Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023849.1 Corchorus olitorius cultivar O-4 contig23882, 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, 1000
Length: 2655
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:751 original size:7 final size:7
Alignment explanation
Indices: 745--1045 Score: 433
Period size: 7 Copynumber: 43.0 Consensus size: 7
735 GAGCCATGAA
*
745 TTTTGAA
1 TTTTGAG
752 TTTTGAG
1 TTTTGAG
759 TTTTGTA-
1 TTTTG-AG
766 TTTTGAG
1 TTTTGAG
*
773 TTTTGAA
1 TTTTGAG
780 TTTTGAG
1 TTTTGAG
*
787 TTTGGAG
1 TTTTGAG
794 TTTTGAG
1 TTTTGAG
801 TTTTGAG
1 TTTTGAG
808 TTTTGAG
1 TTTTGAG
815 TTTTGAG
1 TTTTGAG
822 TTTTGAG
1 TTTTGAG
829 TTTTGAG
1 TTTTGAG
836 TTTTGAG
1 TTTTGAG
843 TTTTGAG
1 TTTTGAG
850 TTTTGAG
1 TTTTGAG
857 TTTTGAG
1 TTTTGAG
864 TTTTGAG
1 TTTTGAG
871 TTTTGAG
1 TTTTGAG
878 TTTTGAG
1 TTTTGAG
885 TTTTGAG
1 TTTTGAG
892 TTTTGAG
1 TTTTGAG
899 TTTTGAG
1 TTTTGAG
906 TTTTGAG
1 TTTTGAG
913 TTTTGAG
1 TTTTGAG
920 TTTTGAG
1 TTTTGAG
927 TTTTGAG
1 TTTTGAG
934 TTTTGAG
1 TTTTGAG
*
941 TTTTGAA
1 TTTTGAG
*
948 TTTTGAA
1 TTTTGAG
*
955 TTTTGAA
1 TTTTGAG
*
962 TTTTGAA
1 TTTTGAG
*
969 TTTTGAA
1 TTTTGAG
*
976 TTTTGAA
1 TTTTGAG
*
983 TTTTGAA
1 TTTTGAG
*
990 TTTTGAA
1 TTTTGAG
*
997 TTTTGAA
1 TTTTGAG
*
1004 TTTTGAA
1 TTTTGAG
*
1011 TTTTGAA
1 TTTTGAG
*
1018 TTTTGAA
1 TTTTGAG
*
1025 TTTTGAA
1 TTTTGAG
*
1032 TTTTGAA
1 TTTTGAG
1039 TTTTGAG
1 TTTTGAG
1046 CAATGAAATG
Statistics
Matches: 285, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
6 1 0.00
7 283 0.99
8 1 0.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (7 bp):
TTTTGAG
Found at i:1222 original size:33 final size:33
Alignment explanation
Indices: 1180--1257 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
1170 AGAAACTGTG
* * * *
1180 GATTCTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1213 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
1246 AATTTTGAACTT
1 GATTTTGAACTT
1258 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:1419 original size:54 final size:54
Alignment explanation
Indices: 1328--1620 Score: 387
Period size: 54 Copynumber: 5.4 Consensus size: 54
1318 ATGACCGCAT
* *
1328 TGGGTCAGT-TTAGAGATCAACTCT-GATCATC-GTAAACTTCT-TGGAATGACCACAC
1 TGGGTCA-TCTTA-AGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAAGACCACAC
* * * * *
1383 TGGATCAACTTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACAC
1 TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
* * * *
1437 AGGGTCATCTGAAGATCAACTTAGATCTCAGAAAACTTCTATGAAAGATCACAC
1 TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
* *
1491 TGGGTCATCTTAAGATTAACATAGATCTCTGAAAACTTCTATGAAAGACCACAC
1 TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
1545 TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
1 TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
*
1599 TGGGTCAACTTAAGATCAACTT
1 TGGGTCATCTTAAGATCAACTT
1621 TCTAGAGAGA
Statistics
Matches: 209, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.01
54 197 0.94
55 10 0.05
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (54 bp):
TGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
Found at i:1672 original size:20 final size:18
Alignment explanation
Indices: 1652--1693 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1642 CATTTTAAAC
*
1652 ACAAAACATGAATTTTGA
1 ACAAAAAATGAATTTTGA
* *
1670 ACAAGAAATGGATTTTGA
1 ACAAAAAATGAATTTTGA
1688 ACAAAA
1 ACAAAA
1694 TTTTGATAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (18 bp):
ACAAAAAATGAATTTTGA
Found at i:1721 original size:37 final size:37
Alignment explanation
Indices: 1679--1882 Score: 182
Period size: 37 Copynumber: 5.6 Consensus size: 37
1669 AACAAGAAAT
* *
1679 GGATTTTGAACAAAATTTTGATAAGAAACCTAAACTG
1 GGATTTTGAACAAGATTTTGATAAGAAACCTAAACAG
* *
1716 GGATTTTG-A-AGGA-TTTAATAAGAAACCTAAACAG
1 GGATTTTGAACAAGATTTTGATAAGAAACCTAAACAG
* * *
1750 GAATTTTGAACAAGATTTTGATGAGACACCTAAACAG
1 GGATTTTGAACAAGATTTTGATAAGAAACCTAAACAG
* * ** * * *
1787 GGATCTTGAACCAGATTTCAATGAGACACCTAAACAT
1 GGATTTTGAACAAGATTTTGATAAGAAACCTAAACAG
** * * *
1824 GGACCTTAAAAAAGGA-TTTGATAAGATACCTAAACAG
1 GGATTTTGAACAA-GATTTTGATAAGAAACCTAAACAG
* *
1861 GAATCTTGAACAAGATTTTGAT
1 GGATTTTGAACAAGATTTTGAT
1883 GAAACTGAAT
Statistics
Matches: 134, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
34 26 0.19
35 3 0.02
36 6 0.04
37 97 0.72
38 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (37 bp):
GGATTTTGAACAAGATTTTGATAAGAAACCTAAACAG
Done.