Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011229.1 Corchorus capsularis cultivar CVL-1 contig11250, 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, 821

Length: 1369
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35


Found at i:279 original size:37 final size:37

Alignment explanation


    Indices: 187--280  Score: 86
    Period size: 37  Copynumber: 2.5  Consensus size: 37

        177 TGGATCGATT

                     **           *            * 
        187 AACTGAAGATGGACCACCCTGGGTCAATTTGAAAATC
          1 AACTGAAGAAAGACCACCCTGGATCAATTTGAAAAGC

                        *  *                        
        224 -ACTTTG-AGAACGATCACCCTGGATCAAATTTG-AAAGC
          1 AAC--TGAAGAAAGACCACCCTGGATC-AATTTGAAAAGC

                                
        261 AACTGAAGAAAGACCACCCT
          1 AACTGAAGAAAGACCACCCT

        281 AGGTCCATTG


Statistics
Matches: 45,  Mismatches: 7, Indels: 10
        0.73            0.11        0.16

Matches are distributed among these distances:
  36    4  0.09
  37   31  0.69
  38   10  0.22

ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20


Consensus pattern (37 bp):   
AACTGAAGAAAGACCACCCTGGATCAATTTGAAAAGC

Found at i:303 original size:34 final size:34

Alignment explanation


    Indices: 264--329  Score: 80
    Period size: 34  Copynumber: 1.9  Consensus size: 34

        254 TGAAAGCAAC

                                   *           
        264 TGAAGAAAGACCACCCTAGG-TCCATTGAAATTAT
          1 TGAAGAAAGACCACCCT-GGATCAATTGAAATTAT

                  *   * *                   
        298 TGAAGAGAGATCGCCCTGGATCAATTGAAATT
          1 TGAAGAAAGACCACCCTGGATCAATTGAAATT

        330 TACTGAATGG


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  33    2  0.07
  34   25  0.93

ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24


Consensus pattern (34 bp):   
TGAAGAAAGACCACCCTGGATCAATTGAAATTAT

Found at i:1358 original size:17 final size:16

Alignment explanation


    Indices: 1324--1365  Score: 57
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1314 ACCCTAGAGC

                            
       1324 TTCTTTTTTCTTCTTT
          1 TTCTTTTTTCTTCTTT

                              
       1340 TTCTTTTCTTCTTTCTTT
          1 TTCTTTT-TTC-TTCTTT

                    
       1358 TCTCTTTT
          1 T-TCTTTT

       1366 CTCT


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

Matches are distributed among these distances:
  16    7  0.30
  17    3  0.13
  18    7  0.30
  19    6  0.26

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (16 bp):   
TTCTTTTTTCTTCTTT

Found at i:1366 original size:12 final size:11

Alignment explanation


    Indices: 1324--1367  Score: 54
    Period size: 12  Copynumber: 3.9  Consensus size: 11

       1314 ACCCTAGAGC

                      *
       1324 TTCTTTTT-TC
          1 TTCTTTTTCTT

                       
       1334 TTCTTTTTCTT
          1 TTCTTTTTCTT

                        
       1345 TTCTTCTTTCTT
          1 TTCTT-TTTCTT

                       
       1357 TTCTCTTTTCT
          1 TTCT-TTTTCT

       1368 CT


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  10    8  0.27
  11    6  0.20
  12   15  0.50
  13    1  0.03

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (11 bp):   
TTCTTTTTCTT
Done.