Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011229.1 Corchorus olitorius cultivar O-4 contig11262, 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: 3196
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36


Found at i:1287 original size:52 final size:52

Alignment explanation


    Indices: 1132--1287  Score: 143
    Period size: 48  Copynumber: 3.1  Consensus size: 52

       1122 GTTAAATTAG

                                                                
       1132 TTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTGTT
          1 TTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTGTT

                   *           *   *                   * *  *        
       1184 TTCTT-TAAT--T--TTGTTCATGCATT-TTTGTGCAATT--CTTGTTAAATTAG--
          1 TTCTTGTCATCCTAATTG-GCATTC-TTATTT-TGC-ATTAGCATATTTAATT-GTT

                                                                
       1231 TTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTGTT
          1 TTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTGTT

                 
       1283 TTCTT
          1 TTCTT

       1288 TAATTTTGTT


Statistics
Matches: 77,  Mismatches: 12, Indels: 30
        0.65            0.10        0.25

Matches are distributed among these distances:
  47    8  0.10
  48   18  0.23
  49   10  0.13
  50   10  0.13
  51   18  0.23
  52   13  0.17

ACGTcount: A:0.21, C:0.14, G:0.12, T:0.54


Consensus pattern (52 bp):   
TTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTGTT

Found at i:1288 original size:99 final size:99

Alignment explanation


    Indices: 1117--1316  Score: 400
    Period size: 99  Copynumber: 2.0  Consensus size: 99

       1107 TGAATTTTAG

                                                                             
       1117 TTCTTGTTAAATTAGTTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTG
          1 TTCTTGTTAAATTAGTTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTG

                                              
       1182 TTTTCTTTAATTTTGTTCATGCATTTTTGTGCAA
         66 TTTTCTTTAATTTTGTTCATGCATTTTTGTGCAA

                                                                             
       1216 TTCTTGTTAAATTAGTTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTG
          1 TTCTTGTTAAATTAGTTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTG

                                              
       1281 TTTTCTTTAATTTTGTTCATGCATTTTTGTGCAA
         66 TTTTCTTTAATTTTGTTCATGCATTTTTGTGCAA

              
       1315 TT
          1 TT

       1317 AATTGTATCA


Statistics
Matches: 101,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  99  101  1.00

ACGTcount: A:0.21, C:0.13, G:0.12, T:0.54


Consensus pattern (99 bp):   
TTCTTGTTAAATTAGTTCTTGTCATCCTAATTGGCATTCTTATTTTGCATTAGCATATTTAATTG
TTTTCTTTAATTTTGTTCATGCATTTTTGTGCAA

Done.