Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010650.1 Corchorus capsularis cultivar CVL-1 contig10671, 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: 10191
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:755 original size:29 final size:31

Alignment explanation


    Indices: 713--786  Score: 107
    Period size: 29  Copynumber: 2.5  Consensus size: 31

        703 CACCAAATTA

                                    *   *  
        713 TAAGTAGAGGGACCAAATTGAT-AGTTTTTG
          1 TAAGTAGAGGGACCAAATTGATCACTTTCTG

                                   *       
        743 T-AGTAGAGGGACCAAATTGATCCCTTTCTG
          1 TAAGTAGAGGGACCAAATTGATCACTTTCTG

                          
        773 TAAGTAGAGGGACC
          1 TAAGTAGAGGGACC

        787 TGTACGGTAT


Statistics
Matches: 39,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  29   20  0.51
  30    7  0.18
  31   12  0.31

ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28


Consensus pattern (31 bp):   
TAAGTAGAGGGACCAAATTGATCACTTTCTG

Found at i:911 original size:33 final size:34

Alignment explanation


    Indices: 872--940  Score: 113
    Period size: 34  Copynumber: 2.1  Consensus size: 34

        862 CTAAACAAAT

                                              
        872 AAAGAGTATACAA-AGAGGTTTACTAATAAAAAC
          1 AAAGAGTATACAACAGAGGTTTACTAATAAAAAC

                   *                     *    
        905 AAAGAGTCTACAACAGAGGTTTACTAATATAAAC
          1 AAAGAGTATACAACAGAGGTTTACTAATAAAAAC

              
        939 AA
          1 AA

        941 TTACATTTAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
  33   12  0.36
  34   21  0.64

ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22


Consensus pattern (34 bp):   
AAAGAGTATACAACAGAGGTTTACTAATAAAAAC

Found at i:3375 original size:6 final size:6

Alignment explanation


    Indices: 3366--3398  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       3356 AAAGCAAAGC

                                                  
       3366 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       3399 GCAGATTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:3410 original size:12 final size:13

Alignment explanation


    Indices: 3395--3439  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       3385 AATCTAAATC

                         
       3395 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       3407 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       3420 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       3433 TAAAGCA
          1 TAAAGCA

       3440 AACAAAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Done.