Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009748.1 Corchorus capsularis cultivar CVL-1 contig09769, 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: 11437
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:3277 original size:24 final size:25

Alignment explanation


    Indices: 3222--3284  Score: 65
    Period size: 26  Copynumber: 2.5  Consensus size: 25

       3212 TTAAAAAAAC

                            *         
       3222 ATAAATATATATTTATTATTTTGCAA
          1 ATAAATATATATTTATCATTTT-CAA

             *               *       
       3248 AGAAATATATATTTATCCTTTT-AA
          1 ATAAATATATATTTATCATTTTCAA

            *            
       3272 TTAAATACTATAT
          1 ATAAATA-TATAT

       3285 ATATAATATA


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  24    7  0.23
  25    5  0.16
  26   19  0.61

ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48


Consensus pattern (25 bp):   
ATAAATATATATTTATCATTTTCAA

Found at i:3319 original size:2 final size:2

Alignment explanation


    Indices: 3314--3377  Score: 58
    Period size: 2  Copynumber: 37.0  Consensus size: 2

       3304 TTTCGATCAA

                                                                          
       3314 AT AT AT A- AT AT A- AT A- AT -T AT AT AT AT AT 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 AT AT

                                                           
       3350 AT A- AT AT A- AT A- AT -T AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3378 TCATAGTATA


Statistics
Matches: 52,  Mismatches: 0, Indels: 20
        0.72            0.00        0.28

Matches are distributed among these distances:
   1   10  0.19
   2   42  0.81

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


Consensus pattern (2 bp):   
AT

Found at i:3342 original size:8 final size:8

Alignment explanation


    Indices: 3314--3377  Score: 58
    Period size: 7  Copynumber: 9.2  Consensus size: 8

       3304 TTTCGATCAA

                    
       3314 ATATATA-
          1 ATATATAT

                    
       3321 ATATA-AT
          1 ATATATAT

                    
       3328 A-AT-TAT
          1 ATATATAT

                    
       3334 ATATATAT
          1 ATATATAT

                    
       3342 ATA-ATAT
          1 ATATATAT

                    
       3349 A-ATA-AT
          1 ATATATAT

                    
       3355 ATA-ATA-
          1 ATATATAT

                    
       3361 AT-TATAT
          1 ATATATAT

                    
       3368 ATATATAT
          1 ATATATAT

              
       3376 AT
          1 AT

       3378 TCATAGTATA


Statistics
Matches: 47,  Mismatches: 0, Indels: 19
        0.71            0.00        0.29

Matches are distributed among these distances:
   6   16  0.34
   7   18  0.38
   8   13  0.28

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


Consensus pattern (8 bp):   
ATATATAT

Found at i:3359 original size:32 final size:31

Alignment explanation


    Indices: 3313--3376  Score: 119
    Period size: 32  Copynumber: 2.0  Consensus size: 31

       3303 TTTTCGATCA

                                           
       3313 AATATATAATATAATAATTATATATATATAT
          1 AATATATAATATAATAATTATATATATATAT

                                            
       3344 AATATAATAATATAATAATTATATATATATAT
          1 AATAT-ATAATATAATAATTATATATATATAT

             
       3376 A
          1 A

       3377 TTCATAGTAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  31    5  0.16
  32   27  0.84

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (31 bp):   
AATATATAATATAATAATTATATATATATAT
Done.