: 79  Copynumber: 1.9  Consensus size: 79

       2891 AGAGCTGTAT

                                             *          * *                  
       2901 AAGAGGAACAAATAACAACTTAAATTATAAAATGAAGACATAAATATAATATATACATTAAGTAG
          1 AAGAGGAACAAATAACAACTTAAATTATAAAATCAAGACATAAAGACAATATATACATTAAGTAG

                          
       2966 GAGGCCGCTCTATG
         66 GAGGCCGCTCTATG

                         *                                                   
       2980 AAGAGGAACAAATGACAACTTAAATTATAAAATCAAGACATAAAGACAATATATACATTAAGTAG
          1 AAGAGGAACAAATAACAACTTAAATTATAAAATCAAGACATAAAGACAATATATACATTAAGTAG

                  
       3045 GAGGCC
         66 GAGGCC

       3051 ATTGAGAGTC


Statistics
Matches: 67,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  79   67  1.00

ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22


Consensus pattern (79 bp):   
AAGAGGAACAAATAACAACTTAAATTATAAAATCAAGACATAAAGACAATATATACATTAAGTAG
GAGGCCGCTCTATG
Done.