Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020130.1 Corchorus olitorius cultivar O-4 contig20163, 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: 14114
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:4386 original size:21 final size:21

Alignment explanation


    Indices: 4361--4401  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4351 TTAGAAACCC

                                  
       4361 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
       4382 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

       4402 AGGGCTTCGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:6011 original size:37 final size:37

Alignment explanation


    Indices: 5905--6017  Score: 129
    Period size: 37  Copynumber: 3.1  Consensus size: 37

       5895 TTGGCGCATC

                                      *           
       5905 ACACCTAAACAGGAATCTTGAACAAGATTTTGATGAA-
          1 ACACCTAAACAGGAATCTTGAACAAGGTTTTGAT-AAG

                     *   * *   *  *    *         
       5942 ACACCTAAATAGGGACCTTAAATAAGGATTTGATAAG
          1 ACACCTAAACAGGAATCTTGAACAAGGTTTTGATAAG

                        *                     *  
       5979 ACACCTAAACAGAAATCTTGAACAAGGTTTTGATGAG
          1 ACACCTAAACAGGAATCTTGAACAAGGTTTTGATAAG

              
       6016 AC
          1 AC

       6018 TGAATTTTGT


Statistics
Matches: 60,  Mismatches: 15, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  36    2  0.03
  37   58  0.97

ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24


Consensus pattern (37 bp):   
ACACCTAAACAGGAATCTTGAACAAGGTTTTGATAAG

Found at i:9320 original size:33 final size:33

Alignment explanation


    Indices: 9283--9389  Score: 196
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       9273 ATAAATATAT

                                             
       9283 ATATATATATATATGGTCACTTACTAAGGGCTA
          1 ATATATATATATATGGTCACTTACTAAGGGCTA

                                              
       9316 ATATATATATATATGGTCACTTACTAAGGGCTAA
          1 ATATATATATATATGGTCACTTACTAAGGGCT-A

                                              
       9350 TATATATATATATATGGTCACTTACTAAGGGCTA
          1 -ATATATATATATATGGTCACTTACTAAGGGCTA

                  
       9384 ATATAT
          1 ATATAT

       9390 GGTGCCTTAC


Statistics
Matches: 72,  Mismatches: 0, Indels: 4
        0.95            0.00        0.05

Matches are distributed among these distances:
  33   38  0.53
  34    2  0.03
  35   32  0.44

ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37


Consensus pattern (33 bp):   
ATATATATATATATGGTCACTTACTAAGGGCTA

Found at i:9326 original size:35 final size:35

Alignment explanation


    Indices: 9281--9389  Score: 204
    Period size: 35  Copynumber: 3.2  Consensus size: 35

       9271 CAATAAATAT

                                               
       9281 ATATATATATATATATGGTCACTTACTAAGGGCT-
          1 ATATATATATATATATGGTCACTTACTAAGGGCTA

                                               
       9315 A-ATATATATATATATGGTCACTTACTAAGGGCTA
          1 ATATATATATATATATGGTCACTTACTAAGGGCTA

                                               
       9349 ATATATATATATATATGGTCACTTACTAAGGGCTA
          1 ATATATATATATATATGGTCACTTACTAAGGGCTA

                  
       9384 ATATAT
          1 ATATAT

       9390 GGTGCCTTAC


Statistics
Matches: 73,  Mismatches: 0, Indels: 3
        0.96            0.00        0.04

Matches are distributed among these distances:
  33   32  0.44
  34    2  0.03
  35   39  0.53

ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38


Consensus pattern (35 bp):   
ATATATATATATATATGGTCACTTACTAAGGGCTA

Found at i:9567 original size:13 final size:13

Alignment explanation


    Indices: 9549--9575  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       9539 GTTTAATTAT

                         
       9549 TACTCTTGTGTAA
          1 TACTCTTGTGTAA

                         
       9562 TACTCTTGTGTAA
          1 TACTCTTGTGTAA

             
       9575 T
          1 T

       9576 GTAGTTTTCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48


Consensus pattern (13 bp):   
TACTCTTGTGTAA

Found at i:13962 original size:16 final size:16

Alignment explanation


    Indices: 13943--14004  Score: 70
    Period size: 16  Copynumber: 3.8  Consensus size: 16

      13933 AAATTTTGGG

                    *       
      13943 TACCCGAATCCGAAAT
          1 TACCCGAACCCGAAAT

                             
      13959 TACCCGAACCCGAAAAT
          1 TACCCGAACCCG-AAAT

            *    *     *    
      13976 GACCCAAACCCAAAAT
          1 TACCCGAACCCGAAAT

            *            
      13992 GACCCGAACCCGA
          1 TACCCGAACCCGA

      14005 TCAACCCGAC


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

Matches are distributed among these distances:
  16   26  0.67
  17   13  0.33

ACGTcount: A:0.40, C:0.37, G:0.13, T:0.10


Consensus pattern (16 bp):   
TACCCGAACCCGAAAT
Done.