Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021972.1 Corchorus olitorius cultivar O-4 contig22005, 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: 18052
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:4316 original size:17 final size:16

Alignment explanation


    Indices: 4283--4313  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4273 CTTTTTCGGA

                  *         
       4283 TATGAACTGTTTTTTG
          1 TATGAAATGTTTTTTG

                           
       4299 TATGAAATGTTTTTT
          1 TATGAAATGTTTTTT

       4314 TGTTTCTCTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58


Consensus pattern (16 bp):   
TATGAAATGTTTTTTG

Found at i:6386 original size:30 final size:30

Alignment explanation


    Indices: 6352--6462  Score: 136
    Period size: 30  Copynumber: 3.7  Consensus size: 30

       6342 GCTTCAAGGC

                           *              
       6352 AGATTCCACATCTCACAAACCTTCTCTCAG
          1 AGATTCCACATCTCAAAAACCTTCTCTCAG

                                 *       *
       6382 AGATTCCACATCTCAAAAACCATCTCTCAC
          1 AGATTCCACATCTCAAAAACCTTCTCTCAG

                                *     *   
       6412 AGATTCCACATCTC-AAAACATT-TCCCAG
          1 AGATTCCACATCTCAAAAACCTTCTCTCAG

                     *             
       6440 AGATATCACTCATCTCAAAAACC
          1 AGAT-TC-CACATCTCAAAAACC

       6463 AGCTCCTGCA


Statistics
Matches: 69,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  28    8  0.12
  29    8  0.12
  30   48  0.70
  31    5  0.07

ACGTcount: A:0.36, C:0.34, G:0.05, T:0.24


Consensus pattern (30 bp):   
AGATTCCACATCTCAAAAACCTTCTCTCAG

Found at i:6454 original size:60 final size:60

Alignment explanation


    Indices: 6351--6463  Score: 167
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       6341 GGCTTCAAGG

                                 *     *                                
       6351 CAGATTCCACATCTCACAAACCTTCTCTCAGAGATTCCACATCTCAAAAACCATCTCTCA
          1 CAGATTCCACATCTCACAAACATTCTCCCAGAGATTCCACATCTCAAAAACCATCTCTCA

                                                    *              
       6411 CAGATTCCACATCTCA-AAACATT-TCCCAGAGATATCACTCATCTCAAAAACCA
          1 CAGATTCCACATCTCACAAACATTCTCCCAGAGAT-TC-CACATCTCAAAAACCA

       6464 GCTCCTGCAG


Statistics
Matches: 48,  Mismatches: 3, Indels: 4
        0.87            0.05        0.07

Matches are distributed among these distances:
  58    9  0.19
  59    8  0.17
  60   31  0.65

ACGTcount: A:0.36, C:0.35, G:0.05, T:0.24


Consensus pattern (60 bp):   
CAGATTCCACATCTCACAAACATTCTCCCAGAGATTCCACATCTCAAAAACCATCTCTCA

Found at i:7192 original size:31 final size:29

Alignment explanation


    Indices: 7148--7205  Score: 80
    Period size: 31  Copynumber: 1.9  Consensus size: 29

       7138 TAAATGTAAC

                           *     *       
       7148 TCAAAATTACAAGTTTAGGGGGCAAAATG
          1 TCAAAATTACAAGTTCAGGGGACAAAATG

                                         
       7177 TCAAAATCATACAAGTTCAGGGGACAAAA
          1 TCAAAAT--TACAAGTTCAGGGGACAAAA

       7206 GGGCATTAAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    7  0.28
  31   18  0.72

ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21


Consensus pattern (29 bp):   
TCAAAATTACAAGTTCAGGGGACAAAATG

Found at i:12702 original size:29 final size:28

Alignment explanation


    Indices: 12629--12704  Score: 82
    Period size: 29  Copynumber: 2.6  Consensus size: 28

      12619 TTTTGTCCCT

                            *             
      12629 TAAATTTGTATGATTTTGACGTTCTGCCTC
          1 TAAATTTGTA--ATTTGGACGTTCTGCCTC

                              *   *       
      12659 TAAATTT-TAATTTTGGATGTTTTGCCTTC
          1 TAAATTTGTAA-TTTGGACGTTCTGCC-TC

                             
      12688 TAAATTTGTAATTTGGA
          1 TAAATTTGTAATTTGGA

      12705 ATATTTTAGT


Statistics
Matches: 40,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  27    1  0.03
  28   12  0.30
  29   17  0.43
  30   10  0.25

ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50


Consensus pattern (28 bp):   
TAAATTTGTAATTTGGACGTTCTGCCTC

Found at i:17538 original size:6 final size:6

Alignment explanation


    Indices: 17528--17560  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      17518 TAACTAATTT

                 *                                
      17528 TTGGAT TTGGAA TTGGAA TTGGAA TTGGAA TTG
          1 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA TTG

      17561 AACTAACATT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39


Consensus pattern (6 bp):   
TTGGAA

Done.