Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007461.1 Corchorus olitorius cultivar O-4 contig07486, 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: 2404
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:512 original size:27 final size:29
Alignment explanation
Indices: 482--557 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
472 TATGAACTTA
* *
482 AAATGGCCAAAATGTCCCTG-A-ATGTGC
1 AAATGACCAAAATGCCCCTGTAGATGTGC
** *
509 AAATGATTAAAATGCCCCTGTAGATGTGT
1 AAATGACCAAAATGCCCCTGTAGATGTGC
538 AAATGACCAAAATGCCCCTG
1 AAATGACCAAAATGCCCCTG
558 GATGCCCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 16 0.40
28 1 0.03
29 23 0.57
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCTGTAGATGTGC
Found at i:954 original size:35 final size:34
Alignment explanation
Indices: 913--1252 Score: 434
Period size: 35 Copynumber: 9.7 Consensus size: 34
903 TGAGTCCATA
913 TTGAAGATGCTACACCGAGTCATCTGAATTATTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTA-TCT
*
948 TTGAAGATGCTACACCGAGTCATCTGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATT-ATCT
*
983 TTGAAGATGCTACACCGAGTCATCT-AGATTCGTCT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATT-ATCT
*
1018 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATT-ATCT
* *
1053 TTGAAGATGCTACATCGAGTCATCTGAATATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TATCT
*
1088 TTGAAGATGCTACACCGAGTCATCTGGATTTAAT-T
1 TTGAAGATGCTACACCGAGTCATCT-GAATT-ATCT
* *
1123 TCGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATT-ATCT
* * *
1158 TTGGAGATGCTATACCGAGTCATCTGAGTTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATT--ATCT
* *
1193 TTGAAGATGCTACACCGAGTCATCTGAGTATAACT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TATCT
1228 TTGAAGATGCTACACCGAGTCATCT
1 TTGAAGATGCTACACCGAGTCATCT
1253 TTGGAAAATA
Statistics
Matches: 273, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
34 7 0.03
35 257 0.94
36 9 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (34 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTATCT
Found at i:1095 original size:105 final size:102
Alignment explanation
Indices: 913--1252 Score: 486
Period size: 105 Copynumber: 3.2 Consensus size: 102
903 TGAGTCCATA
*
913 TTGAAGATGCTACACCGAGTCATCTGAATT-ATTCTTTGAAGATGCTACACCGAGTCATCTGAGT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCA-ACTTTGAAGATGCTACACCGAGTCATCTGAGT
*
977 TCATCTTTGAAGATGCTACACCGAGTCATCTAGATTCGTCT
65 TCAACTTTGAAGATGCTACACCGAGTCATCT-GATT--TCT
* *
1018 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACATCGAGTCATCTGAATA
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAGT-
*
1083 T-AACTTTGAAGATGCTACACCGAGTCATCTGGATTTAAT
65 TCAACTTTGAAGATGCTACACCGAGTCATCT-GATTT-CT
* *
1122 TTCGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGGAGATGCTATACCGAGTCATCTGAGT
1 TT-GAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAGT
* *
1187 TCAATTTTGAAGATGCTACACCGAGTCATCTGAGTATAACT
65 TCAACTTTGAAGATGCTACACCGAGTCATCTGA-T-T-TCT
1228 TTGAAGATGCTACACCGAGTCATCT
1 TTGAAGATGCTACACCGAGTCATCT
1253 TTGGAAAATA
Statistics
Matches: 214, Mismatches: 13, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
103 1 0.00
104 6 0.03
105 201 0.94
106 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (102 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAGTT
CAACTTTGAAGATGCTACACCGAGTCATCTGATTTCT
Found at i:1819 original size:50 final size:50
Alignment explanation
Indices: 1756--1902 Score: 204
Period size: 50 Copynumber: 2.9 Consensus size: 50
1746 TAAATGCCCT
* * * * *
1756 TTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTACC
1 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTTACC
* * **
1806 TTGAAAAGTGAATTTTGATCTTGAACTCATAAATGGAAAGAAATTTTATT
1 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTTACC
*
1856 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGGAATCTT
1 TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTT
1903 GTTATAAAAC
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (50 bp):
TTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTTACC
Done.