Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008743.1 Corchorus capsularis cultivar CVL-1 contig08764, 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: 8179
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:1177 original size:24 final size:24

Alignment explanation


    Indices: 1150--1213  Score: 87
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       1140 ACACTGAGTG

                               *    
       1150 TAATATTTCAAAATTTCATGAGGA
          1 TAATATTTCAAAATTTCATAAGGA

                                    
       1174 TAATATTTCAAAATTTCATAAGGA
          1 TAATATTTCAAAATTTCATAAGGA

            * *               
       1198 GAGTA--TCAAAATTTCA
          1 TAATATTTCAAAATTTCA

       1214 CAGATTATCA


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  22   11  0.30
  24   26  0.70

ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36


Consensus pattern (24 bp):   
TAATATTTCAAAATTTCATAAGGA

Found at i:1292 original size:22 final size:22

Alignment explanation


    Indices: 1267--1314  Score: 69
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1257 AGTGTGGTTG

                 *     *          
       1267 TCAAATTTTCATAAGAAAGTTA
          1 TCAAAATTTCACAAGAAAGTTA

                          *       
       1289 TCAAAATTTCACAATAAAGTTA
          1 TCAAAATTTCACAAGAAAGTTA

                
       1311 TCAA
          1 TCAA

       1315 TTCTCAGTGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33


Consensus pattern (22 bp):   
TCAAAATTTCACAAGAAAGTTA

Found at i:1616 original size:205 final size:200

Alignment explanation


    Indices: 1269--1650  Score: 543
    Period size: 205  Copynumber: 1.9  Consensus size: 200

       1259 TGTGGTTGTC

                                                             *  **        *  
       1269 AAATTTTCATAAGAAAGTTATCAAAATTTCACAATAAAGTTATCAATTCTCAGTGTGATTATTAA
          1 AAATTTTCATAAGAAAGTTATCAAAATTTCACAATAAAGTTATCAATTCACAAAGTGATTATAAA

                       *                                                     
       1334 TTTCTACGTTGGAACATGAAAACAACTACCAAAATGACATAGAAATATATTAAAAATTAGTACAA
         66 TTTCTACGTTGAAACATGAAAACAACTACCAAAATGACATAGAAATATATTAAAAATTAGTACAA

                                            *                                
       1399 ATTAAGTTTCCCTT-GATTAAATTTGAATAGAGTTTATTGGAAAGTGGGACTCTCCAATTAAAGC
        131 ATTAAGTTTCCCTTCG-TTAAATTTGAATAGACTTTATTGGAAAGTGGGACTCTCCAATTAAAGC

                  
       1463 TTTTCT
        195 TTTTCT

                       * *                  *  * *                           
       1469 AAATTTTCATACGGAAGTTATCAAAATTTCACTATGAGGTTATCAAATTTTCACAAAGTGATTAT
          1 AAATTTTCATAAGAAAGTTATCAAAATTTCACAATAAAGTTATC-AA--TTCACAAAGTGATTAT

                                              *     *                        
       1534 CAATATTTCTACGTTGAAACATGAAAACAACTACTAAAATTACATA-AAATATATTAAAAAATTA
         63 -AA-ATTTCTACGTTGAAACATGAAAACAACTACCAAAATGACATAGAAATATATT-AAAAATTA

                                    ***                          
       1598 GTACAAATTAAGTTTCCCTTCGTTGCTTTTGAATAGACTTTATTGGAAAGTGG
        125 GTACAAATTAAGTTTCCCTTCGTTAAATTTGAATAGACTTTATTGGAAAGTGG

       1651 AATCTCTTAA


Statistics
Matches: 159,  Mismatches: 16, Indels: 9
        0.86            0.09        0.05

Matches are distributed among these distances:
 200   39  0.25
 201    2  0.01
 203   13  0.08
 204   10  0.06
 205   94  0.59
 206    1  0.01

ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35


Consensus pattern (200 bp):   
AAATTTTCATAAGAAAGTTATCAAAATTTCACAATAAAGTTATCAATTCACAAAGTGATTATAAA
TTTCTACGTTGAAACATGAAAACAACTACCAAAATGACATAGAAATATATTAAAAATTAGTACAA
ATTAAGTTTCCCTTCGTTAAATTTGAATAGACTTTATTGGAAAGTGGGACTCTCCAATTAAAGCT
TTTCT

Found at i:4127 original size:23 final size:23

Alignment explanation


    Indices: 4081--4123  Score: 70
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       4071 TACAACAACT

                                   
       4081 TTACAAATCAAATTTGAATGAGA
          1 TTACAAATCAAATTTGAATGAGA

                      *          
       4104 TTACAAAT-ATATTTGAATGA
          1 TTACAAATCAAATTTGAATGA

       4124 AGATATGTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22   11  0.58
  23    8  0.42

ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35


Consensus pattern (23 bp):   
TTACAAATCAAATTTGAATGAGA
Done.