Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015091.1 Corchorus capsularis cultivar CVL-1 contig15112, 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: 4782
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29


Found at i:1309 original size:26 final size:26

Alignment explanation


    Indices: 1279--1365  Score: 79
    Period size: 26  Copynumber: 3.2  Consensus size: 26

       1269 GTAATCAGTA

                                      
       1279 AATCAGTAATTAAGTAAAAAGAGATT
          1 AATCAGTAATTAAGTAAAAAGAGATT

                    *                *    *
       1305 AATCAG-AGTTAAAGTAATAGTAATCAG-TA
          1 AATCAGTAATT-AAGTAA-A--AA-GAGATT

              *                       
       1334 AACCAGTAATTAAGTAAAAAGAGATT
          1 AATCAGTAATTAAGTAAAAAGAGATT

                  
       1360 AATCAG
          1 AATCAG

       1366 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:1331 original size:55 final size:55

Alignment explanation


    Indices: 1263--1441  Score: 295
    Period size: 55  Copynumber: 3.3  Consensus size: 55

       1253 GGAAATCAAG

                              *                                    
       1263 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

                                                               *   
       1318 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAA
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

              * *                              *  *               *
       1373 GTGACAGTAATCAGTAAACCAGTAATTAAGTAAAAGGAAATTAATCAGAGTTAAG
          1 GTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAA

                          
       1428 GTAATAGTAATCAG
          1 GTAATAGTAATCAG

       1442 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:1908 original size:25 final size:23

Alignment explanation


    Indices: 1851--1908  Score: 55
    Period size: 25  Copynumber: 2.4  Consensus size: 23

       1841 AGGTGATCAG

                                   
       1851 TAATTCA-AAGAGTAAAATGGTA
          1 TAATTCAGAAGAGTAAAATGGTA

                ***                   
       1873 TAGAAAAAGAAGAGTAAAAATGGTAA
          1 TA-ATTCAGAAGAGT-AAAATGGT-A

                      
       1899 TAATTCAGAA
          1 TAATTCAGAA

       1909 TAAGGTAATT


Statistics
Matches: 26,  Mismatches: 6, Indels: 5
        0.70            0.16        0.14

Matches are distributed among these distances:
  22    2  0.08
  23    2  0.08
  24    6  0.23
  25   13  0.50
  26    3  0.12

ACGTcount: A:0.55, C:0.03, G:0.19, T:0.22


Consensus pattern (23 bp):   
TAATTCAGAAGAGTAAAATGGTA
Done.