Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012023.1 Corchorus capsularis cultivar CVL-1 contig12044, 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: 14492
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:1228 original size:111 final size:111

Alignment explanation


    Indices: 1111--1334  Score: 385
    Period size: 111  Copynumber: 2.0  Consensus size: 111

       1101 TAGGGTTTCA

                             *                           *                   
       1111 AAGAAACTAGATGTTGGTGATCGTGATCATCAATTGCAAGTCTGCGCCATAACCGAAGAACAAGC
          1 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC

                                                          
       1176 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG
         66 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

                                                               *           * 
       1222 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATACCCGAAGAACAATC
          1 AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC

                         *     *                       *  
       1287 TGGGCTTGTTGATGCCCCTGTCCCTGATGATGATGATGATTTCGTG
         66 TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

              
       1333 AA
          1 AA

       1335 TAGCTTATTA


Statistics
Matches: 106,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 111  106  1.00

ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28


Consensus pattern (111 bp):   
AAGAAACTAGATGTTGGCGATCGTGATCATCAATTGCAAGTCTGCCCCATAACCGAAGAACAAGC
TGGGCTTGTTGATACCCCTCTCCCTGATGATGATGATGATTTCCTG

Found at i:4134 original size:42 final size:44

Alignment explanation


    Indices: 4083--4181  Score: 118
    Period size: 42  Copynumber: 2.3  Consensus size: 44

       4073 ATAACATTGA

                           *          *                  
       4083 ATGAAATTTGATAACCCCCAATATTAGTTTTGGCAA-CTT-TTGT
          1 ATGAAATTTGATAACACCCAATATTAATTTTGGCAATCTTGTT-T

                               *             *          
       4126 AT-AAATTTGAT--CACCCTATATTAATTTTGGTAATCTTGTTT
          1 ATGAAATTTGATAACACCCAATATTAATTTTGGCAATCTTGTTT

                           
       4167 ATGAAATTTGATAAC
          1 ATGAAATTTGATAAC

       4182 TCTCTTATAT


Statistics
Matches: 47,  Mismatches: 4, Indels: 9
        0.78            0.07        0.15

Matches are distributed among these distances:
  40   18  0.38
  41    6  0.13
  42   20  0.43
  43    2  0.04
  44    1  0.02

ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42


Consensus pattern (44 bp):   
ATGAAATTTGATAACACCCAATATTAATTTTGGCAATCTTGTTT

Found at i:4336 original size:43 final size:44

Alignment explanation


    Indices: 4289--4385  Score: 117
    Period size: 43  Copynumber: 2.2  Consensus size: 44

       4279 ATAATCCATG

                     *       *        *                  
       4289 TATTAGTTTTGTT-AATCTTGAATATTAAATTTGA-AAACCCTCA
          1 TATTAGTTTAGTTGAA-ATTGAATATAAAATTTGATAAACCCTCA

                                *                * *    
       4332 TATTAGTTTAGTTGAAATTGTATATAAAATTTGATAATCTCTCA
          1 TATTAGTTTAGTTGAAATTGAATATAAAATTTGATAAACCCTCA

                      
       4376 TATTAGTTTA
          1 TATTAGTTTA

       4386 TATATTAGGT


Statistics
Matches: 46,  Mismatches: 6, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  43   27  0.59
  44   19  0.41

ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46


Consensus pattern (44 bp):   
TATTAGTTTAGTTGAAATTGAATATAAAATTTGATAAACCCTCA
Done.