Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012649.1 Corchorus capsularis cultivar CVL-1 contig12670, 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: 4501
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:4156 original size:22 final size:22

Alignment explanation


    Indices: 4130--4178  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4120 GAATTTCGAG

                  *             *  
       4130 AACCTTTTTAT-AAATTTTTTTT
          1 AACCTTCTTATGAAA-TTTTGTT

                                  
       4152 AACCTTCTTATGAAATTTTGTT
          1 AACCTTCTTATGAAATTTTGTT

                 
       4174 AACCT
          1 AACCT

       4179 CTCTAAGGAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22   21  0.88
  23    3  0.12

ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53


Consensus pattern (22 bp):   
AACCTTCTTATGAAATTTTGTT

Found at i:4355 original size:22 final size:22

Alignment explanation


    Indices: 4330--4444  Score: 81
    Period size: 23  Copynumber: 5.1  Consensus size: 22

       4320 GAATTGTTAG

                 *    *           
       4330 TAATCGCACTCTGAAATTTTGA
          1 TAATCACACTATGAAATTTTGA

                                   
       4352 TAATCACACTATG-AATTTGTGA
          1 TAATCACACTATGAAATTT-TGA

               * * *              
       4374 TAACCTCGCTATGAAATTTTGA
          1 TAATCACACTATGAAATTTTGA

                   *      *         
       4396 TAAATCTTC-CTATAAAATTTTGA
          1 T-AATC-ACACTATGAAATTTTGA

                * * *    *         
       4419 TAAACCTCCCTATAAAATTTTGA
          1 T-AATCACACTATGAAATTTTGA

               
       4442 TAA
          1 TAA

       4445 CTTTCTTATA


Statistics
Matches: 80,  Mismatches: 8, Indels: 10
        0.82            0.08        0.10

Matches are distributed among these distances:
  21    5  0.06
  22   32  0.40
  23   41  0.51
  24    2  0.03

ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37


Consensus pattern (22 bp):   
TAATCACACTATGAAATTTTGA

Found at i:4408 original size:23 final size:23

Alignment explanation


    Indices: 4382--4466  Score: 109
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       4372 GATAACCTCG

                *                  
       4382 CTATGAAATTTTGATAAATCTTC
          1 CTATAAAATTTTGATAAATCTTC

                              *  * 
       4405 CTATAAAATTTTGATAAACCTCC
          1 CTATAAAATTTTGATAAATCTTC

                             *     
       4428 CTATAAAATTTTGATAACT-TTC
          1 CTATAAAATTTTGATAAATCTTC

            *        *       
       4450 TTATAAAATCTTGATAA
          1 CTATAAAATTTTGATAA

       4467 CTACAAATTT


Statistics
Matches: 54,  Mismatches: 8, Indels: 1
        0.86            0.13        0.02

Matches are distributed among these distances:
  22   17  0.31
  23   37  0.69

ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41


Consensus pattern (23 bp):   
CTATAAAATTTTGATAAATCTTC

Found at i:4456 original size:45 final size:46

Alignment explanation


    Indices: 4365--4466  Score: 136
    Period size: 46  Copynumber: 2.2  Consensus size: 46

       4355 TCACACTATG

                             *    *                        
       4365 AATTTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAA
          1 AATTT-TGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAA

                                              *     *     
       4411 AATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTATAA
          1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAA

               *       
       4456 AATCTTGATAA
          1 AATTTTGATAA

       4467 CTACAAATTT


Statistics
Matches: 50,  Mismatches: 5, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  45   22  0.44
  46   28  0.56

ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40


Consensus pattern (46 bp):   
AATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTATAA

Found at i:4457 original size:22 final size:22

Alignment explanation


    Indices: 4365--4468  Score: 102
    Period size: 23  Copynumber: 4.6  Consensus size: 22

       4355 TCACACTATG

                          *       * 
       4365 AATTTGTGATAAC-CTCGCTATGA
          1 AATTT-TGATAACTTTC-CTATAA

                       *           
       4388 AATTTTGATAAATCTTCCTATAA
          1 AATTTTGATAACT-TTCCTATAA

                         * *       
       4411 AATTTTGATAAACCTCCCTATAA
          1 AATTTTGAT-AACTTTCCTATAA

                            *     
       4434 AATTTTGATAACTTTCTTATAA
          1 AATTTTGATAACTTTCCTATAA

               *         
       4456 AATCTTGATAACT
          1 AATTTTGATAACT

       4469 ACAAATTTTG


Statistics
Matches: 68,  Mismatches: 10, Indels: 7
        0.80            0.12        0.08

Matches are distributed among these distances:
  22   28  0.41
  23   36  0.53
  24    4  0.06

ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40


Consensus pattern (22 bp):   
AATTTTGATAACTTTCCTATAA
Done.