Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012335.1 Corchorus capsularis cultivar CVL-1 contig12356, 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: 3112
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28


Found at i:1653 original size:20 final size:21

Alignment explanation


    Indices: 1617--1656  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1607 TGGTTAAATG

                                 
       1617 ATAAATCATAATAAATCATAA
          1 ATAAATCATAATAAATCATAA

                                 
       1638 ATAAA-CATAA-ATAATCATA
          1 ATAAATCATAATA-AATCATA

       1657 GAAATAAAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    1  0.06
  20   12  0.67
  21    5  0.28

ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28


Consensus pattern (21 bp):   
ATAAATCATAATAAATCATAA

Found at i:2227 original size:24 final size:27

Alignment explanation


    Indices: 2185--2234  Score: 70
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       2175 TATAATTAAG

                                        
       2185 TAATAGATAACTATAAAAAAG-TAAAAA
          1 TAATAGATAAC-ATAAAAAAGATAAAAA

                                     
       2212 TAATAGATAA-AT-AAAAAGATAAA
          1 TAATAGATAACATAAAAAAGATAAA

       2235 TAGATATATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  24    6  0.27
  25    6  0.27
  27   10  0.45

ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22


Consensus pattern (27 bp):   
TAATAGATAACATAAAAAAGATAAAAA

Found at i:2370 original size:17 final size:17

Alignment explanation


    Indices: 2348--2412  Score: 72
    Period size: 17  Copynumber: 4.2  Consensus size: 17

       2338 AGATAGATAA

                     *       
       2348 ATAATAGTATTAAATAG
          1 ATAATAGTACTAAATAG

                             
       2365 ATAATAGTACTAAATAG
          1 ATAATAGTACTAAATAG

                             
       2382 ATAATA--A-TAAATA-
          1 ATAATAGTACTAAATAG

                             
       2395 ATAAT--TAC-AAATAG
          1 ATAATAGTACTAAATAG

                
       2409 ATAA
          1 ATAA

       2413 GAAAATGAAT


Statistics
Matches: 44,  Mismatches: 1, Indels: 9
        0.81            0.02        0.17

Matches are distributed among these distances:
  13   11  0.25
  14   10  0.23
  15    1  0.02
  17   22  0.50

ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31


Consensus pattern (17 bp):   
ATAATAGTACTAAATAG

Found at i:2390 original size:27 final size:27

Alignment explanation


    Indices: 2360--2412  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       2350 AATAGTATTA

                *                       
       2360 AATAGATAAT-AGTACTAAATAGATAAT
          1 AATAAATAATAAGTAC-AAATAGATAAT

                        *             
       2387 AATAAATAATAATTACAAATAGATAA
          1 AATAAATAATAAGTACAAATAGATAA

       2413 GAAAATGAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27   19  0.83
  28    4  0.17

ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28


Consensus pattern (27 bp):   
AATAAATAATAAGTACAAATAGATAAT

Found at i:2492 original size:22 final size:21

Alignment explanation


    Indices: 2455--2497  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       2445 AACTAAGTAG

                                  
       2455 ATAGATAGATAGATAATAATAA
          1 ATAGATAGATAGATAA-AATAA

                                  
       2477 ATAGATAGAT-GAATAAAATAA
          1 ATAGATAGATAG-ATAAAATAA

       2498 TTTAATAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  21    6  0.30
  22   14  0.70

ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26


Consensus pattern (21 bp):   
ATAGATAGATAGATAAAATAA
Done.