Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014418.1 Corchorus capsularis cultivar CVL-1 contig14439, 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: 22865
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:9426 original size:230 final size:229

Alignment explanation


    Indices: 9010--9503  Score: 527
    Period size: 230  Copynumber: 2.2  Consensus size: 229

       9000 AGTTACTTGA

                *      *                         *  *                *       
       9010 TTGATGAAGACTGCCGGAAAAAGTCGATGAAAGGCCGTGATTCCTTTGAAAGCAACTGAGTTTTG
          1 TTGACGAAGACAGCCGGAAAAAGTCGATGAAAGGCCGCGAGTCCTTTGAAAGCAACTCAGTTTTG

                           *          *                                *   * 
       9075 GGTACTGGTGACCCAGACTCCATGCTCTCTCCTCTCAAAACAATAAAATCAAAAGATATTTTAGA
         66 GGTACTGGTGACCCACACTCCATGCTATCTCCTCTCAAAACAATAAAATCAAAAGATATATTAAA

                                                                            *
       9140 GAAAAAAAAAAAAACAAACAAACGCCCCCACAACAAAAACAAAATCATTTTTGAAAAACCAAAAC
        131 GAAAAAAAAAAAAACAAACAAACGCCCCCACAACAAAAACAAAATCATTTTTG-AAAACCAAAAA

                      *  *                    * *
       9205 GCAA-GGTGAGAATTGAGTTTGGTTCAGA-TACCTGT
        195 GCAATGG-GAAAACTGAGTTTGGTTCA-ATTACCCGG

               *      *                       **                  **         
       9240 TTGGCGAAGAGAGCCGGAAAAAGTCGATGAAAGGTTGCGAGTCC-TTGAAAAGCTTCTCAGTTTT
          1 TTGACGAAGACAGCCGGAAAAAGTCGATGAAAGGCCGCGAGTCCTTTG-AAAGCAACTCAGTTTT

                       *                        *   *  * *                   
       9304 GGGTACTGGTGGCCCACACTCCATGCTATCTCCTCTGAAAGCAGTGAAATC-AAA-ATA-ATTAA
         65 GGGTACTGGTGACCCACACTCCATGCTATCTCCTCTCAAAACAATAAAATCAAAAGATATATTAA

              ***   **                        *    *                       * 
       9366 AGGGGAAATTAAAAACAAA-AAAC-CCCACAACAGAACTCAAAACAAAATCATTTCTTGAAAATC
        130 AGAAAAAAAAAAAAACAAACAAACGCCC-C--CACAAC-AAAAACAAAATCATTT-TTGAAAACC

                                *                   
       9429 AAAAAGCAATGGGAAAACTGGGTTTGGTTCAATTACCCGG
        190 AAAAAGCAATGGGAAAACTGAGTTTGGTTCAATTACCCGG

                *      *                       
       9469 TTGATGAAGACTGCCGGAAAAAGTCGATGAAAGGC
          1 TTGACGAAGACAGCCGGAAAAAGTCGATGAAAGGC

       9504 GGTTTTCCAG


Statistics
Matches: 217,  Mismatches: 39, Indels: 17
        0.79            0.14        0.06

Matches are distributed among these distances:
 225    3  0.01
 226    5  0.02
 227   17  0.08
 228    9  0.04
 229   85  0.39
 230   98  0.45

ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22


Consensus pattern (229 bp):   
TTGACGAAGACAGCCGGAAAAAGTCGATGAAAGGCCGCGAGTCCTTTGAAAGCAACTCAGTTTTG
GGTACTGGTGACCCACACTCCATGCTATCTCCTCTCAAAACAATAAAATCAAAAGATATATTAAA
GAAAAAAAAAAAAACAAACAAACGCCCCCACAACAAAAACAAAATCATTTTTGAAAACCAAAAAG
CAATGGGAAAACTGAGTTTGGTTCAATTACCCGG

Found at i:9903 original size:15 final size:14

Alignment explanation


    Indices: 9883--9912  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       9873 TGTTGGGCCA

                           
       9883 TTTCTTTTTTTCTTT
          1 TTTCTTTTTTT-TTT

                          
       9898 TTTCTTTTTTTTTT
          1 TTTCTTTTTTTTTT

             
       9912 T
          1 T

       9913 CCTTTTAAAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.27
  15   11  0.73

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (14 bp):   
TTTCTTTTTTTTTT

Found at i:13374 original size:19 final size:20

Alignment explanation


    Indices: 13347--13385  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      13337 GAAAATATTG

                     *          
      13347 AAAATATTACAAAAAAAAAT
          1 AAAATATTAAAAAAAAAAAT

                                
      13367 AAAA-ATTAAAAAAAAAAAT
          1 AAAATATTAAAAAAAAAAAT

      13386 CAAAGAAATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18


Consensus pattern (20 bp):   
AAAATATTAAAAAAAAAAAT

Found at i:17980 original size:31 final size:31

Alignment explanation


    Indices: 17920--17980  Score: 86
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      17910 TCGTGCTATA

                                 *         
      17920 TGTACCAAAAAGTGACACATGTCACGCCACG
          1 TGTACCAAAAAGTGACACATGGCACGCCACG

                *             *     *     
      17951 TGTATCAAAAAGTGACACGTGGCATGCCAC
          1 TGTACCAAAAAGTGACACATGGCACGCCAC

      17981 ACGTGCACAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18


Consensus pattern (31 bp):   
TGTACCAAAAAGTGACACATGGCACGCCACG
Done.