Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023152.1 Corchorus olitorius cultivar O-4 contig23185, 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: 18665
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:759 original size:30 final size:29

Alignment explanation


    Indices: 677--760  Score: 105
    Period size: 30  Copynumber: 2.8  Consensus size: 29

        667 TACATACCAC

                           *              
        677 TAATAATTATTATTATTATAATAATAAGTT
          1 TAATAATTATTA-TAATATAATAATAAGTT

                      *   **              
        707 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATAATA-TAATAATAAGTT

                                    
        737 TAATAATTATTATAATAGTAATAA
          1 TAATAATTATTATAATA-TAATAA

        761 GTCTAAATTA


Statistics
Matches: 46,  Mismatches: 7, Indels: 2
        0.84            0.13        0.04

Matches are distributed among these distances:
  29    3  0.07
  30   43  0.93

ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43


Consensus pattern (29 bp):   
TAATAATTATTATAATATAATAATAAGTT

Found at i:1342 original size:11 final size:11

Alignment explanation


    Indices: 1318--1352  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       1308 TTGACAGCAC

                       
       1318 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
       1329 AACGAAAACGA
          1 AACAAAAACAA

                       
       1340 AACAAAAACAA
          1 AACAAAAACAA

              
       1351 AA
          1 AA

       1353 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:1431 original size:2 final size:2

Alignment explanation


    Indices: 1424--1466  Score: 59
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1414 AGTTTGGACT

                        *               *                                  
       1424 TA TA TA TA GA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1467 AAATCGTTGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:6376 original size:272 final size:273

Alignment explanation


    Indices: 5890--6434  Score: 995
    Period size: 272  Copynumber: 2.0  Consensus size: 273

       5880 TGGAACTAGC

                                      *                         *            
       5890 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
          1 ACTGATATCTACAACAAAATTTTGTTATCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAA

                                                                             
       5955 TCAAAGAAATTGCAAAATTACAAATTTGAACATGAAGAAAATGTTGACACATCTAAACATTTTCG
         66 TCAAAGAAATTGCAAAATTACAAATTTGAACATGAAGAAAATGTTGACACATCTAAACATTTTCG

                                                                *            
       6020 TGGAAAAGAAAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGGAATGTAGATGCA
        131 TGGAAAAGAAAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA

                                                                   *       * 
       6085 GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACC-AAACGAAAAAAGG
        196 GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG

                         
       6149 AGTTGCAAGAAAA
        261 AGTTGCAAGAAAA

                                                                             
       6162 ACTGATATCTACAACAAAATTTTGTTATCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAA
          1 ACTGATATCTACAACAAAATTTTGTTATCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAA

                                          *                       *          
       6227 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
         66 TCAAAGAAATTGCAAAATTACAAATTTGAACATGAAGAAAATGTTGACACATCTAAACATTTTCG

                     *                                                       
       6292 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGAT-GAAAGTGTAGATGC
        131 TGGAAAAGAAAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAA-TGTAGATGC

                                                                             
       6356 AGACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAA
        195 AGACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAA

                          
       6421 GAGTTGCAAGAAAA
        260 GAGTTGCAAGAAAA

       6435 GCCAAGTTAG


Statistics
Matches: 263,  Mismatches: 8, Indels: 3
        0.96            0.03        0.01

Matches are distributed among these distances:
 271    3  0.01
 272  236  0.90
 273   24  0.09

ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25


Consensus pattern (273 bp):   
ACTGATATCTACAACAAAATTTTGTTATCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAA
TCAAAGAAATTGCAAAATTACAAATTTGAACATGAAGAAAATGTTGACACATCTAAACATTTTCG
TGGAAAAGAAAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA
GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
AGTTGCAAGAAAA

Found at i:17646 original size:2 final size:2

Alignment explanation


    Indices: 17639--17670  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      17629 CTATTATTAG

                                                              
      17639 TA TA TA TA -A TA TA TA TA TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17671 CTAGTAAAAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   26  0.93

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


Consensus pattern (2 bp):   
TA

Found at i:18351 original size:25 final size:25

Alignment explanation


    Indices: 18300--18351  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      18290 AATAAATATC

                          *          
      18300 AAATTAATTTGTAATATAATATGAA
          1 AAATTAATTTGTAAAATAATATGAA

                      *       *       
      18325 AAATTAATTTTTATAAATCATAT-AA
          1 AAATTAATTTGTA-AAATAATATGAA

              
      18350 AA
          1 AA

      18352 TAAAAAAATA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  25   16  0.70
  26    7  0.30

ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40


Consensus pattern (25 bp):   
AAATTAATTTGTAAAATAATATGAA
Done.