Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001302.1 Corchorus capsularis cultivar CVL-1 contig01302, 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, 628

Length: 1047
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31


Found at i:268 original size:22 final size:23

Alignment explanation


    Indices: 240--284  Score: 83
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        230 ATAAAGATAG

                                   
        240 TAAAAAAAGGAGG-ACATAATGA
          1 TAAAAAAAGGAGGAACATAATGA

                                   
        262 TAAAAAAAGGAGGAACATAATGA
          1 TAAAAAAAGGAGGAACATAATGA

        285 GCGTTCTACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  22   13  0.59
  23    9  0.41

ACGTcount: A:0.60, C:0.04, G:0.22, T:0.13


Consensus pattern (23 bp):   
TAAAAAAAGGAGGAACATAATGA

Found at i:407 original size:27 final size:27

Alignment explanation


    Indices: 322--400  Score: 140
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        312 GGAATCGAGC

                              *        
        322 AAAGATAGTGATAGAAATGCCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                                       
        349 AAAGATAGTGATAGAAATACCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                         *           
        376 AAAGATAGTGATAAAAATACCAATA
          1 AAAGATAGTGATAGAAATACCAATA

        401 ACGAAGAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   50  1.00

ACGTcount: A:0.56, C:0.08, G:0.18, T:0.19


Consensus pattern (27 bp):   
AAAGATAGTGATAGAAATACCAATAGA

Found at i:664 original size:33 final size:33

Alignment explanation


    Indices: 643--772  Score: 129
    Period size: 33  Copynumber: 3.8  Consensus size: 33

        633 TGCAAATGGT

                                       *  *        
        643 AATGATTTAGAAAGTTCTAATGATAATGATTTCGACGAA
          1 AATGATTTAGAAAGTTCTAATGAT--TCA-AT-GA-G-A

                                       * *    
        682 AATGATTTAGAAAGTTCTAATGATTTCGACGA-A
          1 AATGATTTAGAAAGTTCTAATGA-TTCAATGAGA

                                       *      
        715 AATGATTTAGAAAGTTCTAATGATTTCGATGAG-
          1 AATGATTTAGAAAGTTCTAATGA-TTCAATGAGA

                                     
        748 AATGATTTAGAAAGTTCTAATGATT
          1 AATGATTTAGAAAGTTCTAATGATT

        773 TCGACGAAAA


Statistics
Matches: 84,  Mismatches: 5, Indels: 11
        0.84            0.05        0.11

Matches are distributed among these distances:
  32    2  0.02
  33   55  0.65
  36    2  0.02
  38    1  0.01
  39   23  0.27
  40    1  0.01

ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35


Consensus pattern (33 bp):   
AATGATTTAGAAAGTTCTAATGATTCAATGAGA

Found at i:705 original size:18 final size:18

Alignment explanation


    Indices: 682--773  Score: 72
    Period size: 18  Copynumber: 5.4  Consensus size: 18

        672 TTTCGACGAA

                              
        682 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *   *   **
        700 AATGATTTCG-ACG--AA
          1 AATGATTTAGAAAGTTCT

                              
        715 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *   *      
        733 AATGATTTCGATGAG----
          1 AATGATTTAGA-AAGTTCT

                              
        748 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    
        766 AATGATTT
          1 AATGATTT

        774 CGACGAAAAT


Statistics
Matches: 54,  Mismatches: 12, Indels: 16
        0.66            0.15        0.20

Matches are distributed among these distances:
  14    2  0.04
  15   19  0.35
  16    2  0.04
  17    2  0.04
  18   27  0.50
  19    2  0.04

ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37


Consensus pattern (18 bp):   
AATGATTTAGAAAGTTCT

Found at i:773 original size:33 final size:33

Alignment explanation


    Indices: 666--784  Score: 220
    Period size: 33  Copynumber: 3.6  Consensus size: 33

        656 GTTCTAATGA

                                             
        666 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                             
        699 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                        *  *                 
        732 TAATGATTTCGATGAGAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                
        765 TAATGATTTCGACGAAAATG
          1 TAATGATTTCGACGAAAATG

        785 GTAATGATTT


Statistics
Matches: 82,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   82  1.00

ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34


Consensus pattern (33 bp):   
TAATGATTTCGACGAAAATGATTTAGAAAGTTC
Done.