Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021382.1 Corchorus olitorius cultivar O-4 contig21415, 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: 45908
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1464 original size:24 final size:24
Alignment explanation
Indices: 1432--1481 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1422 AAATAAGTGG
1432 AAGAAGTAGATATCACTTTAGAAC
1 AAGAAGTAGATATCACTTTAGAAC
1456 AAGAAGTAGATATCACTTTAGAAC
1 AAGAAGTAGATATCACTTTAGAAC
1480 AA
1 AA
1482 TTCCTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (24 bp):
AAGAAGTAGATATCACTTTAGAAC
Found at i:10112 original size:14 final size:15
Alignment explanation
Indices: 10088--10116 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10078 GGTGCTGAAA
10088 GTGGAAGGTTTTGGG
1 GTGGAAGGTTTTGGG
10103 GTGG-AGGTTTTGGG
1 GTGGAAGGTTTTGGG
10117 TATGAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.00, G:0.55, T:0.34
Consensus pattern (15 bp):
GTGGAAGGTTTTGGG
Found at i:16560 original size:1 final size:1
Alignment explanation
Indices: 16554--16578 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16544 AATATAAAAG
16554 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
16579 AAGCGCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16856 original size:12 final size:12
Alignment explanation
Indices: 16841--16866 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16831 TTTTTCCCTC
16841 TTTTTTGTTTTT
1 TTTTTTGTTTTT
16853 TTTTTTGTTTTT
1 TTTTTTGTTTTT
16865 TT
1 TT
16867 ATCTATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:36239 original size:41 final size:41
Alignment explanation
Indices: 36194--36275 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
36184 ATCCAATAGT
*
36194 GTAAAATAGAAACATGATATCATCAACAAAAAAAATGGAGG
1 GTAAAATAGAAAAATGATATCATCAACAAAAAAAATGGAGG
* * *
36235 GTAAAATAGAAAAATGATATTATCAACCAAGAAAATGGAGG
1 GTAAAATAGAAAAATGATATCATCAACAAAAAAAATGGAGG
36276 AAGAGGCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (41 bp):
GTAAAATAGAAAAATGATATCATCAACAAAAAAAATGGAGG
Found at i:38879 original size:3 final size:3
Alignment explanation
Indices: 38871--38905 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38861 TTCTGGCCAA
38871 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38906 ATCATTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43800 original size:3 final size:3
Alignment explanation
Indices: 43792--43817 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43782 TTTTCTTGGC
43792 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
43818 ATTAACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Done.