Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019770.1 Corchorus olitorius cultivar O-4 contig19803, 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: 21723
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Found at i:9260 original size:176 final size:176

Alignment explanation


    Indices: 8922--9274  Score: 681
    Period size: 176  Copynumber: 2.0  Consensus size: 176

       8912 TTGAGTGGGC

                                                                             
       8922 CATGGCCCCCCTAAAAGTTTTGAAAAACCATTATTAGTACATATAATTTTGCTAATTGTTCTTTT
          1 CATGGCCCCCCTAAAAGTTTTGAAAAACCATTATTAGTACATATAATTTTGCTAATTGTTCTTTT

                                                                             
       8987 ATTTCTATGTTTTTGTTAATGATCTATACTAAAAATTTCATATTGGCTCCCCCAAATTGAAATTC
         66 ATTTCTATGTTTTTGTTAATGATCTATACTAAAAATTTCATATTGGCTCCCCCAAATTGAAATTC

                                                          
       9052 TATCAAGGGAATTTTTGATTGGCCCCCCTAAACTACATATCAAGAT
        131 TATCAAGGGAATTTTTGATTGGCCCCCCTAAACTACATATCAAGAT

                            *                                                
       9098 CATGGCCCCCCTAAAATTTTTGAAAAACCATTATTAGTACATATAATTTTGCTAATTGTTCTTTT
          1 CATGGCCCCCCTAAAAGTTTTGAAAAACCATTATTAGTACATATAATTTTGCTAATTGTTCTTTT

                                                                             
       9163 ATTTCTATGTTTTTGTTAATGATCTATACTAAAAATTTCATATTGGC-CCCCCAAATTGAAATTC
         66 ATTTCTATGTTTTTGTTAATGATCTATACTAAAAATTTCATATTGGCTCCCCCAAATTGAAATTC

                                                           
       9227 TATCAAGGGAATTTTTGATTGGCCCCGCCTAAACTACATATCAAGAT
        131 TATCAAGGGAATTTTTGATTGGCCCC-CCTAAACTACATATCAAGAT

             
       9274 C
          1 C

       9275 TGCCCCTGTT


Statistics
Matches: 175,  Mismatches: 1, Indels: 2
        0.98            0.01        0.01

Matches are distributed among these distances:
 175   43  0.25
 176  132  0.75

ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39


Consensus pattern (176 bp):   
CATGGCCCCCCTAAAAGTTTTGAAAAACCATTATTAGTACATATAATTTTGCTAATTGTTCTTTT
ATTTCTATGTTTTTGTTAATGATCTATACTAAAAATTTCATATTGGCTCCCCCAAATTGAAATTC
TATCAAGGGAATTTTTGATTGGCCCCCCTAAACTACATATCAAGAT

Found at i:9551 original size:2 final size:2

Alignment explanation


    Indices: 9544--9568  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       9534 AGTATAGTAA

                                                 
       9544 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       9569 CTAGTTAAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:14916 original size:57 final size:57

Alignment explanation


    Indices: 14823--14936  Score: 174
    Period size: 58  Copynumber: 2.0  Consensus size: 57

      14813 ATTAATCAAA

                                                         *           
      14823 TATCGAGTGACATGTTCTTTATTAGATGCATAAAAAACACGTTTTCGGACCGAGGCT
          1 TATCGAGTGACATGTTCTTTATTAGATGCATAAAAAACACGTTTTAGGACCGAGGCT

                             *            *       *          *       
      14880 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGGCCGAGGC
          1 TATCGAGTGACATG-TTCTTTATTAGATGCATAAAAAACACGTTTTAGGACCGAGGC

      14937 ATGATGCTAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  57   14  0.27
  58   37  0.73

ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32


Consensus pattern (57 bp):   
TATCGAGTGACATGTTCTTTATTAGATGCATAAAAAACACGTTTTAGGACCGAGGCT

Found at i:16236 original size:36 final size:36

Alignment explanation


    Indices: 16189--16258  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      16179 TTCAATAATC

                         *      *               
      16189 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
      16225 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

      16259 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:19918 original size:13 final size:13

Alignment explanation


    Indices: 19900--19927  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      19890 CATGATCACA

                         
      19900 TTGGTTTACCCTT
          1 TTGGTTTACCCTT

                         
      19913 TTGGTTTACCCTT
          1 TTGGTTTACCCTT

              
      19926 TT
          1 TT

      19928 TTCTTTGGTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.07, C:0.21, G:0.14, T:0.57


Consensus pattern (13 bp):   
TTGGTTTACCCTT
Done.