Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003022.1 Corchorus capsularis cultivar CVL-1 contig03030, 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, 776

Length: 1294
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34


Found at i:1066 original size:33 final size:32

Alignment explanation


    Indices: 969--1073  Score: 129
    Period size: 33  Copynumber: 3.2  Consensus size: 32

        959 TTACAAAGAG

                                           * 
        969 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC

              *   *            *    *        
       1002 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
          1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC

                              *              
       1035 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC

                  
       1068 TGTTTT
          1 TGTTTT

       1074 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    3  0.05
  33   52  0.87
  34    5  0.08

ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46


Consensus pattern (32 bp):   
TGTTTTAGTGTTGTTTGCGATGATACTAAATC

Found at i:1140 original size:66 final size:66

Alignment explanation


    Indices: 1066--1211  Score: 152
    Period size: 66  Copynumber: 2.2  Consensus size: 66

       1056 TGATACTAAA

                         *    *  *              *                     ** *   
       1066 TCTGTTTTGGATGCTAATTGTTATGAAAATAATTCTGTTTTGGTTGATCATA-ACATTGCACATA
          1 TCTGTTTTGGATGATAATAG-CATGAAAATAATTCTATTTTGGTTGATCATAGACATTAAAAATA

              
       1130 AT
         65 AT

                            *       **                      *    *           
       1132 TCTGTTTT-GATTGATCATAGCATTCAAATAATTCTATTTTGGTTGATTATAGGCATTAAAAATA
          1 TCTGTTTTGGA-TGATAATAGCATGAAAATAATTCTATTTTGGTTGATCATAGACATTAAAAATA

              
       1196 AT
         65 AT

                          
       1198 TCTGTTTTGGATGA
          1 TCTGTTTTGGATGA

       1212 AAATGAAAGA


Statistics
Matches: 65,  Mismatches: 12, Indels: 6
        0.78            0.14        0.07

Matches are distributed among these distances:
  65   28  0.43
  66   35  0.54
  67    2  0.03

ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45


Consensus pattern (66 bp):   
TCTGTTTTGGATGATAATAGCATGAAAATAATTCTATTTTGGTTGATCATAGACATTAAAAATAA
T

Found at i:1172 original size:32 final size:33

Alignment explanation


    Indices: 1092--1207  Score: 153
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       1082 ATTGTTATGA

                                      *    * 
       1092 AAATAATTCTGTTTTGGTTGATCATAACATTGC
          1 AAATAATTCTGTTTTGGTTGATCATAGCATTAC

             *              *                
       1125 ACATAATTCTGTTTTGATTGATCATAGCATT-C
          1 AAATAATTCTGTTTTGGTTGATCATAGCATTAC

                      *           *          *
       1157 AAATAATTCTATTTTGGTTGATTATAGGCATTAA
          1 AAATAATTCTGTTTTGGTTGATCATA-GCATTAC

                             
       1191 AAATAATTCTGTTTTGG
          1 AAATAATTCTGTTTTGG

       1208 ATGAAAATGA


Statistics
Matches: 72,  Mismatches: 9, Indels: 3
        0.86            0.11        0.04

Matches are distributed among these distances:
  32   23  0.32
  33   33  0.46
  34   16  0.22

ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44


Consensus pattern (33 bp):   
AAATAATTCTGTTTTGGTTGATCATAGCATTAC
Done.