Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006649.1 Corchorus capsularis cultivar CVL-1 contig06670, 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, 733

Length: 1222
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23


Found at i:991 original size:155 final size:153

Alignment explanation


    Indices: 3--1222  Score: 1745
    Period size: 155  Copynumber: 7.8  Consensus size: 153

          1 AA

                  *                       *                                  
          3 AAATAAAAAGTGTTCTGAATGAGACTAAAACCTTCACAATGGACTAATCTCATACAAAATAATTA
          1 AAATAACAAGTGTTCTGAATG-G-CTAAAAACTTCACAATGGACTAATCTCAT-CAAAATAATTA

                  **                       *                           *     
         68 TAGTTAAACCAGAAACAAT-GGAAAGAAAAGTTTTGTGGTTTGCCAAATCGAAGACGATCCAAAA
         63 TAGTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAA

                                        
        132 CAGACACTAATGGGCCCCGAAA-GCCCG
        127 CAG-CACTAATGGGCCCCGAAAGGCCCG

                                                                             
        159 AAATAA-AAGTGTTCTGAATGAGGCGTAAAAAACTTCACAATGGACTAATCTCATCAAAATAATT
          1 AAATAACAAGTGTTCTGAAT--GGC-T-AAAAACTTCACAATGGACTAATCTCATCAAAATAATT

                                                             *               
        223 ATAGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTTAGTGGTTTTGGGCAAAATCGAAGACGATT
         62 ATAGTTAGGCCAGAAACAATAGGAAGAAAAGC-TTT-GTGG-TTT--GCCAAATCGAAGACGATT

                                           *
        288 CAAAACAGCACTAATGGGCCCCGAAAGGCCCA
        122 CAAAACAGCACTAATGGGCCCCGAAAGGCCCG

                                                                             
        320 AAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCTAAAATAATTAT
          1 AAATAACAAGTGTTCTGAATG-GCTAAAAACTTCACAATGGACTAATCTCATC-AAAATAATTAT

                                                       *                     
        385 AGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGGCAAAATCGAAAGACGATTCAAAA
         64 AGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTT-GCCAAATCG-AAGACGATTCAAAA

                                      *
        450 CAGCACTAATGGGCCCCGAAAGGCCCA
        127 CAGCACTAATGGGCCCCGAAAGGCCCG

                                                                *      *     
        477 AAATAACAAGTGTTCTGAATGAGCCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTAT
          1 AAATAACAAGTGTTCTGAATG-G-CTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTAT

              *    *     *      * *                              *    *     *
        542 AGCTAGGTC-GTATACAAATTGAAAGAAAAAGACTTTGTTGG-TTG-CAAATTAGAAGCCGATTT
         64 AGTTAGGCCAG-AAAC-AATAGGAAG-AAAAG-CTTTG-TGGTTTGCCAAA-TCGAAGACGATTC

              *                 *            
        604 AACACAGCACTAATGGGCCGTCGAAAGGACCCG
        123 AAAACAGCACTAATGGGCC-CCGAAAGG-CCCG

                                                                             
        637 AAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA
          1 AAATAACAAGTGTTCTGAATG-GCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA

                                     *               *                       
        702 GTTAGGCCAGAAACAATA-GAATGATAAGCTTTGTGGTTTGGCAAATCGAAGACGATTCAAAACA
         65 GTTAGGCCAGAAACAATAGGAA-GAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACA

                                     
        766 GCACTAATGGGCCCCGAAAGGCCCG
        129 GCACTAATGGGCCCCGAAAGGCCCG

                                  *                        *                 
        791 AAATAACAAGTGTTCTGAATGACCTAAAAACTTCACAATGGACTAATATCATCAAAATAATTATA
          1 AAATAACAAGTGTTCTGAATG-GCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA

                     *               *                                       
        856 GTTAGGCCATAAACAA-AGGAAAGATAAGCTTTGTGGTTTGCCAAATCGAAAGACGATTCAAAAC
         65 GTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTGTGGTTTGCCAAATCG-AAGACGATTCAAAAC

                                      
        920 AGCACTAATGGGCCCCGAAAGGCCCG
        128 AGCACTAATGGGCCCCGAAAGGCCCG

                            *     *                                          
        946 AAATAACAAGTGTTCTAAACTGTCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA
          1 AAATAACAAGTGTTCTGAA-TGGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA

                                                     *                       
       1011 GTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTTGGCAAATCGAAGACGATTCAAAACA
         65 GTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGG-TTTGCCAAATCGAAGACGATTCAAAACA

                                     
       1076 GCACTAATGGGCCCCGAAAGGCCCG
        129 GCACTAATGGGCCCCGAAAGGCCCG

                               *                                             
       1101 AAATAACAAGTGTTCTGAACGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA
          1 AAATAACAAGTGTTCTGAATG-GCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATA

                                 *                  *        *       
       1166 GTTAGGCCAGAAACAATAGGAGGAAAAGCTTTGTGGTTTGGCAAATCGAGGACGATT
         65 GTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATT


Statistics
Matches: 980,  Mismatches: 49, Indels: 72
        0.89            0.04        0.07

Matches are distributed among these distances:
 153    1  0.00
 154  129  0.13
 155  292  0.30
 156  107  0.11
 157  129  0.13
 158   77  0.08
 159   98  0.10
 160   95  0.10
 161   39  0.04
 162   13  0.01

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23


Consensus pattern (153 bp):   
AAATAACAAGTGTTCTGAATGGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAG
TTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
ACTAATGGGCCCCGAAAGGCCCG

Done.