Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007377.1 Corchorus capsularis cultivar CVL-1 contig07398, 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: 15269
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:4128 original size:14 final size:12

Alignment explanation


    Indices: 4100--4142  Score: 68
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       4090 GAGAAACTGT

                        
       4100 GAGAAAAACAGA
          1 GAGAAAAACAGA

                        
       4112 GAGAAAAACAGA
          1 GAGAAAAACAGA

                *    *  
       4124 GAGAGAAACTGA
          1 GAGAAAAACAGA

                   
       4136 GAGAAAA
          1 GAGAAAA

       4143 TGGAAATCTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.63, C:0.07, G:0.28, T:0.02


Consensus pattern (12 bp):   
GAGAAAAACAGA

Found at i:4229 original size:18 final size:19

Alignment explanation


    Indices: 4206--4245  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       4196 TTCCATACCC

                               
       4206 AAAAACAAAACAAA-AAGA
          1 AAAAACAAAACAAAGAAGA

                      *        
       4224 AAAAACAAAAGAAAGAAGA
          1 AAAAACAAAACAAAGAAGA

               
       4243 AAA
          1 AAA

       4246 TTAGTTAGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18   13  0.65
  19    7  0.35

ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00


Consensus pattern (19 bp):   
AAAAACAAAACAAAGAAGA

Found at i:6615 original size:33 final size:33

Alignment explanation


    Indices: 6578--6706  Score: 201
    Period size: 33  Copynumber: 4.0  Consensus size: 33

       6568 AAGGAGAAGT

                                             
       6578 GCAAAGCTGATGAGGAGGAATCAATAAGACGTC
          1 GCAAAGCTGATGAGGAGGAATCAATAAGACGTC

                     *             *         
       6611 GCAAAGCTGCT---GAGGAATCATTAAGACGTC
          1 GCAAAGCTGATGAGGAGGAATCAATAAGACGTC

                                   *         
       6641 GCAAAGCTGATGAGGAGGAATCATTAAGACGTC
          1 GCAAAGCTGATGAGGAGGAATCAATAAGACGTC

                                     *       
       6674 GCAAAGCTGATGAGGAGGAATCAATGAGACGTC
          1 GCAAAGCTGATGAGGAGGAATCAATAAGACGTC

       6707 TTTTGAAACA


Statistics
Matches: 88,  Mismatches: 5, Indels: 6
        0.89            0.05        0.06

Matches are distributed among these distances:
  30   28  0.32
  33   60  0.68

ACGTcount: A:0.36, C:0.16, G:0.30, T:0.17


Consensus pattern (33 bp):   
GCAAAGCTGATGAGGAGGAATCAATAAGACGTC

Found at i:12046 original size:27 final size:27

Alignment explanation


    Indices: 12016--12069  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      12006 TATCTTACCT

                     **  *   *         
      12016 TTCATATATTTATTTTTTTTTATTTTG
          1 TTCATATATAAATATTTATTTATTTTG

                                       
      12043 TTCATATATAAATATTTATTTATTTTG
          1 TTCATATATAAATATTTATTTATTTTG

      12070 ACAAACAAAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67


Consensus pattern (27 bp):   
TTCATATATAAATATTTATTTATTTTG
Done.