Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011322.1 Corchorus capsularis cultivar CVL-1 contig11343, 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: 15325
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30


Found at i:1097 original size:26 final size:26

Alignment explanation


    Indices: 1067--1153  Score: 79
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       1057 GTAATCAGTA

                                      
       1067 AATCAGTAATTAAGTAAAAAGAGATT
          1 AATCAGTAATTAAGTAAAAAGAGATT

                    *                *    *
       1093 AATCAG-AGTTAAAGTAATAGTAATCAG-TA
          1 AATCAGTAATT-AAGTAA-A--AA-GAGATT

              *                       
       1122 AACCAGTAATTAAGTAAAAAGAGATT
          1 AATCAGTAATTAAGTAAAAAGAGATT

                  
       1148 AATCAG
          1 AATCAG

       1154 AGTCAAAGTG


Statistics
Matches: 46,  Mismatches: 8, Indels: 14
        0.68            0.12        0.21

Matches are distributed among these distances:
  25    5  0.11
  26   20  0.43
  27    1  0.02
  28    1  0.02
  29   14  0.30
  30    5  0.11

ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25


Consensus pattern (26 bp):   
AATCAGTAATTAAGTAAAAAGAGATT

Found at i:1119 original size:55 final size:55

Alignment explanation


    Indices: 1051--1229  Score: 295
    Period size: 55  Copynumber: 3.3  Consensus size: 55

       1041 GGAAATCAAG

                              *                                    
       1051 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

                                                               *   
       1106 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAA
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

              * *                              *  *               *
       1161 GTGACAGTAATCAGTAAACCAGTAATTAAGTAAAAGGAAATTAATCAGAGTTAAG
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

                          
       1216 GTAATAGTAATCAG
          1 GTAATAGTAATCAG

       1230 CAAATAGGTA


Statistics
Matches: 114,  Mismatches: 10, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  55  114  1.00

ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25


Consensus pattern (55 bp):   
GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

Found at i:14541 original size:30 final size:30

Alignment explanation


    Indices: 14505--14606  Score: 122
    Period size: 30  Copynumber: 3.4  Consensus size: 30

      14495 CTGTGTTACA

                   *                      
      14505 TGTGTTTGGGGACTTTAGTATAGATGCCTC
          1 TGTGTTTAGGGACTTTAGTATAGATGCCTC

                             *            
      14535 TGTGTTTAGGGACTTTAATATAGATGCC-C
          1 TGTGTTTAGGGACTTTAGTATAGATGCCTC

                                              
      14564 TTGTGTTT-GAGGACTTTGATGTA-A-ATGCCTC
          1 -TGTGTTTAG-GGACTTT-A-GTATAGATGCCTC

                        
      14595 TGTGTTTAGGGA
          1 TGTGTTTAGGGA

      14607 TGAATACCCT


Statistics
Matches: 63,  Mismatches: 3, Indels: 12
        0.81            0.04        0.15

Matches are distributed among these distances:
  29    2  0.03
  30   55  0.87
  31    4  0.06
  32    2  0.03

ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40


Consensus pattern (30 bp):   
TGTGTTTAGGGACTTTAGTATAGATGCCTC

Found at i:14579 original size:60 final size:57

Alignment explanation


    Indices: 14505--14691  Score: 221
    Period size: 60  Copynumber: 3.3  Consensus size: 57

      14495 CTGTGTTACA

                    *                                                   
      14505 TGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTTAGGGACTTTAATATAGATGCCCT
          1 TGTGTTTGAGGACTTTAGTATAGATGCCTCTGTGTTTAGGGAC-TT-ATATA-ATGCCCT

                                                          *            
      14565 TGTGTTTGAGGACTTTGATGTA-A-ATGCCTCTGTGTTTAGGGA-TGA-AT-A--CCCT
          1 TGTGTTTGAGGACTTT-A-GTATAGATGCCTCTGTGTTTAGGGACTTATATAATGCCCT

                                                                        
      14617 TGTGTTTGAGGACTTT-GATATAGAATTGCCTCTGTGTTTAGGGACTTATA-AATGCCCT
          1 TGTGTTTGAGGACTTTAG-TATAG-A-TGCCTCTGTGTTTAGGGACTTATATAATGCCCT

                             
      14675 TGTGTTTGAGGACTTTA
          1 TGTGTTTGAGGACTTTA

      14692 ATTATTGGGT


Statistics
Matches: 111,  Mismatches: 3, Indels: 27
        0.79            0.02        0.19

Matches are distributed among these distances:
  49    1  0.01
  50    2  0.02
  51    1  0.01
  52   20  0.18
  53    1  0.01
  54   19  0.17
  55    2  0.02
  56    4  0.04
  57    1  0.01
  58   21  0.19
  60   34  0.31
  61    2  0.02
  62    3  0.03

ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40


Consensus pattern (57 bp):   
TGTGTTTGAGGACTTTAGTATAGATGCCTCTGTGTTTAGGGACTTATATAATGCCCT
Done.