Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015217.1 Corchorus capsularis cultivar CVL-1 contig15238, 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: 39073
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:12023 original size:35 final size:35

Alignment explanation


    Indices: 11980--12315  Score: 459
    Period size: 35  Copynumber: 9.7  Consensus size: 35

      11970 GGTAATAAGT

                         *          *           
      11980 AACTTAATTCAGGCTAATTAAGTAGGTCAGTGAAT-
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATC

              *        *           *           
      12015 AATTTAATTCAAGGTAATTAAGTCAGTCAGTAATC
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

                                               
      12050 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

                                              *
      12085 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATA
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

                                               
      12120 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

                  *                           *
      12155 AACTTAGTTCAGGGTAATTAAGTAAGTCAGTAATA
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

              *                                
      12190 AAATTAATTCAGGGTAA-T---TAAGTCAGTAATC
          1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

                                    *           
      12221 AACTTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
          1 AAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAATC

            *      *    *                 *      
      12257 GACTTAAATCGAAGGTAATTAAGTAAGTCAATAAAT-
          1 AACTTAATTC-AGGGTAATTAAGTAAGTCAGT-AATC

                     *             
      12293 AACTTAATTTAGGGTAATTAAGT
          1 AACTTAATTCAGGGTAATTAAGT

      12316 CAGTTAAAAA


Statistics
Matches: 267,  Mismatches: 26, Indels: 16
        0.86            0.08        0.05

Matches are distributed among these distances:
  31   14  0.05
  32   14  0.05
  33    1  0.00
  34    4  0.01
  35  192  0.72
  36   39  0.15
  37    3  0.01

ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32


Consensus pattern (35 bp):   
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC

Found at i:24060 original size:19 final size:18

Alignment explanation


    Indices: 24036--24071  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      24026 TGAAGATTTC

                               
      24036 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      24055 TTGAAGATTATTGAAGA
          1 TTGAAGATAATTGAAGA

      24072 ATCATTTCAA


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:0.00, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:30192 original size:29 final size:29

Alignment explanation


    Indices: 30146--30201  Score: 69
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      30136 ACAAACAATT

                         *      *        
      30146 GCAATTCAATCGATCAATAGCAAGATAAG
          1 GCAATTCAATCGAACAATAGAAAGATAAG

                               *        
      30175 GCAATTCAAATC-AACAATTGAAAGATA
          1 GCAATTC-AATCGAACAATAGAAAGATA

      30202 GAATAAGCAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  29   19  0.83
  30    4  0.17

ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21


Consensus pattern (29 bp):   
GCAATTCAATCGAACAATAGAAAGATAAG

Found at i:36549 original size:15 final size:15

Alignment explanation


    Indices: 36529--36558  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      36519 ATCAGGCTGC

                      *    
      36529 CACGATACACGATAT
          1 CACGATACACAATAT

                           
      36544 CACGATACACAATAT
          1 CACGATACACAATAT

      36559 TTCAACCGAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20


Consensus pattern (15 bp):   
CACGATACACAATAT
Done.