Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015567.1 Corchorus olitorius cultivar O-4 contig15600, 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: 3821
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:1045 original size:41 final size:41

Alignment explanation


    Indices: 1000--1148  Score: 165
    Period size: 41  Copynumber: 3.6  Consensus size: 41

        990 TTTCTAAAAC

                   *                                 
       1000 CAGGGACCAAATTGAATCAAATAGTAACTAAAATCCTAATT
          1 CAGGGACTAAATTGAATCAAATAGTAACTAAAATCCTAATT

                          *      *     *  *    *   * 
       1041 CAGGGACTAAATTGCATCAAAAAGTAAATAGAATCTTAAAT
          1 CAGGGACTAAATTGAATCAAATAGTAACTAAAATCCTAATT

                        *      *  * *                 
       1082 CAGGGACTAAATCGAATCACATTGAAACTAAAATCCT-ATAT
          1 CAGGGACTAAATTGAATCAAATAGTAACTAAAATCCTAAT-T

                          * *         
       1123 CAGGGACTAAATTGCACCAAATAGTA
          1 CAGGGACTAAATTGAATCAAATAGTA

       1149 TATAGAATCT


Statistics
Matches: 84,  Mismatches: 23, Indels: 2
        0.77            0.21        0.02

Matches are distributed among these distances:
  40    1  0.01
  41   83  0.99

ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23


Consensus pattern (41 bp):   
CAGGGACTAAATTGAATCAAATAGTAACTAAAATCCTAATT

Found at i:1117 original size:82 final size:82

Alignment explanation


    Indices: 1000--1175  Score: 246
    Period size: 82  Copynumber: 2.1  Consensus size: 82

        990 TTTCTAAAAC

                   *    *           *                                 *      
       1000 CAGGGACCAAATTGAATCAAATAGTAACTAAAATCCTA-ATTCAGGGACTAAATTGCATCAAAAA
          1 CAGGGACTAAATCGAATCAAATAGAAACTAAAATCCTATA-TCAGGGACTAAATTGCACCAAAAA

                              
       1064 GTAAATAGAATCTTAAAT
         65 GTAAATAGAATCTTAAAT

                               *  *                                       *  
       1082 CAGGGACTAAATCGAATCACATTGAAACTAAAATCCTATATCAGGGACTAAATTGCACCAAATAG
          1 CAGGGACTAAATCGAATCAAATAGAAACTAAAATCCTATATCAGGGACTAAATTGCACCAAAAAG

              *          *   
       1147 TATATAGAATCTTTAAT
         66 TAAATAGAATCTTAAAT

              *         
       1164 CAAGGACTAAAT
          1 CAGGGACTAAAT

       1176 TGTAAACGGA


Statistics
Matches: 83,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  82   82  0.99
  83    1  0.01

ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25


Consensus pattern (82 bp):   
CAGGGACTAAATCGAATCAAATAGAAACTAAAATCCTATATCAGGGACTAAATTGCACCAAAAAG
TAAATAGAATCTTAAAT

Found at i:1171 original size:41 final size:41

Alignment explanation


    Indices: 1000--1177  Score: 164
    Period size: 41  Copynumber: 4.3  Consensus size: 41

        990 TTTCTAAAAC

                   *      *            *  *     *     
       1000 CAGGGACCAAATTGAATCAAATAGTAACTAAAATC-CTAATT
          1 CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTTAA-T

                                 *               *   
       1041 CAGGGACTAAATTGCATCAAAAAGTAAATAGAATCTTAAAT
          1 CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTTAAT

                        * *    *  *        *     *     
       1082 CAGGGACTAAATCGAATCACATTG-AAACTAAAATC-CTATAT
          1 CAGGGACTAAATTGCATCAAATAGTAAA-TAGAATCTTTA-AT

                            *         *              
       1123 CAGGGACTAAATTGCACCAAATAGTATATAGAATCTTTAAT
          1 CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTTAAT

              *           
       1164 CAAGGACTAAATTG
          1 CAGGGACTAAATTG

       1178 TAAACGGAAA


Statistics
Matches: 108,  Mismatches: 24, Indels: 10
        0.76            0.17        0.07

Matches are distributed among these distances:
  40    4  0.04
  41   98  0.91
  42    6  0.06

ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25


Consensus pattern (41 bp):   
CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTTAAT

Found at i:3445 original size:40 final size:40

Alignment explanation


    Indices: 3389--3464  Score: 134
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       3379 GATTCAAAGT

                       *                            
       3389 ACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATGAGGC
          1 ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATGAGGC

                  *                             
       3429 ACTATGCAAGGAAAAAGGAATTGTAAATAAAAGATG
          1 ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATG

       3465 GACCAATACT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  40   34  1.00

ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18


Consensus pattern (40 bp):   
ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATGAGGC
Done.