Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011037.1 Corchorus olitorius cultivar O-4 contig11070, 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, 660

Length: 1101
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35


Found at i:518 original size:154 final size:155

Alignment explanation


    Indices: 1--658  Score: 1027
    Period size: 154  Copynumber: 4.2  Consensus size: 155

                                 *                                           
          1 AAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
          1 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC

                                                                             
         66 ACTGTGAAGTTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGGCCCATTAGTG
         66 ACTGTGAAG-TTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGGCCCATTAGTG

                                       
        131 ACGCTTTTGAATCGTCTTCGATTTGGC
        130 ACG-TTTTGAATCGTCTTCGATTTGGC

                                         *                                   
        158 AAACCTCAATGCTTTTCTTTCCATTG-TTGTGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
          1 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC

                                                       *                    *
        222 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGACCCTATCGGGGGCCCATTAGTT
         66 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GAGCCTATCGGGGGCCCATTAGTG

            *                         
        287 CCGTTTTGAATCGTCTTCGATTTGGC
        130 ACGTTTTGAATCGTCTTCGATTTGGC

                            *                                                
        313 AAACCTCAATGCTTTTATTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
          1 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC

             *               *                                       *       
        378 AATGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGAGCCTATC-GGGGCCCTTTAGTGA
         66 ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGGCCCATTAGTGA

            *          *      *      
        442 TGTTTTGAATCATCTTCGCTTTGG-
        131 CGTTTTGAATCGTCTTCGATTTGGC

            *      *     *                                        *          
        466 TAACCGTTAATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGGGAGATTAGTC
          1 AAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC

                                    *  *              *                  *  *
        531 CACTGTGAAGTTTTTAGCTCATTTTGAGCACTTGTTATTTTGGGCCTATC-GGGGCCCATTTGTT
         65 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGGCCCATTAGTG

            *                         
        595 CCGTTTTGAATCGTCTTCGATTTGGC
        130 ACGTTTTGAATCGTCTTCGATTTGGC

              *              *              *     
        621 AACCCTCAATGCTTTTCATTCCATTGTTTATGACCTAA
          1 AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAA

        659 TGATGCGCCA


Statistics
Matches: 458,  Mismatches: 39, Indels: 11
        0.90            0.08        0.02

Matches are distributed among these distances:
 153    4  0.01
 154  194  0.42
 155   90  0.20
 156  145  0.32
 157   25  0.05

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41


Consensus pattern (155 bp):   
AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGGCCCATTAGTGA
CGTTTTGAATCGTCTTCGATTTGGC

Found at i:791 original size:21 final size:21

Alignment explanation


    Indices: 765--898  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

        755 TGCTAGAAGT

                                  
        765 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
        786 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        807 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        828 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        849 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        870 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        891 TCATTGGA
          1 TCATTGGA

        899 ATTGCCTAAG


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  106  0.98

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.