Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005370.1 Corchorus capsularis cultivar CVL-1 contig05388, 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, 991

Length: 1652
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:917 original size:31 final size:31

Alignment explanation


    Indices: 882--941  Score: 86
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        872 ATGTTTTCGG

                            **              
        882 ATTGTACCCTTATT-TTTAAAACATATTTCCA
          1 ATTGTACCCTT-TTCTAAAAAACATATTTCCA

                                         
        913 ATTGTACCCTTTTCTAAAAAACATATTTC
          1 ATTGTACCCTTTTCTAAAAAACATATTTC

        942 TAAATTGCCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  30    2  0.08
  31   24  0.92

ACGTcount: A:0.33, C:0.20, G:0.03, T:0.43


Consensus pattern (31 bp):   
ATTGTACCCTTTTCTAAAAAACATATTTCCA

Found at i:1242 original size:22 final size:22

Alignment explanation


    Indices: 1217--1339  Score: 90
    Period size: 22  Copynumber: 5.6  Consensus size: 22

       1207 TGGTCCAATT

                 *        *       
       1217 TCAAATTTTCAAAGTGAGGTTA
          1 TCAAAATTTCAAAGAGAGGTTA

                    *       *       
       1239 TCAAAATTACATAATGTGA--TTA
          1 TCAAAATTTCA-AA-GAGAGGTTA

                       *    *   * 
       1261 TCAAAATTTCATAGAGGGGTCA
          1 TCAAAATTTCAAAGAGAGGTTA

            *        * *          
       1283 ACAAAATTTGATAGAGAGGTTA
          1 TCAAAATTTCAAAGAGAGGTTA

                     *             
       1305 TCAAAATTTGATAA-AGAGGTTA
          1 TCAAAATTTCA-AAGAGAGGTTA

                 *       
       1327 TCAAATTTTCAAA
          1 TCAAAATTTCAAA

       1340 ATATTATTAC


Statistics
Matches: 81,  Mismatches: 15, Indels: 11
        0.76            0.14        0.10

Matches are distributed among these distances:
  20    2  0.02
  21    3  0.04
  22   69  0.85
  23    3  0.04
  24    4  0.05

ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33


Consensus pattern (22 bp):   
TCAAAATTTCAAAGAGAGGTTA

Found at i:1334 original size:21 final size:22

Alignment explanation


    Indices: 1232--1331  Score: 101
    Period size: 22  Copynumber: 4.5  Consensus size: 22

       1222 TTTTCAAAGT

                           **    *
       1232 GAGGTTATCAAAATTACATAAT
          1 GAGGTTATCAAAATTTGATAAA

             * *            *   * 
       1254 GTGATTATCAAAATTTCATAGA
          1 GAGGTTATCAAAATTTGATAAA

             *   * *            * 
       1276 GGGGTCAACAAAATTTGATAGA
          1 GAGGTTATCAAAATTTGATAAA

                                  
       1298 GAGGTTATCAAAATTTGATAAA
          1 GAGGTTATCAAAATTTGATAAA

                        
       1320 GAGGTTATCAAA
          1 GAGGTTATCAAA

       1332 TTTTCAAAAT


Statistics
Matches: 64,  Mismatches: 14, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  22   64  1.00

ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30


Consensus pattern (22 bp):   
GAGGTTATCAAAATTTGATAAA

Found at i:1526 original size:22 final size:21

Alignment explanation


    Indices: 1501--1598  Score: 60
    Period size: 22  Copynumber: 4.6  Consensus size: 21

       1491 AATAGTGTAA

                                  
       1501 TTATCATAATTTCATAGGAATG
          1 TTATCATAATTTCATAGGAA-G

                   *         *     
       1523 TTATCAAAAATTTCATAAGAACG
          1 TTATC-ATAATTTCATAGGAA-G

             *          *     *  *
       1546 TCATCA-AA---AATAGCAAAA
          1 TTATCATAATTTCATAG-GAAG

                        *        
       1564 TTATCATAATTTAATAGGAAG
          1 TTATCATAATTTCATAGGAAG

                          
       1585 ATTATCATAATTTC
          1 -TTATCATAATTTC

       1599 GTATGAGATT


Statistics
Matches: 57,  Mismatches: 12, Indels: 14
        0.69            0.14        0.17

Matches are distributed among these distances:
  18    8  0.14
  19    4  0.07
  21    4  0.07
  22   23  0.40
  23   18  0.32

ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35


Consensus pattern (21 bp):   
TTATCATAATTTCATAGGAAG

Found at i:1533 original size:63 final size:63

Alignment explanation


    Indices: 1462--1591  Score: 183
    Period size: 63  Copynumber: 2.1  Consensus size: 63

       1452 TCAGGGAGGA

                              *                ***              *           
       1462 TATC-AAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCATAATTTCATAGGAATG-T
          1 TATCAAAAATTTCATAAGAACGTCATAAAAAATAGCAAAATTATCATAATTTAATAGGAA-GAT

                                      *                                    
       1524 TATCAAAAATTTCATAAGAACGTCATCAAAAATAGCAAAATTATCATAATTTAATAGGAAGAT
          1 TATCAAAAATTTCATAAGAACGTCATAAAAAATAGCAAAATTATCATAATTTAATAGGAAGAT

                 
       1587 TATCA
          1 TATCA

       1592 TAATTTCGTA


Statistics
Matches: 60,  Mismatches: 6, Indels: 3
        0.87            0.09        0.04

Matches are distributed among these distances:
  62    5  0.08
  63   55  0.92

ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32


Consensus pattern (63 bp):   
TATCAAAAATTTCATAAGAACGTCATAAAAAATAGCAAAATTATCATAATTTAATAGGAAGAT

Found at i:1538 original size:23 final size:23

Alignment explanation


    Indices: 1508--1556  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1498 TAATTATCAT

                     *   *  *      
       1508 AATTTCATAGGAATGTTATCAAA
          1 AATTTCATAAGAACGTCATCAAA

                                   
       1531 AATTTCATAAGAACGTCATCAAA
          1 AATTTCATAAGAACGTCATCAAA

               
       1554 AAT
          1 AAT

       1557 AGCAAAATTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31


Consensus pattern (23 bp):   
AATTTCATAAGAACGTCATCAAA
Done.