Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009056.1 Corchorus olitorius cultivar O-4 contig09084, 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, 996

Length: 1661
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34


Found at i:1189 original size:322 final size:323

Alignment explanation


    Indices: 498--1293  Score: 965
    Period size: 322  Copynumber: 2.4  Consensus size: 323

        488 TTCTTCTTTT

                          *                      *                           
        498 TTTTTTTCCGAATTTATTTTTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATCCT
          1 TTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT

                 **          *         *                    *                
        563 TAAATATAATGTGGCTGAGAGCCTGAGATTGGTTAT-ATGAATATAGAAATTTCAAGGAGTCTTT
         66 T-AATCCAATGTGG-T-TGA--C--A-TTTGGTT-TGATGAATATAGATATTTCAAGGAGTCTTT

                                                        *             *    * 
        627 CTGCCAAAAATCATGCAAAACTGAACCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAATCCATTA
        122 C-GCCAAAAATCATGCAAAACTGAACCGGGG-CCCCGAAACGCGGTTTTAGCCCAAAAACCATGA

                                                   ***        *        *     
        692 TGGTTAGTACACGATTTTCGACTAAAAACTTACCCGAATTTTTTTTTTCTGAATTTTTTCCCACA
        185 TGGTTAGTACACGATTTTCGACTAAAAACTTACCCGAATAAGTTTTTTCTCAATTTTTTACCACA

                                                    *  *            *     *  
        757 ATACTCAGAAAAATATATAATTCAACACCAAAAATATTGATGGTCTTTTCACGCTTTTAATATCA
        250 ATACTCAGAAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTTCACGCTTCTAATAACA

                     
        822 TTTTTCCAA
        315 TTTTTCCAA

                             * *                             *       *       
        831 TTTTTTTCCGAATTAATATCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAATAAATCCT
          1 TTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT

                                           *                                *
        896 TATATCCAATGTGGTTGACATTTGGTTTGATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAT
         66 TA-ATCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAA

                        *   **       *                           *           
        961 AATCATGCAAAATTGAGTCGGGG-CTCGAGAACGCGGTTTTAG-CCAAAAACCGTGATGGTTAGT
        129 AATCATGCAAAACTGAACCGGGGCCCCGA-AACGCGGTTTTAGCCCAAAAACCATGATGGTTAGT

                        *           * *                                   *  
       1024 ACACGA-TTTCGGCTAAAAACTTATCGGAA-AAGTTTTTTCTCAATTTTTTACCACAATACTTAG
        193 ACACGATTTTCGACTAAAAACTTACCCGAATAAGTTTTTTCTCAATTTTTTACCACAATACTCAG

                               *                                           * 
       1087 AAAAAATATATAATTCAACGCCAAAAATATTGACGGGCTTTTCACGCTTCTAATAACATTTTTTC
        258 -AAAAATATATAATTCAACACCAAAAATATTGACGGGCTTTTCACGCTTCTAATAACATTTTTCC

              
       1152 -A
        322 AA

                                         *                                * *
       1153 TTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACG
          1 TTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT

                 *  *    *  **    *   *         *               *      *     
       1218 TAATCGAACGTGGCTGGGATTTTGTTCGATGAATATTGATATTTCAAGGAGTATTTACGTCAAAA
         66 TAATCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAA

                       
       1283 ATCATGCAAAA
        130 ATCATGCAAAA

       1294 ACAAAAAAAA


Statistics
Matches: 402,  Mismatches: 56, Indels: 22
        0.84            0.12        0.05

Matches are distributed among these distances:
 321   61  0.15
 322   89  0.22
 323   78  0.19
 324   28  0.07
 325   13  0.03
 326   57  0.14
 327    2  0.00
 329    1  0.00
 331    2  0.00
 332    2  0.00
 333   69  0.17

ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Consensus pattern (323 bp):   
TTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
TAATCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTCGCCAAAAA
TCATGCAAAACTGAACCGGGGCCCCGAAACGCGGTTTTAGCCCAAAAACCATGATGGTTAGTACA
CGATTTTCGACTAAAAACTTACCCGAATAAGTTTTTTCTCAATTTTTTACCACAATACTCAGAAA
AATATATAATTCAACACCAAAAATATTGACGGGCTTTTCACGCTTCTAATAACATTTTTCCAA

Found at i:1536 original size:239 final size:233

Alignment explanation


    Indices: 1146--1661  Score: 727
    Period size: 239  Copynumber: 2.2  Consensus size: 233

       1136 CTAATAACAT

                                        *  *      *                          
       1146 TTTTTC-ATTTTTTTCCGAAT-TAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAA
          1 TTTTTCTATTTTTTTCCGAATCTAA-TTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAA

                                *       *  *   *         *                   
       1209 ACAAATACGTAATCGAACGTGGCTGGGATTTTGTTCGATGAATATTGATATTTCAAGGAGTATTT
         65 ACAAATACGTAATCGAACGTAGCTGGGAATTGGTTAGATGAATATAGATATTTCAAGGAGTATTT

               *                            *                                
       1274 ACGTCAAAAATCATGCAAAAACAAAAAAAATATATTTTCGGCAAAAAATACACAATTCAAAGC-A
        130 ACGCCAAAAATCATGCAAAAACAAAAAAAATACATTTTCGGCAAAAAATACACAATTCAAAGCAA

                  *                                
       1338 AAAAAATTTTTG-AAATATTTTTCTCGCTTTAAATATCA
        195 AAAAAAATTTTGAAAATATTTTTCTCGCTTTAAATATCA

                                                         *                   
       1376 TTTTTCTATTTTTTTCCGAATCTAATTCTATTTAAATCGAAACAATATTCAGATGCTCGTAAAAA
          1 TTTTTCTATTTTTTTCCGAATCTAATTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA

                 * *      *                                               *  
       1441 CAAATCCTTAAATCTAACGTAGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCATGG
         66 CAAATACGT-AATCGAACGTAGCT--G-G---GA-ATTGGTTAGATGAATATAGATATTTCAAGG

               *                                                             
       1506 AGTCTTT-CTGCCAAAAATCATGCAAAAACAAAAAAAATACATTTTCGGCAAAAAATACACAATT
        123 AGTATTTAC-GCCAAAAATCATGCAAAAACAAAAAAAATACATTTTCGGCAAAAAATACACAATT

                                                           
       1570 CAAAGCAAAAAAAAATTTTGAAAATATTTTTCTCGCTTTAAATATCA
        187 CAAAGCAAAAAAAAATTTTGAAAATATTTTTCTCGCTTTAAATATCA

                                                    *    
       1617 TTTTTCTATTTTTTTTCCCGAATCTAATTCTATTTAAATCAAAAC
          1 TTTTTCTA-TTTTTTT-CCGAATCTAATTCTATTTAAATCGAAAC


Statistics
Matches: 253,  Mismatches: 18, Indels: 17
        0.88            0.06        0.06

Matches are distributed among these distances:
 230    6  0.02
 231   57  0.23
 232   15  0.06
 234    1  0.00
 235    1  0.00
 238    3  0.01
 239   90  0.36
 240   12  0.05
 241   34  0.13
 242    7  0.03
 243   27  0.11

ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35


Consensus pattern (233 bp):   
TTTTTCTATTTTTTTCCGAATCTAATTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATACGTAATCGAACGTAGCTGGGAATTGGTTAGATGAATATAGATATTTCAAGGAGTATTTA
CGCCAAAAATCATGCAAAAACAAAAAAAATACATTTTCGGCAAAAAATACACAATTCAAAGCAAA
AAAAAATTTTGAAAATATTTTTCTCGCTTTAAATATCA
Done.