Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018312.1 Corchorus olitorius cultivar O-4 contig18345, 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: 7659
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:1196 original size:38 final size:38

Alignment explanation


    Indices: 1146--1266  Score: 170
    Period size: 46  Copynumber: 3.0  Consensus size: 38

       1136 GACATGCACA

                                                  
       1146 ACATACATGTATATTCATAACAAATTTATAATTAATTT
          1 ACATACATGTATATTCATAACAAATTTATAATTAATTT

                                                          
       1184 ACATACATGTATATTCATAACAAATTTATAAATTTATAATTAATTT
          1 ACATACATGTATATTCATAAC--------AAATTTATAATTAATTT

                                                 
       1230 ACATACATGTATATTCATAACAAATTTATAATTAATT
          1 ACATACATGTATATTCATAACAAATTTATAATTAATT

       1267 GATGATTATT


Statistics
Matches: 75,  Mismatches: 0, Indels: 16
        0.82            0.00        0.18

Matches are distributed among these distances:
  38   37  0.49
  46   38  0.51

ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42


Consensus pattern (38 bp):   
ACATACATGTATATTCATAACAAATTTATAATTAATTT

Found at i:1203 original size:27 final size:27

Alignment explanation


    Indices: 1173--1249  Score: 80
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       1163 TAACAAATTT

                                       
       1173 ATAATTAATTTACATACATGTATATTC
          1 ATAATTAATTTACATACATGTATATTC

                **                     
       1200 ATAACAAATTT--ATA-A---AT-TT-
          1 ATAATTAATTTACATACATGTATATTC

                                       
       1219 ATAATTAATTTACATACATGTATATTC
          1 ATAATTAATTTACATACATGTATATTC

                
       1246 ATAA
          1 ATAA

       1250 CAAATTTATA


Statistics
Matches: 38,  Mismatches: 4, Indels: 16
        0.66            0.07        0.28

Matches are distributed among these distances:
  19    9  0.24
  20    2  0.05
  21    5  0.13
  22    1  0.03
  24    1  0.03
  25    5  0.13
  26    2  0.05
  27   13  0.34

ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43


Consensus pattern (27 bp):   
ATAATTAATTTACATACATGTATATTC

Found at i:1234 original size:46 final size:46

Alignment explanation


    Indices: 1167--1260  Score: 188
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       1157 TATTCATAAC

                                                          
       1167 AAATTTATAATTAATTTACATACATGTATATTCATAACAAATTTAT
          1 AAATTTATAATTAATTTACATACATGTATATTCATAACAAATTTAT

                                                          
       1213 AAATTTATAATTAATTTACATACATGTATATTCATAACAAATTTAT
          1 AAATTTATAATTAATTTACATACATGTATATTCATAACAAATTTAT

              
       1259 AA
          1 AA

       1261 TTAATTGATG


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   48  1.00

ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43


Consensus pattern (46 bp):   
AAATTTATAATTAATTTACATACATGTATATTCATAACAAATTTAT

Found at i:3920 original size:2 final size:2

Alignment explanation


    Indices: 3913--3947  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       3903 ACGTTGATTT

                                                                
       3913 TA TA TA 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 TA TA TA T

       3948 TTATTATTAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:6794 original size:2 final size:2

Alignment explanation


    Indices: 6787--6814  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       6777 ATTTAGGATC

                                                     
       6787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       6815 TTGCTGATCG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.