Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015626.1 Corchorus capsularis cultivar CVL-1 contig15647, 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: 7738
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:263 original size:7 final size:7

Alignment explanation


    Indices: 247--317  Score: 56
    Period size: 7  Copynumber: 9.6  Consensus size: 7

        237 CCGACTAAAG

                   
        247 ATAT-TT
          1 ATATATT

                   
        253 ATATATT
          1 ATATATT

                    
        260 ATATATAT
          1 ATATAT-T

                      
        268 ATTATAATTT
          1 A-TAT-A-TT

                 *   
        278 ATATGTTAT
          1 ATAT-AT-T

                   
        287 ATATATT
          1 ATATATT

                   
        294 ATATATT
          1 ATATATT

                   
        301 -TATATT
          1 ATATATT

            *      
        307 TTATATT
          1 ATATATT

                
        314 ATAT
          1 ATAT

        318 TTAATTTGTT


Statistics
Matches: 54,  Mismatches: 4, Indels: 13
        0.76            0.06        0.18

Matches are distributed among these distances:
   6   10  0.19
   7   25  0.46
   8    4  0.07
   9   11  0.20
  10    3  0.06
  11    1  0.02

ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59


Consensus pattern (7 bp):   
ATATATT

Found at i:286 original size:25 final size:25

Alignment explanation


    Indices: 249--345  Score: 103
    Period size: 23  Copynumber: 3.9  Consensus size: 25

        239 GACTAAAGAT

                                     
        249 ATTTATATATTATATATATATTATA
          1 ATTTATATATTATATATATATTATA

                     *               
        274 ATTTATAT-GT-TATATATATTATA
          1 ATTTATATATTATATATATATTATA

                     *                
        297 TATTTATATTTTATAT-TATATT-TA
          1 -ATTTATATATTATATATATATTATA

                * *                  
        321 ATTTGTTTATATATATATAATATTA
          1 ATTTATATAT-TATATAT-ATATTA

        346 GAATATATCA


Statistics
Matches: 60,  Mismatches: 5, Indels: 12
        0.78            0.06        0.16

Matches are distributed among these distances:
  23   20  0.33
  24   16  0.27
  25   16  0.27
  26    8  0.13

ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59


Consensus pattern (25 bp):   
ATTTATATATTATATATATATTATA

Found at i:353 original size:2 final size:2

Alignment explanation


    Indices: 247--343  Score: 50
    Period size: 2  Copynumber: 53.0  Consensus size: 2

        237 CCGACTAAAG

                  *                                         *        *    
        247 AT AT TT AT AT AT -T AT AT AT AT AT -T AT A- AT TT AT AT GT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                    *           *                 *       
        285 AT AT AT AT -T AT AT AT TT AT AT -T TT AT AT -T AT AT TT A- AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *  *  *                         
        323 TT GT TT AT AT AT AT AT A- AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT

        344 TAGAATATAT


Statistics
Matches: 72,  Mismatches: 14, Indels: 18
        0.69            0.13        0.17

Matches are distributed among these distances:
   1    9  0.12
   2   63  0.88

ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59


Consensus pattern (2 bp):   
AT

Found at i:1580 original size:22 final size:22

Alignment explanation


    Indices: 1552--1600  Score: 89
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1542 TTAACATTCA

                                  
       1552 CTGATTATATACTGTTATAGTG
          1 CTGATTATATACTGTTATAGTG

                                  
       1574 CTGATTATATACTGTTATAGTG
          1 CTGATTATATACTGTTATAGTG

            *    
       1596 TTGAT
          1 CTGAT

       1601 AATAGTTGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   26  1.00

ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47


Consensus pattern (22 bp):   
CTGATTATATACTGTTATAGTG

Found at i:6912 original size:17 final size:18

Alignment explanation


    Indices: 6884--6920  Score: 67
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       6874 CCTCCCCATA

                              
       6884 GTACCTAGGTAGTATGAG
          1 GTACCTAGGTAGTATGAG

                              
       6902 GTACC-AGGTAGTATGAG
          1 GTACCTAGGTAGTATGAG

              
       6919 GT
          1 GT

       6921 GATAGGCTGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17   14  0.74
  18    5  0.26

ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27


Consensus pattern (18 bp):   
GTACCTAGGTAGTATGAG
Done.