Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011473.1 Corchorus capsularis cultivar CVL-1 contig11494, 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: 40585
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:5177 original size:21 final size:20

Alignment explanation


    Indices: 5140--5178  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5130 TTTAGAAGCA

                       *        
       5140 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
       5160 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

       5179 GGAAGGGAAA


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

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC

Found at i:5283 original size:73 final size:73

Alignment explanation


    Indices: 5198--5339  Score: 214
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       5188 ATGTGTAGTC

                   *                  *                   *                  
       5198 ACGAAAAGGGTAGAAGGAAAAGGAATGTGGGAAACTCATAAAGGGGTTTTTTAGTCATCC-GAAA
          1 ACGAAAAAGGTAGAAGGAAAAGGAATATGGGAAACTCATAAAGGGGCTTTTTAGTCA-CCTGAAA

                     
       5262 AGTGTAATT
         65 AGTGTAATT

                                 *              *   *                        
       5271 ACGAAAAAGGTAGAAGGAAAATGAATATGGGAAACTTATAGAGGGGCTTTTTAGTCACCTGAAAA
          1 ACGAAAAAGGTAGAAGGAAAAGGAATATGGGAAACTCATAAAGGGGCTTTTTAGTCACCTGAAAA

                
       5336 GTGT
         66 GTGT

       5340 GAAAAGACTA


Statistics
Matches: 62,  Mismatches: 6, Indels: 2
        0.89            0.09        0.03

Matches are distributed among these distances:
  72    2  0.03
  73   60  0.97

ACGTcount: A:0.40, C:0.08, G:0.28, T:0.23


Consensus pattern (73 bp):   
ACGAAAAAGGTAGAAGGAAAAGGAATATGGGAAACTCATAAAGGGGCTTTTTAGTCACCTGAAAA
GTGTAATT

Found at i:5484 original size:2 final size:2

Alignment explanation


    Indices: 5473--5501  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       5463 TTACATTTAC

                                                        
       5473 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5502 GCAATTGAGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:10027 original size:17 final size:17

Alignment explanation


    Indices: 10005--10039  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       9995 CATTGACCCA

                             
      10005 AGGACTGAGAGTCATAT
          1 AGGACTGAGAGTCATAT

                             
      10022 AGGACTGAGAGTCATAT
          1 AGGACTGAGAGTCATAT

             
      10039 A
          1 A

      10040 AATTAAAAAT


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

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23


Consensus pattern (17 bp):   
AGGACTGAGAGTCATAT

Found at i:10441 original size:48 final size:48

Alignment explanation


    Indices: 10385--10484  Score: 200
    Period size: 48  Copynumber: 2.1  Consensus size: 48

      10375 TTAAGTAATC

                                                            
      10385 AAATTTTGTTGTGGAATGATAACAAAACAAAGCAATTGAGTAAAATTG
          1 AAATTTTGTTGTGGAATGATAACAAAACAAAGCAATTGAGTAAAATTG

                                                            
      10433 AAATTTTGTTGTGGAATGATAACAAAACAAAGCAATTGAGTAAAATTG
          1 AAATTTTGTTGTGGAATGATAACAAAACAAAGCAATTGAGTAAAATTG

                
      10481 AAAT
          1 AAAT

      10485 ATGTAAAAGA


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   52  1.00

ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29


Consensus pattern (48 bp):   
AAATTTTGTTGTGGAATGATAACAAAACAAAGCAATTGAGTAAAATTG

Found at i:11345 original size:18 final size:18

Alignment explanation


    Indices: 11322--11360  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      11312 CATGTGCATG

                              
      11322 CAAATCCAAAAACTTAAT
          1 CAAATCCAAAAACTTAAT

                              
      11340 CAAATCCAAAAACTTAAT
          1 CAAATCCAAAAACTTAAT

               
      11358 CAA
          1 CAA

      11361 TTAAGAACTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21


Consensus pattern (18 bp):   
CAAATCCAAAAACTTAAT

Found at i:34735 original size:2 final size:2

Alignment explanation


    Indices: 34728--34781  Score: 72
    Period size: 2  Copynumber: 27.0  Consensus size: 2

      34718 TTACCTAGGT

                                       *     *                     *     *
      34728 TA TA TA TA TA TA TA TA TA CA TA CA TA TA TA TA TA TA TG TA TG
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                             
      34770 TA TA TA TA TA TA
          1 TA TA TA TA TA TA

      34782 CACACTCCAA


Statistics
Matches: 44,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46


Consensus pattern (2 bp):   
TA

Done.