Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009437.1 Corchorus capsularis cultivar CVL-1 contig09458, 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: 6602
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:140 original size:66 final size:66

Alignment explanation


    Indices: 1--198  Score: 217
    Period size: 66  Copynumber: 3.0  Consensus size: 66

                             **                              *             * 
          1 CCCAGTGGGGCGGCCTTTTCATGGTGAAGCCGCCCCAGTGGGGCGGC-CTGCCCATGGTGAAGTC
          1 CCCAGTGGGGCGGCCTTCCCATGGTGAAGCCGCCCCAGTGGGGCGGCTCCG-CCATGGTGAAGCC

              
         65 GC
         65 GC

              *             *                  *                 *           
         67 CCTAGTGGGGCGGCCTGCCCATGGTGAAGCCGCCCTAGTGGGGCGGCTCCGCCGTGGTTG-AGCC
          1 CCCAGTGGGGCGGCCTTCCCATGGTGAAGCCGCCCCAGTGGGGCGGCTCCGCCATGG-TGAAGCC

            * 
        131 TC
         65 GC

                                  *         *                *     *         
        133 CCCAGTGGGGCGG-CTTCGCCACGGT-AAGCCTCCCCAGTGGGGCGGCTTCGCCACGGT-AAGCC
          1 CCCAGTGGGGCGGCCTTC-CCATGGTGAAGCCGCCCCAGTGGGGCGGCTCCGCCATGGTGAAGCC

              
        195 GC
         65 GC

              
        197 CC
          1 CC

        199 TCTTGGGACG


Statistics
Matches: 110,  Mismatches: 18, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
  64    8  0.07
  65   29  0.26
  66   69  0.63
  67    4  0.04

ACGTcount: A:0.11, C:0.35, G:0.37, T:0.17


Consensus pattern (66 bp):   
CCCAGTGGGGCGGCCTTCCCATGGTGAAGCCGCCCCAGTGGGGCGGCTCCGCCATGGTGAAGCCG
C

Found at i:168 original size:32 final size:32

Alignment explanation


    Indices: 1--198  Score: 195
    Period size: 33  Copynumber: 6.1  Consensus size: 32

                             **              
          1 CCCAGTGGGGCGGCCTTTTCATGGTGAAGCCGC
          1 CCCAGTGGGGCGG-CTTGCCATGGTGAAGCCGC

                          *              *   
         34 CCCAGTGGGGCGGCCTGCCCATGGTGAAGTCGC
          1 CCCAGTGGGGCGGCTTG-CCATGGTGAAGCCGC

              *           *                  
         67 CCTAGTGGGGCGGCCTGCCCATGGTGAAGCCGC
          1 CCCAGTGGGGCGGCTTG-CCATGGTGAAGCCGC

              *             *   *           * 
        100 CCTAGTGGGGCGGCTCCGCCGTGGTTG-AGCCTC
          1 CCCAGTGGGGCGGCT-TGCCATGG-TGAAGCCGC

                                 *         * 
        133 CCCAGTGGGGCGGCTTCGCCACGGT-AAGCCTC
          1 CCCAGTGGGGCGGCTT-GCCATGGTGAAGCCGC

                                 *           
        165 CCCAGTGGGGCGGCTTCGCCACGGT-AAGCCGC
          1 CCCAGTGGGGCGGCTT-GCCATGGTGAAGCCGC

              
        197 CC
          1 CC

        199 TCTTGGGACG


Statistics
Matches: 145,  Mismatches: 15, Indels: 11
        0.85            0.09        0.06

Matches are distributed among these distances:
  32   42  0.29
  33  100  0.69
  34    3  0.02

ACGTcount: A:0.11, C:0.35, G:0.37, T:0.17


Consensus pattern (32 bp):   
CCCAGTGGGGCGGCTTGCCATGGTGAAGCCGC

Found at i:1031 original size:46 final size:47

Alignment explanation


    Indices: 937--1031  Score: 156
    Period size: 47  Copynumber: 2.0  Consensus size: 47

        927 ATTTTGGGAG

                                                           
        937 AAACAGAAAACAAAGAGTGAGAAGAAGAAGAGAGGGTTTTCGCGCTT
          1 AAACAGAAAACAAAGAGTGAGAAGAAGAAGAGAGGGTTTTCGCGCTT

                   *                      *            *   
        984 AAACAGAGAACAAAGAGTGAGAAG-AGAAGGGAGGGTTTTCGCTCTT
          1 AAACAGAAAACAAAGAGTGAGAAGAAGAAGAGAGGGTTTTCGCGCTT

              
       1030 AA
          1 AA

       1032 CTGTCTTCTG


Statistics
Matches: 45,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  46   22  0.49
  47   23  0.51

ACGTcount: A:0.43, C:0.11, G:0.31, T:0.16


Consensus pattern (47 bp):   
AAACAGAAAACAAAGAGTGAGAAGAAGAAGAGAGGGTTTTCGCGCTT

Found at i:4550 original size:20 final size:20

Alignment explanation


    Indices: 4525--4589  Score: 53
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       4515 CAATTTTTGA

                                
       4525 ATAAACTAACCATTAATTGG
          1 ATAAACTAACCATTAATTGG

                          *    *   *
       4545 ATAAAC-AATTTGCAATT-TTTGA
          1 ATAAACTAA----CCATTAATTGG

                                
       4567 ATAAACTAACCATTAATTGG
          1 ATAAACTAACCATTAATTGG

               
       4587 ATA
          1 ATA

       4590 GACAAGGGGA


Statistics
Matches: 33,  Mismatches: 6, Indels: 12
        0.65            0.12        0.24

Matches are distributed among these distances:
  19    6  0.18
  20   12  0.36
  22    9  0.27
  23    6  0.18

ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34


Consensus pattern (20 bp):   
ATAAACTAACCATTAATTGG

Found at i:4568 original size:42 final size:42

Alignment explanation


    Indices: 4509--4594  Score: 163
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       4499 AAACTCTTGA

                                                      
       4509 AATTTGCAATTTTTGAATAAACTAACCATTAATTGGATAAAC
          1 AATTTGCAATTTTTGAATAAACTAACCATTAATTGGATAAAC

                                                   *  
       4551 AATTTGCAATTTTTGAATAAACTAACCATTAATTGGATAGAC
          1 AATTTGCAATTTTTGAATAAACTAACCATTAATTGGATAAAC

              
       4593 AA
          1 AA

       4595 GGGGATTTTG


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35


Consensus pattern (42 bp):   
AATTTGCAATTTTTGAATAAACTAACCATTAATTGGATAAAC
Done.