Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013683.1 Corchorus capsularis cultivar CVL-1 contig13704, 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: 53090
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:31594 original size:24 final size:25

Alignment explanation


    Indices: 31561--31620  Score: 104
    Period size: 24  Copynumber: 2.4  Consensus size: 25

      31551 TAAAGCTGCG

                                     
      31561 TTTCTGTTCTTAAATATGTAATACC
          1 TTTCTGTTCTTAAATATGTAATACC

                                     
      31586 -TTCTGTTCTTAAATATGTAATACC
          1 TTTCTGTTCTTAAATATGTAATACC

                 *     
      31610 TTTCTTTTCTT
          1 TTTCTGTTCTT

      31621 TTCTTTTTTT


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

Matches are distributed among these distances:
  24   24  0.73
  25    9  0.27

ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53


Consensus pattern (25 bp):   
TTTCTGTTCTTAAATATGTAATACC

Found at i:38468 original size:3 final size:3

Alignment explanation


    Indices: 38460--38497  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

      38450 TTGGTTTCTT

                                                              
      38460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

      38498 CTAATAGCTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:40743 original size:30 final size:28

Alignment explanation


    Indices: 40672--40749  Score: 86
    Period size: 29  Copynumber: 2.7  Consensus size: 28

      40662 GAATTTACAC

                *                       
      40672 AAAACGGCCAAATAAGCCCCTGAACTCT
          1 AAAAAGGCCAAATAAGCCCCTGAACTCT

               **                           
      40700 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
          1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T

                               
      40731 AAAAAGGCCAAATAAGCCC
          1 AAAAAGGCCAAATAAGCCC

      40750 TTTTCTGATG


Statistics
Matches: 41,  Mismatches: 4, Indels: 8
        0.77            0.08        0.15

Matches are distributed among these distances:
  27    3  0.07
  29   21  0.51
  30   13  0.32
  31    1  0.02
  32    3  0.07

ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17


Consensus pattern (28 bp):   
AAAAAGGCCAAATAAGCCCCTGAACTCT

Found at i:43962 original size:25 final size:24

Alignment explanation


    Indices: 43924--43972  Score: 71
    Period size: 25  Copynumber: 2.0  Consensus size: 24

      43914 AATGGGAGGG

                     *        *     
      43924 TTGGCTGCCCTGCCCTGCTCTGCC
          1 TTGGCTGCCATGCCCTGCCCTGCC

                                     
      43948 TTGGCTTGCCATGCCCTGCCCTGCC
          1 TTGGC-TGCCATGCCCTGCCCTGCC

      43973 CCGGCCCCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    5  0.23
  25   17  0.77

ACGTcount: A:0.02, C:0.45, G:0.24, T:0.29


Consensus pattern (24 bp):   
TTGGCTGCCATGCCCTGCCCTGCC

Found at i:44261 original size:26 final size:26

Alignment explanation


    Indices: 44221--44271  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      44211 TATTTTGCTT

                                       
      44221 CCTTTGCTTTCCTTTCCTTCATTTTTC
          1 CCTTTGCTTTCCTTTCCTTC-TTTTTC

                 *          *        
      44248 CCTTTTCTTT-CTTTCTTTCTTTTT
          1 CCTTTGCTTTCCTTTCCTTCTTTTT

      44272 AATTAATTTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  25    5  0.23
  26    8  0.36
  27    9  0.41

ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67


Consensus pattern (26 bp):   
CCTTTGCTTTCCTTTCCTTCTTTTTC

Found at i:50829 original size:2 final size:2

Alignment explanation


    Indices: 50822--50856  Score: 54
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      50812 ATGTTGATAC

                                                                 
      50822 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A- AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A

      50857 ATAATGTATC


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.90
   3    2  0.06

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (2 bp):   
AT

Done.