Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014322.1 Corchorus capsularis cultivar CVL-1 contig14343, 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: 15472
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:11596 original size:241 final size:239

Alignment explanation


    Indices: 11024--11721  Score: 1174
    Period size: 237  Copynumber: 2.9  Consensus size: 239

      11014 AGAGACGAGT

                                                                             
      11024 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT
          1 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT

                                                                             
      11089 GCAAAGAGATTTGAGATGAATGAACTTGATGCATCACATGCGCATGACCATGTTATCGATTGATC
         66 GCAAAGAGATTTGAGATGAATGAACTTGATGCATCACATGCGCATGACCATGTTATCGATTGATC

                           *                                                 
      11154 TAATC-TAAGTCAATGATGATGCAATTGTGAATTTCAGACGGGAATTAGATATATTAGCCCCTAT
        131 TAATCTTAAGTCAATAATGATGCAATTGTGAATTTCAGACGGGAATTAGATATATTAGCCCCTAT

                                    *                   
      11218 ATTAAGTTGTACTACAAAACATA-ATTACGTCCTATGATTAAGG
        196 ATTAAGTTGTACTACAAAACATAGTTTACGTCCTATGATTAAGG

                                                                             
      11261 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT
          1 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT

                                  *                              *  **       
      11326 GCAAAGAGATTTGAGATGAATGGACTTGATGCATCACATGCGCATGACCATGTCATTAATTGATC
         66 GCAAAGAGATTTGAGATGAATGAACTTGATGCATCACATGCGCATGACCATGTTATCGATTGATC

                                                   *                         
      11391 TAATCTTAAGTCAATAATGATGCAATTGTGAATTTCAGATGGGAATTAGATATATTAGCCCCTAT
        131 TAATCTTAAGTCAATAATGATGCAATTGTGAATTTCAGACGGGAATTAGATATATTAGCCCCTAT

                                           *  *           
      11456 ATTAAGTTGTACTACAAAACATAGTTTACGTTCTGTGATTAAGGTG
        196 ATTAAGTTGTACTACAAAACATAGTTTACGTCCTATGATTAA-G-G

                                                           *    *            
      11502 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCTTAGACCGTGATATATGT
          1 TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT

                             *             *   *               *             
      11567 GCAAAGAGATTTGAGATTAATGAACTTGATGAATCGCATGCGCATGACCATTTTATCGATTGATC
         66 GCAAAGAGATTTGAGATGAATGAACTTGATGCATCACATGCGCATGACCATGTTATCGATTGATC

                       *                                     *               
      11632 TAATCTT-AGTTAATAATGATGCAATTGTGAATTTCAGACGGGAATTAGTTATATTA-CCTCCTA
        131 TAATCTTAAGTCAATAATGATGCAATTGTGAATTTCAGACGGGAATTAGATATATTAGCC-CCTA

                                         
      11695 TATTAAG-T-TACTACAAAACATAGTTTA
        195 TATTAAGTTGTACTACAAAACATAGTTTA

      11722 ATTCTAAAGT


Statistics
Matches: 434,  Mismatches: 22, Indels: 9
        0.93            0.05        0.02

Matches are distributed among these distances:
 237  131  0.30
 238   99  0.23
 239   18  0.04
 240   58  0.13
 241  128  0.29

ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34


Consensus pattern (239 bp):   
TGTTCAAATGAAGTTAGTTTGAAGTCCCTCAAAAAAGTTTGAAGTTCCTAGATCGTGATATATGT
GCAAAGAGATTTGAGATGAATGAACTTGATGCATCACATGCGCATGACCATGTTATCGATTGATC
TAATCTTAAGTCAATAATGATGCAATTGTGAATTTCAGACGGGAATTAGATATATTAGCCCCTAT
ATTAAGTTGTACTACAAAACATAGTTTACGTCCTATGATTAAGG

Found at i:14223 original size:2 final size:2

Alignment explanation


    Indices: 14216--14243  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14206 TTATAATTAG

                                                     
      14216 TA TA TA 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

      14244 GTAGTATAGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Done.