Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007428.1 Corchorus capsularis cultivar CVL-1 contig07449, 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: 17428
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30


Found at i:5320 original size:5 final size:5

Alignment explanation


    Indices: 5310--5354  Score: 56
    Period size: 5  Copynumber: 9.0  Consensus size: 5

       5300 TTTCCTCTTC

                                      *                *          
       5310 CTTTT CTTTT CTTTT CTTTT -TCTT CTTTT CCTTTT ATTTT CTTTT
          1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT -CTTTT CTTTT CTTTT

       5355 TCCTTCTCCT


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
   4    3  0.09
   5   26  0.76
   6    5  0.15

ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78


Consensus pattern (5 bp):   
CTTTT

Found at i:5333 original size:25 final size:25

Alignment explanation


    Indices: 5292--5361  Score: 81
    Period size: 25  Copynumber: 2.7  Consensus size: 25

       5282 AAAATTATAA

                                        
       5292 TTATTTT-TTTTCCTCTTCCTTTT-CTT
          1 TTATTTTCTTTT--TCTT-CTTTTCCTT

              *                      
       5318 TTCTTTTCTTTTTCTTCTTTTCCTT
          1 TTATTTTCTTTTTCTTCTTTTCCTT

                               
       5343 TTATTTTCTTTTTCCTTCT
          1 TTATTTTCTTTTT-CTTCT

       5362 CCTTCTTCGT


Statistics
Matches: 39,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  24    5  0.13
  25   19  0.49
  26   11  0.28
  27    4  0.10

ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74


Consensus pattern (25 bp):   
TTATTTTCTTTTTCTTCTTTTCCTT

Found at i:5350 original size:19 final size:19

Alignment explanation


    Indices: 5313--5352  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5303 CCTCTTCCTT

                         *     
       5313 TTCTTTTCTTTTCTTTTTC
          1 TTCTTTTCTTTTCATTTTC

                                
       5332 TTCTTTTCCTTTT-ATTTTC
          1 TTCTTTT-CTTTTCATTTTC

              
       5351 TT
          1 TT

       5353 TTTCCTTCTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19   14  0.74
  20    5  0.26

ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78


Consensus pattern (19 bp):   
TTCTTTTCTTTTCATTTTC

Found at i:7425 original size:31 final size:31

Alignment explanation


    Indices: 7385--7453  Score: 93
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       7375 AAAATCTAAA

                *        *                 
       7385 TTGATCCAATTTTGAAACATTTAGTACCTAT
          1 TTGAGCCAATTTTAAAACATTTAGTACCTAT

                              *   *      * 
       7416 TTGAGCCAATTTTAAAACGTTTGGTACCTGT
          1 TTGAGCCAATTTTAAAACATTTAGTACCTAT

                   
       7447 TTGAGCC
          1 TTGAGCC

       7454 GGTTTAAAAT


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39


Consensus pattern (31 bp):   
TTGAGCCAATTTTAAAACATTTAGTACCTAT

Found at i:7462 original size:30 final size:31

Alignment explanation


    Indices: 7385--7462  Score: 77
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7375 AAAATCTAAA

                *    *   *                 
       7385 TTGATCCAATTTTGAAACATTTAGTACCTAT
          1 TTGAGCCAAGTTTAAAACATTTAGTACCTAT

                     *        *   *      * 
       7416 TTGAGCCAATTTTAAAACGTTTGGTACCTGT
          1 TTGAGCCAAGTTTAAAACATTTAGTACCTAT

                    *        
       7447 TTGAGCC-GGTTTAAAA
          1 TTGAGCCAAGTTTAAAA

       7463 TATAAAAGTA


Statistics
Matches: 40,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  30    7  0.17
  31   33  0.82

ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38


Consensus pattern (31 bp):   
TTGAGCCAAGTTTAAAACATTTAGTACCTAT

Found at i:7500 original size:10 final size:10

Alignment explanation


    Indices: 7487--7528  Score: 61
    Period size: 10  Copynumber: 4.4  Consensus size: 10

       7477 AAAATAAAAC

                      
       7487 AAATATTTAA
          1 AAATATTTAA

                      
       7497 AAATATTTAA
          1 AAATATTTAA

                   *  
       7507 AAATA--AAA
          1 AAATATTTAA

                      
       7515 AAATATTTAA
          1 AAATATTTAA

                
       7525 AAAT
          1 AAAT

       7529 GCCACGTAGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
   8    7  0.25
  10   21  0.75

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (10 bp):   
AAATATTTAA
Done.