Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007003.1 Corchorus capsularis cultivar CVL-1 contig07024, 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: 35621
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:1023 original size:171 final size:171

Alignment explanation


    Indices: 697--1025  Score: 398
    Period size: 171  Copynumber: 1.9  Consensus size: 171

        687 TTTTTGCATG

                        *         **                       *                 
        697 TAATTCTCGGCATAAACCCTAATTTTGCCAAAAATTATACCAAACTAGATCAATTCATTGAATCA
          1 TAATTCTCGGCACAAACCCTAAGCTTGCCAAAAATTATACCAAACTAAATCAATTCATTGAATCA

              *                  *              *    *  *                    
        762 TAGAGTAAATTGCATGAAAATTTGATCAAAATTTGATAAGGGATTAAACCCTAATTTTACCGCAA
         66 TAAAGTAAATTGCATGAAAATATGATCAAAATTTGAGAAGGAATGAAACCCTAATTTTACCGCAA

                                                     
        827 ACACTAATTGCATGGGGCAGCAAAATTGTTGAATTTGTATA
        131 ACACTAATTGCATGGGGCAGCAAAATTGTTGAATTTGTATA

                 *               *               *       *                   
        868 TAATTTTCGGCACAAACCCTAGGCTTGCCAAAAATTGGTACCAAATTAAATCAATTCA-TGAAAT
          1 TAATTCTCGGCACAAACCCTAAGCTTGCCAAAAATT-ATACCAAACTAAATCAATTCATTG-AAT

                                         **                  *            * *
        932 CATAAAGTAAATTGCATG-AAATCATGATTGAAA-TTGAGGAA-GAATGGAACCCTAATTTTGCT
         64 CATAAAGTAAATTGCATGAAAAT-ATGATCAAAATTTGA-GAAGGAATGAAACCCTAATTTTACC

                  *                *         
        994 GC-AACCCTTAATTGCATGGGGCGGCAAAATTG
        127 GCAAACAC-TAATTGCATGGGGCAGCAAAATTG

       1026 CCTTCAAGTC


Statistics
Matches: 133,  Mismatches: 20, Indels: 10
        0.82            0.12        0.06

Matches are distributed among these distances:
 170    4  0.03
 171   82  0.62
 172   47  0.35

ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29


Consensus pattern (171 bp):   
TAATTCTCGGCACAAACCCTAAGCTTGCCAAAAATTATACCAAACTAAATCAATTCATTGAATCA
TAAAGTAAATTGCATGAAAATATGATCAAAATTTGAGAAGGAATGAAACCCTAATTTTACCGCAA
ACACTAATTGCATGGGGCAGCAAAATTGTTGAATTTGTATA

Found at i:13045 original size:27 final size:26

Alignment explanation


    Indices: 13015--13066  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

      13005 TATTCACTGC

                                        
      13015 TTTCTTATTAATAATTTT-CTTGTTTGA
          1 TTTCTTA--AATAATTTTACTTGTTTGA

                   *                 
      13042 TTTCTTAGATAATTTTACTTGTTTG
          1 TTTCTTAAATAATTTTACTTGTTTG

      13067 TTTGATTTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  25    8  0.35
  26    8  0.35
  27    7  0.30

ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62


Consensus pattern (26 bp):   
TTTCTTAAATAATTTTACTTGTTTGA

Found at i:34244 original size:11 final size:10

Alignment explanation


    Indices: 34226--34259  Score: 50
    Period size: 11  Copynumber: 3.2  Consensus size: 10

      34216 GAAGTTCGTA

                      
      34226 TTTTGAAGAT
          1 TTTTGAAGAT

                       
      34236 TTCTTGAAGAT
          1 TT-TTGAAGAT

                       
      34247 ATTTTGAAGAT
          1 -TTTTGAAGAT

              
      34258 TT
          1 TT

      34260 GAAGATAATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  10    4  0.18
  11   16  0.73
  12    2  0.09

ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50


Consensus pattern (10 bp):   
TTTTGAAGAT

Found at i:35502 original size:25 final size:25

Alignment explanation


    Indices: 35474--35584  Score: 114
    Period size: 25  Copynumber: 4.1  Consensus size: 25

      35464 GTAGCGACGT

                                     
      35474 CTAAAATAGTGGCGTCTGGACGCCG
          1 CTAAAATAGTGGCGTCTGGACGCCG

                 *           *      *
      35499 CTAAAGTAGTGGCGTCTTGACGCCC
          1 CTAAAATAGTGGCGTCTGGACGCCG

                                             
      35524 CTAAAATAGTGGCGTCCTGAAGTCCTGACGCCG
          1 CTAAAATAGTGGCGT-CT---G----GACGCCG

                             *       
      35557 CTAAAATAGTGGCGTCTAGACGCCG
          1 CTAAAATAGTGGCGTCTGGACGCCG

               
      35582 CTA
          1 CTA

      35585 TATGCAAATT


Statistics
Matches: 71,  Mismatches: 7, Indels: 16
        0.76            0.07        0.17

Matches are distributed among these distances:
  25   46  0.65
  26    2  0.03
  32    2  0.03
  33   21  0.30

ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22


Consensus pattern (25 bp):   
CTAAAATAGTGGCGTCTGGACGCCG
Done.