Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010788.1 Corchorus capsularis cultivar CVL-1 contig10809, 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: 15761
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:1811 original size:116 final size:116

Alignment explanation


    Indices: 1602--1816  Score: 340
    Period size: 116  Copynumber: 1.9  Consensus size: 116

       1592 TATAGAAATC

                                                                             
       1602 AAATAATAAACAAAATCACATCTCTTTGGGAACCGAAAAAGATTTAAAAGAACAACAAAAGAAAA
          1 AAATAATAAACAAAATCACATCTCTTTGGGAACCGAAAAAGATTTAAAAGAACAACAAAAGAAAA

                  *        *                                   
       1667 TTGCGTTGAAAACAAGAAGTATACAAGAGTTGGATATTAAAACAAAAAGAA
         66 TTGCGTGGAAAACAAAAAGTATACAAGAGTTGGATATTAAAACAAAAAGAA

                *       *     *            * * *           *                *
       1718 AAATGATAAACACAATCATATCTCTTTGGGATCTGTAAAAGATTTAAGAGAACAACAAAAGAAAT
          1 AAATAATAAACAAAATCACATCTCTTTGGGAACCGAAAAAGATTTAAAAGAACAACAAAAGAAAA

                                              
       1783 TTGCGTGGAAAACAAAAAGTATACAAGAGTTGGA
         66 TTGCGTGGAAAACAAAAAGTATACAAGAGTTGGA

       1817 GCTCGTATTA


Statistics
Matches: 89,  Mismatches: 10, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 116   89  1.00

ACGTcount: A:0.52, C:0.11, G:0.16, T:0.21


Consensus pattern (116 bp):   
AAATAATAAACAAAATCACATCTCTTTGGGAACCGAAAAAGATTTAAAAGAACAACAAAAGAAAA
TTGCGTGGAAAACAAAAAGTATACAAGAGTTGGATATTAAAACAAAAAGAA

Found at i:6236 original size:16 final size:15

Alignment explanation


    Indices: 6208--6253  Score: 51
    Period size: 16  Copynumber: 3.1  Consensus size: 15

       6198 AGAAAAATCT

                           
       6208 CAAACCC-AAGAAAA
          1 CAAACCCGAAGAAAA

                            *
       6222 CAGAACCCGAAGAAACC
          1 CA-AACCCGAAGAAA-A

                           
       6239 CAAACCCGAA-AAAA
          1 CAAACCCGAAGAAAA

             
       6253 C
          1 C

       6254 CCGAATCCGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  14    3  0.11
  15    8  0.30
  16   14  0.52
  17    2  0.07

ACGTcount: A:0.57, C:0.33, G:0.11, T:0.00


Consensus pattern (15 bp):   
CAAACCCGAAGAAAA

Found at i:6254 original size:16 final size:16

Alignment explanation


    Indices: 6225--6266  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6215 AAGAAAACAG

                    *       
       6225 AACCCGAAGAAACCCA
          1 AACCCGAAAAAACCCA

                           *
       6241 AACCCGAAAAAACCCG
          1 AACCCGAAAAAACCCA

              *       
       6257 AATCCGAAAA
          1 AACCCGAAAA

       6267 TTTATGAAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.52, C:0.33, G:0.12, T:0.02


Consensus pattern (16 bp):   
AACCCGAAAAAACCCA

Found at i:6468 original size:32 final size:32

Alignment explanation


    Indices: 6421--6499  Score: 88
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       6411 AGACCGAGCT

                  *   *                      
       6421 CGAACCTGAATTAACCTAACC-CAAATTCAACC
          1 CGAACCCGAACTAACCT-ACCTCAAATTCAACC

               *             *            * 
       6453 CGAGCCCGAACTAACCTGCCTCAAATTCAATC
          1 CGAACCCGAACTAACCTACCTCAAATTCAACC

                      *    
       6485 CGAACCCGAATTAAC
          1 CGAACCCGAACTAAC

       6500 TTGACCTGAC


Statistics
Matches: 39,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  31    2  0.05
  32   37  0.95

ACGTcount: A:0.37, C:0.35, G:0.10, T:0.18


Consensus pattern (32 bp):   
CGAACCCGAACTAACCTACCTCAAATTCAACC

Found at i:10485 original size:25 final size:25

Alignment explanation


    Indices: 10457--10506  Score: 82
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      10447 AGAATTTTGA

                              *      
      10457 TTGAAATGATGAAATGAATCTTTTT
          1 TTGAAATGATGAAATGAAGCTTTTT

                   *                 
      10482 TTGAAATTATGAAATGAAGCTTTTT
          1 TTGAAATGATGAAATGAAGCTTTTT

      10507 AATATAAAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44


Consensus pattern (25 bp):   
TTGAAATGATGAAATGAAGCTTTTT

Found at i:12221 original size:17 final size:17

Alignment explanation


    Indices: 12199--12234  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      12189 AATTTTTGGA

                             
      12199 CATATATCTAATACATG
          1 CATATATCTAATACATG

                         *   
      12216 CATATATCTAATATATG
          1 CATATATCTAATACATG

              
      12233 CA
          1 CA

      12235 AAATGATTGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36


Consensus pattern (17 bp):   
CATATATCTAATACATG
Done.