Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017787.1 Corchorus olitorius cultivar O-4 contig17820, 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: 8355
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35


Found at i:2160 original size:21 final size:21

Alignment explanation


    Indices: 2101--2161  Score: 63
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       2091 GGAGATTAAC

                                   
       2101 AAAATCTCATAGGGAGGTTATCA
          1 AAAAT-TCATA-GGAGGTTATCA

             *                    
       2124 AGAA-TCATAGGAAGGTTA-CA
          1 AAAATTCATAGG-AGGTTATCA

                              
       2144 AAAATTTCATAGGAGGTT
          1 AAAA-TTCATAGGAGGTT

       2162 TTATTAAAAT


Statistics
Matches: 33,  Mismatches: 2, Indels: 8
        0.77            0.05        0.19

Matches are distributed among these distances:
  20    7  0.21
  21   16  0.48
  22    7  0.21
  23    3  0.09

ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26


Consensus pattern (21 bp):   
AAAATTCATAGGAGGTTATCA

Found at i:2249 original size:22 final size:22

Alignment explanation


    Indices: 2218--2288  Score: 74
    Period size: 22  Copynumber: 3.2  Consensus size: 22

       2208 ATCACAATTT

                          *       
       2218 AATTTAATAGGTAAATTATCAA
          1 AATTTAATAGGTAAGTTATCAA

                 *        *       *
       2240 AATTTTATAGTGT-GGTTATCAC
          1 AATTTAATAG-GTAAGTTATCAA

                                   
       2262 AATTTAATAGG-ATAGTTATCAA
          1 AATTTAATAGGTA-AGTTATCAA

                 
       2284 AATTT
          1 AATTT

       2289 TATAATAATA


Statistics
Matches: 39,  Mismatches: 7, Indels: 6
        0.75            0.13        0.12

Matches are distributed among these distances:
  21    1  0.03
  22   36  0.92
  23    2  0.05

ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41


Consensus pattern (22 bp):   
AATTTAATAGGTAAGTTATCAA

Found at i:2694 original size:50 final size:51

Alignment explanation


    Indices: 2605--2704  Score: 175
    Period size: 50  Copynumber: 2.0  Consensus size: 51

       2595 ACTTGAATTA

                                                               
       2605 AAGGATAGCATACAGGAAAAAAAAACATAAAGTTATAGATAATGAGATTTT
          1 AAGGATAGCATACAGGAAAAAAAAACATAAAGTTATAGATAATGAGATTTT

                        *                           *         
       2656 AAGGATAGCATATAGG-AAAAAAAACATAAAGTTATAGATGATGAGATTT
          1 AAGGATAGCATACAGGAAAAAAAAACATAAAGTTATAGATAATGAGATTT

       2705 CTACTTTAAC


Statistics
Matches: 47,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  50   32  0.68
  51   15  0.32

ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24


Consensus pattern (51 bp):   
AAGGATAGCATACAGGAAAAAAAAACATAAAGTTATAGATAATGAGATTTT

Found at i:7313 original size:35 final size:35

Alignment explanation


    Indices: 7248--7314  Score: 89
    Period size: 35  Copynumber: 1.9  Consensus size: 35

       7238 GATCCTCTTT

                   *                 *         
       7248 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
          1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA

                           *  * *           
       7283 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
          1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT

       7315 AAAGAGCTTA


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  35   27  1.00

ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42


Consensus pattern (35 bp):   
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA

Found at i:8332 original size:43 final size:44

Alignment explanation


    Indices: 8246--8347  Score: 125
    Period size: 43  Copynumber: 2.3  Consensus size: 44

       8236 TTCATAAGAA

                   *            *   *             *     
       8246 AGTTTATTAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGG
          1 AGTTTATCAAAATTTTATAGGTAGATTATCAAAGTTTCATATGG

                     *                       *          
       8290 AGTTTATCACAATTTTATAGGTA-ATTATCAAATTTTCATATGG
          1 AGTTTATCAAAATTTTATAGGTAGATTATCAAAGTTTCATATGG

            * *            
       8333 TGGTTATCAAAATTT
          1 AGTTTATCAAAATTT

       8348 CATAAAAA


Statistics
Matches: 49,  Mismatches: 9, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  43   29  0.59
  44   20  0.41

ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46


Consensus pattern (44 bp):   
AGTTTATCAAAATTTTATAGGTAGATTATCAAAGTTTCATATGG

Found at i:8341 original size:22 final size:22

Alignment explanation


    Indices: 8269--8351  Score: 80
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       8259 TTTATAGTTA

                      *    *     *
       8269 GGTTATCAAAGTTTCTTATGGA
          1 GGTTATCAAATTTTCATATGGT

             *                     
       8291 GTTTATCACAATTTT-ATA-GGT
          1 GGTTATCA-AATTTTCATATGGT

            **                    
       8312 AATTATCAAATTTTCATATGGT
          1 GGTTATCAAATTTTCATATGGT

                      *       
       8334 GGTTATCAAAATTTCATA
          1 GGTTATCAAATTTTCATA

       8352 AAAA


Statistics
Matches: 49,  Mismatches: 9, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
  20    6  0.12
  21   11  0.22
  22   27  0.55
  23    5  0.10

ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43


Consensus pattern (22 bp):   
GGTTATCAAATTTTCATATGGT
Done.