Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012110.1 Corchorus capsularis cultivar CVL-1 contig12131, 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: 8378
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:206 original size:30 final size:30

Alignment explanation


    Indices: 170--276  Score: 178
    Period size: 30  Copynumber: 3.6  Consensus size: 30

        160 CCCTCTCCAA

                                          
        170 CATTGTTATCTTCCACTTGCTGCTCGTTTC
          1 CATTGTTATCTTCCACTTGCTGCTCGTTTC

                                          
        200 CATTGTTATCTTCCACTTGCTGCTCGTTTC
          1 CATTGTTATCTTCCACTTGCTGCTCGTTTC

                           *        *     
        230 CATTGTTATCTTCCATTTGCTGCTGGTTTC
          1 CATTGTTATCTTCCACTTGCTGCTCGTTTC

                   *    *    
        260 CATTGTTGTCTTTCACT
          1 CATTGTTATCTTCCACT

        277 ACTACTTCAT


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   72  1.00

ACGTcount: A:0.10, C:0.27, G:0.14, T:0.49


Consensus pattern (30 bp):   
CATTGTTATCTTCCACTTGCTGCTCGTTTC

Found at i:1090 original size:13 final size:13

Alignment explanation


    Indices: 1072--1096  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1062 GCCAGGCAAA

                         
       1072 CAATATTAACATT
          1 CAATATTAACATT

                        
       1085 CAATATTAACAT
          1 CAATATTAACAT

       1097 GGGTAAATCT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36


Consensus pattern (13 bp):   
CAATATTAACATT

Found at i:2479 original size:37 final size:32

Alignment explanation


    Indices: 2435--2535  Score: 150
    Period size: 31  Copynumber: 3.0  Consensus size: 32

       2425 GGGTTATCAG

                                            
       2435 TCTCCAGATCTTTAGATCTTGGATGTTTGAGT
          1 TCTCCAGATCTTTAGATCTTGGATGTTTGAGT

                                                 
       2467 CTCCAGATCCAGATCTTTAGATCTTGGATGTTTGAG-
          1 -T-C---TCCAGATCTTTAGATCTTGGATGTTTGAGT

                                            
       2503 TCTCCAGATCTTTAGATCTTGGATGTTTGAGT
          1 TCTCCAGATCTTTAGATCTTGGATGTTTGAGT

             
       2535 T
          1 T

       2536 TGTTCAGTTT


Statistics
Matches: 63,  Mismatches: 0, Indels: 11
        0.85            0.00        0.15

Matches are distributed among these distances:
  31   29  0.46
  32    1  0.02
  33    1  0.02
  34    2  0.03
  35    1  0.02
  37   29  0.46

ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42


Consensus pattern (32 bp):   
TCTCCAGATCTTTAGATCTTGGATGTTTGAGT

Found at i:2537 original size:37 final size:37

Alignment explanation


    Indices: 2433--2537  Score: 125
    Period size: 37  Copynumber: 3.0  Consensus size: 37

       2423 TTGGGTTATC

                                                **
       2433 AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGTCTCC
          1 AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGT-TTG

               *                                 
       2471 AG-ATCCAGATCTTTAGATCTTGGA----T--GTTTG
          1 AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGTTTG

                                                 
       2501 AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGTTTG
          1 AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGTTTG

       2538 TTCAGTTTGT


Statistics
Matches: 56,  Mismatches: 4, Indels: 15
        0.75            0.05        0.20

Matches are distributed among these distances:
  30    3  0.05
  31   23  0.41
  33    1  0.02
  35    1  0.02
  37   26  0.46
  38    2  0.04

ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41


Consensus pattern (37 bp):   
AGTCTCCAGATCTTTAGATCTTGGATGTTTGAGTTTG

Found at i:5612 original size:55 final size:55

Alignment explanation


    Indices: 5545--5656  Score: 215
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       5535 TGAACCAGTC

                                                                   
       5545 AATATAAATTAAATTAATAATTATTTTGTTAGACTAAATGCTAGGTTCTAATAAA
          1 AATATAAATTAAATTAATAATTATTTTGTTAGACTAAATGCTAGGTTCTAATAAA

                  *                                                
       5600 AATATAGATTAAATTAATAATTATTTTGTTAGACTAAATGCTAGGTTCTAATAAA
          1 AATATAAATTAAATTAATAATTATTTTGTTAGACTAAATGCTAGGTTCTAATAAA

              
       5655 AA
          1 AA

       5657 AAGTTATGAC


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  55   56  1.00

ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39


Consensus pattern (55 bp):   
AATATAAATTAAATTAATAATTATTTTGTTAGACTAAATGCTAGGTTCTAATAAA
Done.