Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012307.1 Corchorus capsularis cultivar CVL-1 contig12328, 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: 16357
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:3398 original size:5 final size:5

Alignment explanation


    Indices: 3388--3414  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

       3378 GCCGTCCAAC

                                            
       3388 ACCTT ACCTT ACCTT ACCTT ACCTT AC
          1 ACCTT ACCTT ACCTT ACCTT ACCTT AC

       3415 ATCATATGTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37


Consensus pattern (5 bp):   
ACCTT

Found at i:9669 original size:31 final size:31

Alignment explanation


    Indices: 9634--9707  Score: 139
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       9624 TTGTGTTTTG

                                           
       9634 AGACCCTTATTTGAGATTTTTATGAAAGTTC
          1 AGACCCTTATTTGAGATTTTTATGAAAGTTC

                                           
       9665 AGACCCTTATTTGAGATTTTTATGAAAGTTC
          1 AGACCCTTATTTGAGATTTTTATGAAAGTTC

               *        
       9696 AGATCCTTATTT
          1 AGACCCTTATTT

       9708 AATATCCGTT


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  31   42  1.00

ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43


Consensus pattern (31 bp):   
AGACCCTTATTTGAGATTTTTATGAAAGTTC

Found at i:11384 original size:29 final size:29

Alignment explanation


    Indices: 11323--11402  Score: 108
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      11313 CAAATAGTGG

                                 **        
      11323 CAAATTGA-CCCTTAACTATCCATTTTGGGA
          1 CAAATTGACCCCTTAACT-T-TTTTTTGGGA

                                         
      11353 CAAATTGACCCCTTAACTTTTTTTTGGGA
          1 CAAATTGACCCCTTAACTTTTTTTTGGGA

                   *             
      11382 CAAATTGGCCCCTTAACTTTT
          1 CAAATTGACCCCTTAACTTTT

      11403 AAAAACAAGA


Statistics
Matches: 46,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  29   28  0.61
  30    9  0.20
  31    9  0.20

ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38


Consensus pattern (29 bp):   
CAAATTGACCCCTTAACTTTTTTTTGGGA

Found at i:12483 original size:103 final size:103

Alignment explanation


    Indices: 12258--12494  Score: 331
    Period size: 103  Copynumber: 2.3  Consensus size: 103

      12248 AAATTTTATT

                 *                                              *        *   
      12258 TTTTAGTTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAGCCCTATAGCTAT
          1 TTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAGATAT

                         *                          
      12321 ATTATTAATTATGGAATTTACCCTTAAAATAAAAATAAAA
         66 ATTATTAATTATGAAATTTACCCTT--AATAAAAATAAAA

                                              * *                            
      12361 TTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATA-ATAA
          1 TTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAGAT-A

                         *                           
      12425 TAAATTATTAATTTTGAAATTTACCCTT-A-AAAAATAAAA
         65 T--ATTATTAATTATGAAATTTACCCTTAATAAAAATAAAA

                                           
      12464 TTTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 TTTTAATTTGGGGCTAAACTTAGTGAAATTA

      12495 AGGCTAAACT


Statistics
Matches: 122,  Mismatches: 7, Indels: 10
        0.88            0.05        0.07

Matches are distributed among these distances:
 103   49  0.40
 104   17  0.14
 105   33  0.27
 107   23  0.19

ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42


Consensus pattern (103 bp):   
TTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAGATAT
ATTATTAATTATGAAATTTACCCTTAATAAAAATAAAA

Found at i:13008 original size:2 final size:2

Alignment explanation


    Indices: 13003--13040  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      12993 TGTTTTTTCA

                                                       *              
      13003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13041 AATAATTATA


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Done.