Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013785.1 Corchorus capsularis cultivar CVL-1 contig13806, 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: 8880
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:1515 original size:8 final size:8

Alignment explanation


    Indices: 1504--1529  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       1494 TTCTTTAATG

                    
       1504 ATCTTCAA
          1 ATCTTCAA

                    
       1512 ATCTTCAA
          1 ATCTTCAA

                    
       1520 ATCTTCAA
          1 ATCTTCAA

              
       1528 AT
          1 AT

       1530 TATCTTCAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38


Consensus pattern (8 bp):   
ATCTTCAA

Found at i:4445 original size:33 final size:33

Alignment explanation


    Indices: 4370--4446  Score: 145
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       4360 AAGGGTCGCG

                     *                       
       4370 TGGCCGGTTATGGCCGGGCATGGCCGAGTCGTT
          1 TGGCCGGTTGTGGCCGGGCATGGCCGAGTCGTT

                                             
       4403 TGGCCGGTTGTGGCCGGGCATGGCCGAGTCGTT
          1 TGGCCGGTTGTGGCCGGGCATGGCCGAGTCGTT

                       
       4436 TGGCCGGTTGT
          1 TGGCCGGTTGT

       4447 AGTCGGCCAT


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   43  1.00

ACGTcount: A:0.06, C:0.23, G:0.44, T:0.26


Consensus pattern (33 bp):   
TGGCCGGTTGTGGCCGGGCATGGCCGAGTCGTT

Found at i:4473 original size:33 final size:34

Alignment explanation


    Indices: 4364--4509  Score: 115
    Period size: 33  Copynumber: 4.4  Consensus size: 34

       4354 TAGACAAAGG

                              *     *    *     
       4364 GTCGCGTGGCCGGTT-ATGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGATAGCCGGACATGTCC-AT

                **            *     *    *     
       4397 GTCGTTTGGCCGGTTG-TGGCCGGGCATGGCCGA-
          1 GTCGCGTGGCCGGTTGATAGCCGGACATGTCC-AT

                **              *   *         
       4430 GTCGTTTGGCCGGTTG-TAGTCGGCCATGTCCAT
          1 GTCGCGTGGCCGGTTGATAGCCGGACATGTCCAT

                              *               
       4463 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
          1 GTCGCGTGGCCGGTTGATAGCCGGACATGTCCAT

                          
       4496 GTCGCGTGGCCGGT
          1 GTCGCGTGGCCGGT

       4510 CTTGTGGCCG


Statistics
Matches: 98,  Mismatches: 11, Indels: 7
        0.84            0.09        0.06

Matches are distributed among these distances:
  32    3  0.03
  33   95  0.97

ACGTcount: A:0.08, C:0.26, G:0.42, T:0.24


Consensus pattern (34 bp):   
GTCGCGTGGCCGGTTGATAGCCGGACATGTCCAT

Found at i:5586 original size:6 final size:6

Alignment explanation


    Indices: 5575--5601  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       5565 ATTAATCTGT

                                           
       5575 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       5602 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Done.