Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001634.1 Corchorus capsularis cultivar CVL-1 contig01634, 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, 635

Length: 1059
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35


Found at i:111 original size:27 final size:25

Alignment explanation


    Indices: 73--122  Score: 66
    Period size: 27  Copynumber: 1.9  Consensus size: 25

         63 TGATGCAATC

                                       
         73 AAAACATGAAATTAGCAAAAAATTAAT
          1 AAAACATGAAATTA--AAAAAATTAAT

                                    
        100 AAAA-ATGAAAATTAAAAAAATTA
          1 AAAACATG-AAATTAAAAAAATTA

        123 TAATTGATTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  25    9  0.41
  26    3  0.14
  27   10  0.45

ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22


Consensus pattern (25 bp):   
AAAACATGAAATTAAAAAAATTAAT

Found at i:127 original size:15 final size:16

Alignment explanation


    Indices: 91--120  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

         81 AAATTAGCAA

                            
         91 AAAATTAATAAAAATG
          1 AAAATTAATAAAAATG

                           
        107 AAAATTAA-AAAAAT
          1 AAAATTAATAAAAAT

        121 TATAATTGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23


Consensus pattern (16 bp):   
AAAATTAATAAAAATG

Found at i:486 original size:20 final size:19

Alignment explanation


    Indices: 451--493  Score: 59
    Period size: 20  Copynumber: 2.2  Consensus size: 19

        441 AAATGTTTAG

                             * 
        451 AAAAGAATATAAAAATATA
          1 AAAAGAATATAAAAATACA

                  *             
        470 AAAAGACTATAAAAAATACA
          1 AAAAGAATAT-AAAAATACA

                
        490 AAAA
          1 AAAA

        494 TGAAAAAAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19    9  0.43
  20   12  0.57

ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16


Consensus pattern (19 bp):   
AAAAGAATATAAAAATACA

Found at i:560 original size:17 final size:17

Alignment explanation


    Indices: 538--599  Score: 83
    Period size: 17  Copynumber: 3.8  Consensus size: 17

        528 TACTATTTTC

                             
        538 TATTTTATATGTTATTT
          1 TATTTTATATGTTATTT

                             
        555 TATTTTATATGTTATTT
          1 TATTTTATATGTTATTT

                 *           
        572 TA--TCATATGTTATTT
          1 TATTTTATATGTTATTT

               *    *    
        587 TATCTTATCTGTT
          1 TATTTTATATGTT

        600 CGGCTTTTTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  15   14  0.35
  17   26  0.65

ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66


Consensus pattern (17 bp):   
TATTTTATATGTTATTT

Found at i:581 original size:15 final size:15

Alignment explanation


    Indices: 544--590  Score: 67
    Period size: 15  Copynumber: 3.0  Consensus size: 15

        534 TTTCTATTTT

                            *
        544 ATATGTTATTTTATTTT
          1 ATATGTTATTTTA--TC

                           
        561 ATATGTTATTTTATC
          1 ATATGTTATTTTATC

                           
        576 ATATGTTATTTTATC
          1 ATATGTTATTTTATC

        591 TTATCTGTTC


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  15   16  0.55
  17   13  0.45

ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64


Consensus pattern (15 bp):   
ATATGTTATTTTATC

Found at i:774 original size:13 final size:13

Alignment explanation


    Indices: 756--780  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        746 CTATAGCAGC

                         
        756 AATAATAAATAAG
          1 AATAATAAATAAG

                        
        769 AATAATAAATAA
          1 AATAATAAATAA

        781 AATTAAGAAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24


Consensus pattern (13 bp):   
AATAATAAATAAG
Done.