Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014090.1 Corchorus capsularis cultivar CVL-1 contig14111, 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: 8197
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:470 original size:82 final size:82

Alignment explanation


    Indices: 382--541  Score: 302
    Period size: 82  Copynumber: 2.0  Consensus size: 82

        372 GCGTCTGGGA

                                                                             
        382 TCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATGGAGTAAAAATGAAGCCTAACA
          1 TCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATGGAGTAAAAATGAAGCCTAACA

                             
        447 AATAGCGGCGTCTTATG
         66 AATAGCGGCGTCTTATG

                     *                                 *                     
        464 TCCCAGACGTCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAAAAATGAAGCCTAACA
          1 TCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATGGAGTAAAAATGAAGCCTAACA

                         
        529 AATAGCGGCGTCT
         66 AATAGCGGCGTCT

        542 AGGCCCTAAA


Statistics
Matches: 76,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  82   76  1.00

ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25


Consensus pattern (82 bp):   
TCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATGGAGTAAAAATGAAGCCTAACA
AATAGCGGCGTCTTATG

Found at i:812 original size:113 final size:113

Alignment explanation


    Indices: 449--818  Score: 616
    Period size: 113  Copynumber: 3.2  Consensus size: 113

        439 GCCTAACAAA

                                    *                                        
        449 TAGCGGCGTCTTATGTCCCAGACGTCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA
          1 TAGCGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA

                                                            
        514 AAATGAAGCCTAACAAATAGCGGCGTCTAGGCCCTAAACGCCGCTATT
         66 AAATGAAGCCTAACAAATAGCGGCGTCTAGGCCCTAAACGCCGCTATT

                                 *                      *       *            
        562 TAGCGGCGTCTTATGTCCCAGTCGCCGCCATAC-TAATTTTTTCAGAGAAATGCAAATTGAGTAA
          1 TAGCGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA

                 **                     *                       
        626 CCCTATTTGAAGCCTAACAAATAGCGGCATCTAGGCCCTAAACGCCGCTATT
         66 ----AAATGAAGCCTAACAAATAGCGGCGTCTAGGCCCTAAACGCCGCTATT

                                                                             
        678 TAGCGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA
          1 TAGCGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA

                                      *                     
        743 AAATGAAGCCTAACAAATAGCGGCGTGTAGGCCCTAAACGCCGCTATT
         66 AAATGAAGCCTAACAAATAGCGGCGTCTAGGCCCTAAACGCCGCTATT

                            *           
        791 TAGCGGCGTCTTATGTACCAGACGCCGC
          1 TAGCGGCGTCTTATGTCCCAGACGCCGC

        819 TAAATGGTGG


Statistics
Matches: 237,  Mismatches: 15, Indels: 10
        0.90            0.06        0.04

Matches are distributed among these distances:
 112   29  0.12
 113  102  0.43
 116   77  0.32
 117   29  0.12

ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25


Consensus pattern (113 bp):   
TAGCGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGAGAAATACAAATTGAGTAA
AAATGAAGCCTAACAAATAGCGGCGTCTAGGCCCTAAACGCCGCTATT

Found at i:1731 original size:15 final size:15

Alignment explanation


    Indices: 1711--1741  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1701 CTTCTCCTTT

                       *   
       1711 CCTTCTCTTCGCTTC
          1 CCTTCTCTTCGATTC

                           
       1726 CCTTCTCTTCGATTC
          1 CCTTCTCTTCGATTC

             
       1741 C
          1 C

       1742 TAAACCCTAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.03, C:0.45, G:0.06, T:0.45


Consensus pattern (15 bp):   
CCTTCTCTTCGATTC

Found at i:4581 original size:58 final size:59

Alignment explanation


    Indices: 4512--4626  Score: 187
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       4502 GCTATATTTA

                               *                                       
       4512 AAAAACCCTTAAA-ATAGCGGCGTCTAAACGCCGCTATATTTAATTTCAGATTTTTTTT
          1 AAAAACCCTTAAATATAGCAGCGTCTAAACGCCGCTATATTTAATTTCAGATTTTTTTT

                *                     *                    *         
       4570 AAAATCCCTTAAATATAGCAGCGTCTGAACGCCGCTATATTTAATTTGAGATTTTTT
          1 AAAAACCCTTAAATATAGCAGCGTCTAAACGCCGCTATATTTAATTTCAGATTTTTT

       4627 CTCAAAATAG


Statistics
Matches: 52,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  58   12  0.23
  59   40  0.77

ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37


Consensus pattern (59 bp):   
AAAAACCCTTAAATATAGCAGCGTCTAAACGCCGCTATATTTAATTTCAGATTTTTTTT

Done.