Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008010.1 Corchorus capsularis cultivar CVL-1 contig08031, 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: 3364
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:1334 original size:10 final size:10

Alignment explanation


    Indices: 1313--1343  Score: 55
    Period size: 10  Copynumber: 3.2  Consensus size: 10

       1303 CTTTTCGCAG

                      
       1313 TAAAAAAT-A
          1 TAAAAAATAA

                      
       1322 TAAAAAATAA
          1 TAAAAAATAA

                      
       1332 TAAAAAATAA
          1 TAAAAAATAA

              
       1342 TA
          1 TA

       1344 TCTACATATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    8  0.38
  10   13  0.62

ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23


Consensus pattern (10 bp):   
TAAAAAATAA

Found at i:2213 original size:84 final size:84

Alignment explanation


    Indices: 2109--2273  Score: 330
    Period size: 84  Copynumber: 2.0  Consensus size: 84

       2099 GAGAAATGAC

                                                                             
       2109 CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG
          1 CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG

                               
       2174 TAGGTAAAGACGAAAAGGA
         66 TAGGTAAAGACGAAAAGGA

                                                                             
       2193 CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG
          1 CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG

                            
       2258 TAGGTAAAGACGAAAA
         66 TAGGTAAAGACGAAAA

       2274 TGATTAGTTC


Statistics
Matches: 81,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  84   81  1.00

ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25


Consensus pattern (84 bp):   
CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG
TAGGTAAAGACGAAAAGGA

Found at i:2547 original size:166 final size:165

Alignment explanation


    Indices: 2193--2617  Score: 582
    Period size: 166  Copynumber: 2.6  Consensus size: 165

       2183 ACGAAAAGGA

                                                                       *     
       2193 CAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTACCAAG
          1 CAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAG

                *           **            *  * ** **  *       * *         *  
       2258 TAGGTAAAGACGAAAATGATTAGTTCTCTAGCTTATCATTAATCCTTGATTGTGATCTTTTATTA
         65 TAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGAAAGCCTTGATAGGGATCTTTTAGTA

                     *      *     *    *        
       2323 ATTCCACTACTCTATTTAAGTCCATTGTGAAATGAC
        130 ATTCCACTAATCTATTAAAGTCAATTGGGAAATGAC

            *    *     *                                        *            
       2359 TAAAAGGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAATAATCTGCCAAG
          1 CAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAG

                                *                            *               
       2424 TAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGAAAGCCTTGGTAGGGATCTTTTAGT
         65 TAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGAAAGCCTTGATAGGGATCTTTTAGT

                                                 
       2489 AATTCCACTAATCTATTAAAGTCAATTGGGAAATGAC
        129 AATTCCACTAATCTATTAAAGTCAATTGGGAAATGAC

                                                                             
       2526 CAAAAAGTCTAGTTA-TTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAG
          1 CAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAG

               *                        
       2590 TAGAAAAAGACGAAAAAAATTAGTTCTC
         65 TAGGAAAAGACGAAAAAAATTAGTTCTC

       2618 CCGCTCCTCA


Statistics
Matches: 226,  Mismatches: 31, Indels: 4
        0.87            0.12        0.02

Matches are distributed among these distances:
 166  162  0.72
 167   64  0.28

ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30


Consensus pattern (165 bp):   
CAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGT
AGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGAAAGCCTTGATAGGGATCTTTTAGTAA
TTCCACTAATCTATTAAAGTCAATTGGGAAATGAC
Done.