Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010922.1 Corchorus capsularis cultivar CVL-1 contig10943, 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: 12942
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:958 original size:21 final size:21

Alignment explanation


    Indices: 934--976  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        924 GGACTCTAAA

                   *         *   
        934 GCTTGAATACTTGCCTCTGTT
          1 GCTTGAAAACTTGCCTCCGTT

                *       *        
        955 GCTTTAAAACTTTCCTCCGTT
          1 GCTTGAAAACTTGCCTCCGTT

             
        976 G
          1 G

        977 GTTTAAAGGC


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42


Consensus pattern (21 bp):   
GCTTGAAAACTTGCCTCCGTT

Found at i:981 original size:21 final size:21

Alignment explanation


    Indices: 942--983  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        932 AAGCTTGAAT

                     *           
        942 ACTTGCCTCTGTTGCTTTAAA
          1 ACTTGCCTCCGTTGCTTTAAA

                *         *      
        963 ACTTTCCTCCGTTGGTTTAAA
          1 ACTTGCCTCCGTTGCTTTAAA

        984 GGCTTCTTCA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43


Consensus pattern (21 bp):   
ACTTGCCTCCGTTGCTTTAAA

Found at i:1649 original size:18 final size:18

Alignment explanation


    Indices: 1626--1669  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1616 TGTTTCAATT

                              
       1626 AACTAATAAACTAAACTA
          1 AACTAATAAACTAAACTA

                       *       
       1644 AACTAACT-AATTAAACTA
          1 AACTAA-TAAACTAAACTA

              *     
       1662 AATTAATA
          1 AACTAATA

       1670 GGACAATTGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  17    1  0.05
  18   20  0.91
  19    1  0.05

ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27


Consensus pattern (18 bp):   
AACTAATAAACTAAACTA

Found at i:2185 original size:27 final size:27

Alignment explanation


    Indices: 2138--2205  Score: 77
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       2128 ATCCTAGGGA

                       *                
       2138 ACTAACTTTGACTGGGAAACTGT-TCTG
          1 ACTAACTTTGAATGGGAAACTGTCT-TG

                *                       
       2165 ACTAGCTTTGAAT-GGAGAACTGTCTTG
          1 ACTAACTTTGAATGGGA-AACTGTCTTG

                    *     
       2192 ACTAACTTGGAATG
          1 ACTAACTTTGAATG

       2206 AGAGTCTGAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 5
        0.79            0.09        0.12

Matches are distributed among these distances:
  26    3  0.09
  27   30  0.88
  28    1  0.03

ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32


Consensus pattern (27 bp):   
ACTAACTTTGAATGGGAAACTGTCTTG

Found at i:8805 original size:31 final size:31

Alignment explanation


    Indices: 8767--8829  Score: 99
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       8757 CAATCAATTC

                              *     *      
       8767 GTCCTGATGGAAAGCCTCTCGATGTTAAGTT
          1 GTCCTGATGGAAAGCCTCCCGATGATAAGTT

                           *               
       8798 GTCCTGATGGAAAGCGTCCCGATGATAAGTT
          1 GTCCTGATGGAAAGCCTCCCGATGATAAGTT

             
       8829 G
          1 G

       8830 CTTTAGAACT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29


Consensus pattern (31 bp):   
GTCCTGATGGAAAGCCTCCCGATGATAAGTT

Found at i:9227 original size:24 final size:24

Alignment explanation


    Indices: 9195--9241  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       9185 TGGAACATCC

                     *              
       9195 TGACCATCAGGACCCAAACTCTTA
          1 TGACCATCAAGACCCAAACTCTTA

                              *    
       9219 TGACCATCAAGACCCAAATTCTT
          1 TGACCATCAAGACCCAAACTCTT

       9242 TGTCCCGATG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23


Consensus pattern (24 bp):   
TGACCATCAAGACCCAAACTCTTA
Done.