Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006118.1 Corchorus olitorius cultivar O-4 contig06143, 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, 893

Length: 1489
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24


Found at i:771 original size:5 final size:5

Alignment explanation


    Indices: 756--792  Score: 58
    Period size: 5  Copynumber: 7.6  Consensus size: 5

        746 GTAAAACATT

                                       *                 
        756 AAAAC -AAAC AAAAC AAAAC AAACC AAAAC AAAAC AAA
          1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA

        793 GCAACCATTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   4    4  0.14
   5   25  0.86

ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:784 original size:15 final size:14

Alignment explanation


    Indices: 756--792  Score: 65
    Period size: 15  Copynumber: 2.6  Consensus size: 14

        746 GTAAAACATT

                          
        756 AAAACAAACAAAAC
          1 AAAACAAACAAAAC

                           
        770 AAAACAAACCAAAAC
          1 AAAACAAA-CAAAAC

                    
        785 AAAACAAA
          1 AAAACAAA

        793 GCAACCATTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  14    8  0.36
  15   14  0.64

ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00


Consensus pattern (14 bp):   
AAAACAAACAAAAC

Found at i:1415 original size:79 final size:80

Alignment explanation


    Indices: 1275--1489  Score: 315
    Period size: 79  Copynumber: 2.7  Consensus size: 80

       1265 AAGGAATAGG

                      *   *  *             ** *     *       *    *           
       1275 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTAGACAACACTTTCCTGTAGGGAAAGG
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTAGGGAAAGG

                           
       1340 CAAACT-GGTATTTA
         66 CAAACTGGGTATTTA

                                                                    *     *  
       1354 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGG
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTAGGGAAAGG

                           
       1419 CAAACTGGGTATTTA
         66 CAAACTGGGTATTTA

                                                                    
       1434 AACAACACCTTCCGGTGGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGG
          1 AACAACACCTTCCGGT-GGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGG


Statistics
Matches: 123,  Mismatches: 11, Indels: 2
        0.90            0.08        0.01

Matches are distributed among these distances:
  79   60  0.49
  80   24  0.20
  81   39  0.32

ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20


Consensus pattern (80 bp):   
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTAGGGAAAGG
CAAACTGGGTATTTA

Found at i:1467 original size:41 final size:40

Alignment explanation


    Indices: 1275--1489  Score: 315
    Period size: 40  Copynumber: 5.4  Consensus size: 40

       1265 AAGGAATAGG

                      *   *  *             ** *     
       1275 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

            *       *    *  *     *                 
       1315 GACAACACTTTCCTGTAGGGAAAGGCAAACT-GGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                                                    
       1354 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                                                    
       1394 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                                                     
       1434 AACAACACCTTCCGGTGGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGT-GGGGAAGGGCAAACTGGGTATTTA

                           
       1475 AACAACACCTTCCGG
          1 AACAACACCTTCCGG


Statistics
Matches: 158,  Mismatches: 15, Indels: 3
        0.90            0.09        0.02

Matches are distributed among these distances:
  39   32  0.20
  40   87  0.55
  41   39  0.25

ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20


Consensus pattern (40 bp):   
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
Done.