Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012190.1 Corchorus capsularis cultivar CVL-1 contig12211, 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: 19965
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:1083 original size:23 final size:23

Alignment explanation


    Indices: 1026--1083  Score: 64
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       1016 TATTGCTTGT

                            *       
       1026 ATATATAGTTATATATTTAGATCA
          1 ATATATA-TTATATATCTAGATCA

                   *          *     
       1050 AGT-TATTTTATATATCTGGATCA
          1 A-TATATATTATATATCTAGATCA

                       
       1073 ATATATATTAT
          1 ATATATATTAT

       1084 TGAAGAGCAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 5
        0.76            0.11        0.14

Matches are distributed among these distances:
  22    1  0.04
  23   22  0.79
  24    4  0.14
  25    1  0.04

ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48


Consensus pattern (23 bp):   
ATATATATTATATATCTAGATCA

Found at i:10030 original size:21 final size:19

Alignment explanation


    Indices: 10005--10062  Score: 62
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       9995 GCTGCTCTAA

                                 
      10005 TAATCTCATATGTACAGTACC
          1 TAATCTCATATGTACAGT--C

                  *  *        *
      10026 TAATCTAATCTGTACAGTG
          1 TAATCTCATATGTACAGTC

                     *        
      10045 TAATCTCATTTGTACAGT
          1 TAATCTCATATGTACAGT

      10063 TGCTAAATAG


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38


Consensus pattern (19 bp):   
TAATCTCATATGTACAGTC

Found at i:10317 original size:25 final size:23

Alignment explanation


    Indices: 10283--10340  Score: 71
    Period size: 25  Copynumber: 2.4  Consensus size: 23

      10273 TCAAACCCTA

                              *     
      10283 AACTTCATTTCTAACAACTTCTTC
          1 AACTTCATTTCTAACAA-ATCTTC

                       *            
      10307 GAACTTCATTTTTAACAAATCTTC
          1 -AACTTCATTTCTAACAAATCTTC

              *       
      10331 AAATTCATTT
          1 AACTTCATTT

      10341 TCCTTCATTT


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  23    9  0.30
  24    5  0.17
  25   16  0.53

ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43


Consensus pattern (23 bp):   
AACTTCATTTCTAACAAATCTTC

Found at i:10417 original size:26 final size:26

Alignment explanation


    Indices: 10381--10483  Score: 97
    Period size: 26  Copynumber: 4.0  Consensus size: 26

      10371 CCAAAAAAAA

                *                     
      10381 TAATCATAAACTAATTAAATACTAAT
          1 TAATAATAAACTAATTAAATACTAAT

                             *        
      10407 TAATAATAAACTAATTAGATACTAAT
          1 TAATAATAAACTAATTAAATACTAAT

                           *        *    
      10433 TAA-ACATAAAC-AAATAAACTAAGTAAT
          1 TAATA-ATAAACTAATTAAA-T-ACTAAT

              *    *                  
      10460 T-TTAATTAACTAATTAAA-ACTAAT
          1 TAATAATAAACTAATTAAATACTAAT

      10484 CATAAACTAA


Statistics
Matches: 63,  Mismatches: 9, Indels: 12
        0.75            0.11        0.14

Matches are distributed among these distances:
  24    5  0.08
  25    6  0.10
  26   39  0.62
  27   13  0.21

ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33


Consensus pattern (26 bp):   
TAATAATAAACTAATTAAATACTAAT

Found at i:10579 original size:11 final size:12

Alignment explanation


    Indices: 10565--10593  Score: 51
    Period size: 11  Copynumber: 2.5  Consensus size: 12

      10555 TCTTTTTTTC

                        
      10565 TTTTTAAAAT-T
          1 TTTTTAAAATAT

                        
      10576 TTTTTAAAATAT
          1 TTTTTAAAATAT

                  
      10588 TTTTTA
          1 TTTTTA

      10594 CATCAACCCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11   10  0.59
  12    7  0.41

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (12 bp):   
TTTTTAAAATAT

Found at i:17856 original size:2 final size:2

Alignment explanation


    Indices: 17845--17873  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      17835 TAACTATAAT

                                                        
      17845 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17874 CACTAATTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.