Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002816.1 Corchorus capsularis cultivar CVL-1 contig02824, 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, 670

Length: 1117
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36


Found at i:384 original size:33 final size:33

Alignment explanation


    Indices: 333--439  Score: 144
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        323 TTGCAAAGAG

                                            * 
        333 TGTTTT-AGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTGAG-TGTTGTTTGCGATGATACTAAATC

              *                *    *        
        366 TGATTTGAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTGAGTGTTGTTTGCGATGATACTAAATC

                  *           *              
        399 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTTGAGTGTTGTTTGCGATGATACTAAATC

                    
        432 TGTTTTGA
          1 TGTTTTGA

        440 ATGCTAATTG


Statistics
Matches: 63,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  33   61  0.97
  34    2  0.03

ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45


Consensus pattern (33 bp):   
TGTTTTGAGTGTTGTTTGCGATGATACTAAATC

Found at i:451 original size:33 final size:34

Alignment explanation


    Indices: 386--471  Score: 95
    Period size: 33  Copynumber: 2.6  Consensus size: 34

        376 GTTGTTTGCA

                *                    * **     
        386 ATGACACTAAATCTGTTTT-AAGTGTTGTTTGTG
          1 ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG

                *                             
        419 ATGATACTAAATCTGTTTTGAA-TGCTAATTGTG
          1 ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG

                  *   *         
        452 ATGAAAATAATTCTGTTTTG
          1 ATGAAACTAAATCTGTTTTG

        472 GTTGATCATA


Statistics
Matches: 45,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  33   43  0.96
  34    2  0.04

ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44


Consensus pattern (34 bp):   
ATGAAACTAAATCTGTTTTGAAGTGCTAATTGTG

Found at i:467 original size:66 final size:66

Alignment explanation


    Indices: 333--470  Score: 152
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        323 TTGCAAAGAG

                                                     *  * **         * *     
        333 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTGATTTGAGTGTTGTTTGCAATGACACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTGATTTGAATGCTAATTGCAATGAAAATAAAT

             
        398 C
         66 C

                               *            *   *               **          *
        399 TGTTTTA-AGTGTTGTTTGTGATGATACTAAATCTGTTTTGAATGCTAATTGTGATGAAAATAAT
          1 TGTTTTAGA-TGTTGTTTGCGATGATACTAAACCTGATTTGAATGCTAATTGCAATGAAAATAAA

              
        463 TC
         65 TC

                  
        465 TGTTTT
          1 TGTTTT

        471 GGTTGATCAT


Statistics
Matches: 59,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  65    1  0.02
  66   58  0.98

ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45


Consensus pattern (66 bp):   
TGTTTTAGATGTTGTTTGCGATGATACTAAACCTGATTTGAATGCTAATTGCAATGAAAATAAAT
C

Found at i:493 original size:33 final size:32

Alignment explanation


    Indices: 456--537  Score: 102
    Period size: 27  Copynumber: 2.7  Consensus size: 32

        446 ATTGTGATGA

                                             
        456 AAATAATTCTGTTTTGGTTGATCATAGCATTAC
          1 AAATAA-TCTGTTTTGGTTGATCATAGCATTAC

                                          * 
        489 AAATAA----TTTT-GTTGATCATAGCATTGC
          1 AAATAATCTGTTTTGGTTGATCATAGCATTAC

                                  
        516 AAATAATCCTGTTTTGGTTGAT
          1 AAATAAT-CTGTTTTGGTTGAT

        538 GGCATTGAAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 12
        0.76            0.02        0.22

Matches are distributed among these distances:
  27   22  0.52
  28    4  0.10
  32    4  0.10
  33   12  0.29

ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43


Consensus pattern (32 bp):   
AAATAATCTGTTTTGGTTGATCATAGCATTAC

Done.