Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005218.1 Corchorus capsularis cultivar CVL-1 contig05236, 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: 7812
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:1396 original size:17 final size:16

Alignment explanation


    Indices: 1374--1408  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1364 TACTTCATTG

                             
       1374 CTCAATTCCCTCTGTTT
          1 CTCAATT-CCTCTGTTT

                   *        
       1391 CTCAATTTCTCTGTTT
          1 CTCAATTCCTCTGTTT

              
       1407 CT
          1 CT

       1409 TGATTTCTCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   10  0.59
  17    7  0.41

ACGTcount: A:0.11, C:0.31, G:0.06, T:0.51


Consensus pattern (16 bp):   
CTCAATTCCTCTGTTT

Found at i:1737 original size:7 final size:7

Alignment explanation


    Indices: 1713--1747  Score: 52
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       1703 CGATACCTTC

                   
       1713 TCTTGTT
          1 TCTTGTT

                     
       1720 TCTTGATTT
          1 TCTTG--TT

                   
       1729 TCTTGTT
          1 TCTTGTT

                   
       1736 TCTTGTT
          1 TCTTGTT

                 
       1743 TCTTG
          1 TCTTG

       1748 ACTTCCCCTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   7   19  0.73
   9    7  0.27

ACGTcount: A:0.03, C:0.14, G:0.14, T:0.69


Consensus pattern (7 bp):   
TCTTGTT

Found at i:2421 original size:39 final size:39

Alignment explanation


    Indices: 2378--2453  Score: 152
    Period size: 39  Copynumber: 1.9  Consensus size: 39

       2368 CCCAATTATC

                                                   
       2378 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA
          1 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA

                                                 
       2417 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGG
          1 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGG

       2454 AAGAGTTGCC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   37  1.00

ACGTcount: A:0.46, C:0.07, G:0.24, T:0.24


Consensus pattern (39 bp):   
AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA

Found at i:2476 original size:39 final size:39

Alignment explanation


    Indices: 2428--2558  Score: 226
    Period size: 39  Copynumber: 3.3  Consensus size: 39

       2418 GTCAAAACAA

                      *      *     *                
       2428 GAATATGAATAATGAGGTGATATTGGAAGAGTTGCCAGTT
          1 GAAT-TGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT

                                                   
       2468 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
          1 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT

                                                   
       2507 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
          1 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT

                         
       2546 GAATTGAATCATG
          1 GAATTGAATCATG

       2559 CTGTTACTTA


Statistics
Matches: 88,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  39   84  0.95
  40    4  0.05

ACGTcount: A:0.33, C:0.08, G:0.31, T:0.27


Consensus pattern (39 bp):   
GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT

Found at i:2489 original size:78 final size:78

Alignment explanation


    Indices: 2389--2558  Score: 189
    Period size: 78  Copynumber: 2.2  Consensus size: 78

       2379 GTCAAAACAA

                      *      *     *  *                              *     * 
       2389 GAATATGAATAATGAGGTGATATTGGCA-AGTCAAAACAAGAATATGAATAATGAGGTGATATTG
          1 GAAT-TGAATCATGAGGCGATATGGGAAGAGTCAAAACAAGAAT-TGAATAATGAGGCGATATGG

                           
       2453 GAAGAGTTGCCAGTT
         64 GAAGAGTTGCCAGTT

                                           **** ***         *                
       2468 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTTGAATTGAATCATGAGGCGATATGGGA
          1 GAATTGAATCATGAGGCGATATGGGAAGAGTCAAAACAAGAATTGAATAATGAGGCGATATGGGA

                         
       2533 AGAGTTGCCAGTT
         66 AGAGTTGCCAGTT

                         
       2546 GAATTGAATCATG
          1 GAATTGAATCATG

       2559 CTGTTACTTA


Statistics
Matches: 76,  Mismatches: 14, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  78   64  0.84
  79   12  0.16

ACGTcount: A:0.36, C:0.08, G:0.29, T:0.26


Consensus pattern (78 bp):   
GAATTGAATCATGAGGCGATATGGGAAGAGTCAAAACAAGAATTGAATAATGAGGCGATATGGGA
AGAGTTGCCAGTT

Done.