Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018256.1 Corchorus olitorius cultivar O-4 contig18289, 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: 4222
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:1406 original size:13 final size:13

Alignment explanation


    Indices: 1388--1426  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       1378 TAGTAGTAAG

                         
       1388 ATAAGATAAGATA
          1 ATAAGATAAGATA

                        * 
       1401 ATAAGAT-AGTAAA
          1 ATAAGATAAG-ATA

                         
       1414 ATAAGATAAGATA
          1 ATAAGATAAGATA

       1427 TAATATATTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  12    2  0.09
  13   18  0.82
  14    2  0.09

ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23


Consensus pattern (13 bp):   
ATAAGATAAGATA

Found at i:1417 original size:26 final size:26

Alignment explanation


    Indices: 1369--1426  Score: 84
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       1359 TTCGTAATAG

                               *      
       1369 TAAGAT-ATATAGTAGTAAGATAAGA
          1 TAAGATAATATAGTAGTAAAATAAGA

                                       
       1394 TAAGATAATA-AGATAGTAAAATAAGA
          1 TAAGATAATATAG-TAGTAAAATAAGA

                   
       1420 TAAGATA
          1 TAAGATA

       1427 TAATATATTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  25    8  0.27
  26   22  0.73

ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26


Consensus pattern (26 bp):   
TAAGATAATATAGTAGTAAAATAAGA

Found at i:4186 original size:221 final size:219

Alignment explanation


    Indices: 3690--4222  Score: 870
    Period size: 221  Copynumber: 2.4  Consensus size: 219

       3680 TGATTTGGGT

                                               *                             
       3690 TTAATTGAATAAACCCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATT
          1 TTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATT

                         * *                              *                  
       3755 CAGTATCCTCAAACTGATATACTTTATACCCAAATCATTTCTCATCCTCCCCAAATAATCATATG
         66 CAGTATCC-CAAAGTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATG

               *                      *                                     *
       3820 CACTATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATACACCCAAAATTGACTTTAAAAAG
        130 CACCATCCCCAAATTCTTTAGAGATTCACATTTTTTCTCATACACCCAAAATTGACTTTAAAAAA

                                     
       3885 TGCTAATCCATACTTTTCATCCTAA
        195 TGCTAATCCATACTTTTCATCCTAA

                               *                          *                  
       3910 TTAATTGAATAAACCCCGTTTATATGATTTTAGTGTCATCTAATAACTAAACAAAATGCAAAATT
          1 TTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATT

                                                                        *    
       3975 CAGTATCTCCAAAGTAATATACTTTATACCCAAATCATTTCT-ATCATCCCCAAATAATCTTATG
         66 CAGTATC-CCAAAGTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATG

                                 *                    *                      
       4039 CACCATCCCCAAATTCTTTAGTGATTCACATTTTTTCTCATATACCCAAAATTGACTTTAAAAAA
        130 CACCATCCCCAAATTCTTTAGAGATTCACATTTTTTCTCATACACCCAAAATTGACTTTAAAAAA

                          *           *
       4104 TGCTTTAATCCATATTTTTCATCCTAG
        195 TGC--TAATCCATACTTTTCATCCTAA

                                                         *           *       
       4131 TTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTAATAGTTAAACAAAATACAAAATT
          1 TTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATT

                                       
       4196 CAGTATCCCCAAAGTAATATACTTTAT
         66 CAGTAT-CCCAAAGTAATATACTTTAT


Statistics
Matches: 291,  Mismatches: 18, Indels: 7
        0.92            0.06        0.02

Matches are distributed among these distances:
 219   83  0.29
 220  100  0.34
 221  107  0.37
 222    1  0.00

ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35


Consensus pattern (219 bp):   
TTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATT
CAGTATCCCAAAGTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGC
ACCATCCCCAAATTCTTTAGAGATTCACATTTTTTCTCATACACCCAAAATTGACTTTAAAAAAT
GCTAATCCATACTTTTCATCCTAA
Done.