Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009624.1 Corchorus capsularis cultivar CVL-1 contig09645, 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: 23029
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:2075 original size:28 final size:28

Alignment explanation


    Indices: 2035--2092  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       2025 AATTTCTCCA

                                        
       2035 TTACCAAACAAGCTCTAACTTCCTGTAT
          1 TTACCAAACAAGCTCTAACTTCCTGTAT

                                        
       2063 TTACCAAACAAGCTCTAACTTCCTGTAT
          1 TTACCAAACAAGCTCTAACTTCCTGTAT

              
       2091 TT
          1 TT

       2093 GAGGTTTGAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34


Consensus pattern (28 bp):   
TTACCAAACAAGCTCTAACTTCCTGTAT

Found at i:7694 original size:29 final size:29

Alignment explanation


    Indices: 7662--7721  Score: 102
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       7652 CAATTCCTCC

                                         
       7662 TTTCCACACATCAACCATGTGTTATCTAA
          1 TTTCCACACATCAACCATGTGTTATCTAA

                   *   *                 
       7691 TTTCCACGCATTAACCATGTGTTATCTAA
          1 TTTCCACACATCAACCATGTGTTATCTAA

              
       7720 TT
          1 TT

       7722 ATTATTATAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38


Consensus pattern (29 bp):   
TTTCCACACATCAACCATGTGTTATCTAA

Found at i:10893 original size:53 final size:51

Alignment explanation


    Indices: 10819--10923  Score: 183
    Period size: 53  Copynumber: 2.0  Consensus size: 51

      10809 GCTAAACTAT

                                                               
      10819 ATTATATTATATATAAACCCTTTAATTATACACAAAAGGCTTTGATCCTAA
          1 ATTATATTATATATAAACCCTTTAATTATACACAAAAGGCTTTGATCCTAA

                                                  *              
      10870 ATTATATTATATATATAAACCCTTTAATTATACACAAATGGCTTTGATCCTAA
          1 ATTATA-T-TATATATAAACCCTTTAATTATACACAAAAGGCTTTGATCCTAA

             
      10923 A
          1 A

      10924 ATAACTTCCA


Statistics
Matches: 51,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  51    6  0.12
  52    1  0.02
  53   44  0.86

ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38


Consensus pattern (51 bp):   
ATTATATTATATATAAACCCTTTAATTATACACAAAAGGCTTTGATCCTAA

Found at i:21386 original size:2 final size:2

Alignment explanation


    Indices: 21379--21407  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      21369 TCACAGATTT

                                                       
      21379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      21408 CTTCCAATCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:22417 original size:29 final size:30

Alignment explanation


    Indices: 22358--22430  Score: 76
    Period size: 29  Copynumber: 2.4  Consensus size: 30

      22348 TGGACTGGAT

                     *                *    
      22358 TTATTTGACCTTGTTCGATAAGTTCGTGCCC
          1 TTATTTGACATT-TTCGATAAGTTCGGGCCC

                           *       *      
      22389 TTATTTGACATTTTCTA-AAGTTTGGGCCC
          1 TTATTTGACATTTTCGATAAGTTCGGGCCC

             *      *    
      22418 TGATTTGAGATTT
          1 TTATTTGACATTT

      22431 ACCGTAATTC


Statistics
Matches: 36,  Mismatches: 6, Indels: 2
        0.82            0.14        0.05

Matches are distributed among these distances:
  29   21  0.58
  30    4  0.11
  31   11  0.31

ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45


Consensus pattern (30 bp):   
TTATTTGACATTTTCGATAAGTTCGGGCCC

Found at i:22718 original size:2 final size:2

Alignment explanation


    Indices: 22711--22739  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      22701 TTGAAGCAAA

                                                        
      22711 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      22740 TAAGAAATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

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


Consensus pattern (2 bp):   
AT

Done.