Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011126.1 Corchorus capsularis cultivar CVL-1 contig11147, 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: 2539
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29


Found at i:1344 original size:8 final size:8

Alignment explanation


    Indices: 1316--1349  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       1306 GAATCGGCTA

                    
       1316 TGAATTTT
          1 TGAATTTT

                    *
       1324 TGAAGTTTC
          1 TGAA-TTTT

                    
       1333 TGAATTTT
          1 TGAATTTT

                    
       1341 TGAATTTT
          1 TGAATTTT

             
       1349 T
          1 T

       1350 CAAGAAGGTG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:2349 original size:33 final size:34

Alignment explanation


    Indices: 2312--2385  Score: 91
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       2302 CGCCAAGTGA

                                  *            
       2312 TGGCCGGTTG-TGGCCAGACATGTCC-ATGTCGCG
          1 TGGCCGGTTGATGGCCAGACATCTCCGA-GTCGCG

                            * *               
       2345 TGGCCGG-TGATGGCCGGGCATCTCCGAGTCGCG
          1 TGGCCGGTTGATGGCCAGACATCTCCGAGTCGCG

                    
       2378 TGGCCGGT
          1 TGGCCGGT

       2386 GTTGGCCGGT


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  32    2  0.06
  33   32  0.91
  34    1  0.03

ACGTcount: A:0.09, C:0.28, G:0.41, T:0.22


Consensus pattern (34 bp):   
TGGCCGGTTGATGGCCAGACATCTCCGAGTCGCG

Found at i:2392 original size:43 final size:43

Alignment explanation


    Indices: 2345--2428  Score: 123
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       2335 CCATGTCGCG

                                     *      *          
       2345 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCGTGGCCGGTGT
          1 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCATGGCCGGTGT

                     *       * *                     
       2388 TGGCCGGTGTTGGCCGGTCTTCTCCAAGTCGCATGGCCGGT
          1 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCATGGCCGGT

       2429 TACTCGCACC


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  43   36  1.00

ACGTcount: A:0.07, C:0.29, G:0.40, T:0.24


Consensus pattern (43 bp):   
TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCATGGCCGGTGT

Found at i:2393 original size:10 final size:10

Alignment explanation


    Indices: 2378--2405  Score: 56
    Period size: 10  Copynumber: 2.8  Consensus size: 10

       2368 CCGAGTCGCG

                      
       2378 TGGCCGGTGT
          1 TGGCCGGTGT

                      
       2388 TGGCCGGTGT
          1 TGGCCGGTGT

                    
       2398 TGGCCGGT
          1 TGGCCGGT

       2406 CTTCTCCAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.00, C:0.21, G:0.50, T:0.29


Consensus pattern (10 bp):   
TGGCCGGTGT
Done.