Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009526.1 Corchorus capsularis cultivar CVL-1 contig09547, 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: 48691
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:3585 original size:19 final size:20

Alignment explanation


    Indices: 3553--3590  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3543 TTCCCCTTTT

                                
       3553 CTATATTTCTCA-TTATCTC
          1 CTATATTTCTCATTTATCTC

                                
       3572 CTATACTTTC-CATTTATCT
          1 CTATA-TTTCTCATTTATCT

       3591 ATCTTTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53


Consensus pattern (20 bp):   
CTATATTTCTCATTTATCTC

Found at i:17029 original size:6 final size:6

Alignment explanation


    Indices: 17018--17058  Score: 73
    Period size: 6  Copynumber: 6.8  Consensus size: 6

      17008 AACAGAACTG

                                                    *      
      17018 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTA GGTTT
          1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTT

      17059 GGAGTTTGGG


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.02, C:0.00, G:0.34, T:0.63


Consensus pattern (6 bp):   
GGTTTT

Found at i:17066 original size:18 final size:18

Alignment explanation


    Indices: 17018--17067  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 18

      17008 AACAGAACTG

                    *        *
      17018 GGTTTTGGTTTTGGTTTT
          1 GGTTTTGGGTTTGGTTTA

                    *         
      17036 GGTTTTGGTTTTGGTTTA
          1 GGTTTTGGGTTTGGTTTA

                           
      17054 GG-TTTGGAGTTTGG
          1 GGTTTTGG-GTTTGG

      17068 GGTTGGGGAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.17
  18   24  0.83

ACGTcount: A:0.04, C:0.00, G:0.38, T:0.58


Consensus pattern (18 bp):   
GGTTTTGGGTTTGGTTTA

Found at i:38562 original size:32 final size:30

Alignment explanation


    Indices: 38517--38591  Score: 87
    Period size: 31  Copynumber: 2.4  Consensus size: 30

      38507 GCCCCCTCTG

                   *        *        *     
      38517 TCAGGGGTAAAATGTATTGAATTTTGGAAGT
          1 TCAGGGGCAAAATGTACTGAA-TTTAGAAGT

                            *              
      38548 TCAGGGTGCAAAATGTCCTGAATTTAGAAGT
          1 TCAGGG-GCAAAATGTACTGAATTTAGAAGT

                         
      38579 TCAGGGGGCAAAA
          1 TCA-GGGGCAAAA

      38592 AGGCTAATAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  31   23  0.61
  32   15  0.39

ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28


Consensus pattern (30 bp):   
TCAGGGGCAAAATGTACTGAATTTAGAAGT

Found at i:43257 original size:17 final size:17

Alignment explanation


    Indices: 43235--43270  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      43225 TATAATAAAC

                             
      43235 AAAACATTTAGAAAATT
          1 AAAACATTTAGAAAATT

                             
      43252 AAAACATTTAGAAAATT
          1 AAAACATTTAGAAAATT

              
      43269 AA
          1 AA

      43271 CTATTGATAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28


Consensus pattern (17 bp):   
AAAACATTTAGAAAATT
Done.