Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007319.1 Corchorus capsularis cultivar CVL-1 contig07340, 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: 12292
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:307 original size:33 final size:33

Alignment explanation


    Indices: 226--366  Score: 169
    Period size: 33  Copynumber: 4.3  Consensus size: 33

        216 AACGGATCAT

                                  **  *    **
        226 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
          1 GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCGC

               *                   *       *  
        259 GTGACCGGTTGTGGCCGGGCATGGTCC-AGTTGC
          1 GTGGCCGGTTGTGGCCGGGCAT-CTCCAAGTCGC

                *                             
        292 GTGGTCGG-TGATGGCCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTTG-TGGCCGGGCATCTCCAAGTCGC

                                             
        325 GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCGC

                     
        358 GTGGCCGGT
          1 GTGGCCGGT

        367 CACAAGTGCT


Statistics
Matches: 94,  Mismatches: 10, Indels: 8
        0.84            0.09        0.07

Matches are distributed among these distances:
  32    5  0.05
  33   84  0.89
  34    5  0.05

ACGTcount: A:0.09, C:0.26, G:0.43, T:0.22


Consensus pattern (33 bp):   
GTGGCCGGTTGTGGCCGGGCATCTCCAAGTCGC

Found at i:5729 original size:10 final size:10

Alignment explanation


    Indices: 5714--5748  Score: 52
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       5704 TCTGGTCGAA

                       
       5714 TTTTTTTTATT
          1 TTTTTTTTA-T

                      
       5725 TTTTTTTTAT
          1 TTTTTTTTAT

                  *   
       5735 TTTTTTATAT
          1 TTTTTTTTAT

                
       5745 TTTT
          1 TTTT

       5749 CGATATAACT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  10   14  0.61
  11    9  0.39

ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89


Consensus pattern (10 bp):   
TTTTTTTTAT

Found at i:5730 original size:11 final size:11

Alignment explanation


    Indices: 5714--5740  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       5704 TCTGGTCGAA

                       
       5714 TTTTTTTTATT
          1 TTTTTTTTATT

                       
       5725 TTTTTTTTATT
          1 TTTTTTTTATT

                 
       5736 TTTTT
          1 TTTTT

       5741 ATATTTTTCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93


Consensus pattern (11 bp):   
TTTTTTTTATT

Found at i:10200 original size:33 final size:33

Alignment explanation


    Indices: 10158--10266  Score: 157
    Period size: 33  Copynumber: 3.3  Consensus size: 33

      10148 GTGTTTTAGA

                                             
      10158 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
          1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG

                      *    *      *   *   *  
      10191 TGTTGTTTGCAATGACACTAAATCT-GTTTTAG
          1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG

                                              
      10223 ATGTTGTTTGCGATGATACTAAACCTAATTTGAG
          1 -TGTTGTTTGCGATGATACTAAACCTAATTTGAG

                      
      10257 TGTTGTTTGC
          1 TGTTGTTTGC

      10267 AATAAAACTA


Statistics
Matches: 64,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  32    5  0.08
  33   54  0.84
  34    5  0.08

ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42


Consensus pattern (33 bp):   
TGTTGTTTGCGATGATACTAAACCTAATTTGAG

Found at i:10231 original size:66 final size:66

Alignment explanation


    Indices: 10149--10291  Score: 259
    Period size: 66  Copynumber: 2.2  Consensus size: 66

      10139 TTGAAAAGAG

                                                                   * *       
      10149 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT

             
      10214 C
         66 C

                                                                             
      10215 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT

             
      10280 C
         66 C

                  *    
      10281 TGTTTTGGATG
          1 TGTTTTAGATG

      10292 CTAATTGTGA


Statistics
Matches: 74,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  66   74  1.00

ACGTcount: A:0.27, C:0.10, G:0.20, T:0.42


Consensus pattern (66 bp):   
TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
C

Found at i:10405 original size:30 final size:31

Alignment explanation


    Indices: 10302--10421  Score: 125
    Period size: 33  Copynumber: 3.8  Consensus size: 31

      10292 CTAATTGTGA

                                             
      10302 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT

             *                           *   
      10335 TAAAAACAATTCTGTTTTGGTTGATTATAACAT
          1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT

            *     *   *                    
      10368 AGAAAATAATCCTGTTTTGGTTG-ATAGCAT
          1 TGAAAACAATTCTGTTTTGGTTGAATAGCAT

                  *  *        *     
      10398 TGAAAATAAATCTGTTTTAGTTGA
          1 TGAAAACAATTCTGTTTTGGTTGA

      10422 CGAGAAAGAG


Statistics
Matches: 73,  Mismatches: 12, Indels: 6
        0.80            0.13        0.07

Matches are distributed among these distances:
  30   25  0.34
  32    1  0.01
  33   47  0.64

ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39


Consensus pattern (31 bp):   
TGAAAACAATTCTGTTTTGGTTGAATAGCAT
Done.