Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016317.1 Corchorus capsularis cultivar CVL-1 contig16338, 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: 13418
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:2306 original size:24 final size:27

Alignment explanation


    Indices: 2279--2331  Score: 67
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       2269 TTCTAGTGAT

                                 *     
       2279 GAGAAT-AAG-GAAGGAAAA-GAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

                   *                   
       2303 GAGAATCGAGAGAAGGAAAATAAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

              
       2330 GA
          1 GA

       2332 ATTTCATCCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  24    6  0.25
  25    2  0.08
  26    9  0.38
  27    7  0.29

ACGTcount: A:0.53, C:0.02, G:0.40, T:0.06


Consensus pattern (27 bp):   
GAGAATCAAGAGAAGGAAAATAAGGAG

Found at i:3245 original size:1 final size:1

Alignment explanation


    Indices: 3239--3270  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

       3229 ATTTTCTAGT

                                            
       3239 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       3271 CATCCATTGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4083 original size:19 final size:18

Alignment explanation


    Indices: 4059--4094  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4049 TGAAGATTTC

                               
       4059 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       4078 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       4095 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:12299 original size:33 final size:33

Alignment explanation


    Indices: 12223--12346  Score: 135
    Period size: 33  Copynumber: 3.7  Consensus size: 33

      12213 TAGACAAAGG

                                   *    *     
      12223 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT

                **           *     *         
      12256 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT

                                *             
      12289 GTCGCGTGGCCGG-TGATGGTCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT

                                     
      12322 GTCGCGTGGCCGGTCTTGTGGCCGG
          1 GTCGCGTGGCCGG--TTGTGGCCGG

      12347 TGTTGCGCGG


Statistics
Matches: 75,  Mismatches: 11, Indels: 8
        0.80            0.12        0.09

Matches are distributed among these distances:
  32    3  0.04
  33   64  0.85
  35    6  0.08
  36    2  0.03

ACGTcount: A:0.07, C:0.27, G:0.42, T:0.24


Consensus pattern (33 bp):   
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Done.