Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011865.1 Corchorus olitorius cultivar O-4 contig11898, 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: 6875
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1128 original size:13 final size:13
Alignment explanation
Indices: 1107--1140 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1097 CTTTGAATTG
1107 AAAAA-AAAAAGA
1 AAAAAGAAAAAGA
1119 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
*
1132 AAGAAGAAA
1 AAAAAGAAA
1141 GTCAAGCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:1134 original size:17 final size:17
Alignment explanation
Indices: 1108--1141 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1098 TTTGAATTGA
1108 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
* *
1125 AAAAAGAAAGAAGAAAG
1 AAAAAAAAAGAAAAAAG
1142 TCAAGCTCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:1306 original size:10 final size:10
Alignment explanation
Indices: 1271--1307 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1261 TTTTACATAC
*
1271 ATATATGCAT
1 ATATATGTAT
1281 ATATA--TAT
1 ATATATGTAT
1289 ATATATGTAT
1 ATATATGTAT
1299 ATATATGTA
1 ATATATGTA
1308 CATGTGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 7 0.29
10 17 0.71
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (10 bp):
ATATATGTAT
Found at i:1867 original size:11 final size:10
Alignment explanation
Indices: 1846--1880 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
1836 CCACAGTAGG
1846 AAATACAAAA
1 AAATACAAAA
1856 AAATACCAAAA
1 AAATA-CAAAA
1867 AAAGTACAAAA
1 AAA-TACAAAA
1878 AAA
1 AAA
1881 AGGAGAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 16 0.70
12 2 0.09
ACGTcount: A:0.77, C:0.11, G:0.03, T:0.09
Consensus pattern (10 bp):
AAATACAAAA
Found at i:4603 original size:16 final size:15
Alignment explanation
Indices: 4565--4606 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
4555 ACAGAGATTG
*
4565 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
4580 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4595 ACTAGAAAACAA
1 AC-AGAAAACAA
4607 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:5372 original size:11 final size:11
Alignment explanation
Indices: 5356--5381 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5346 CCTTTGCCTA
5356 AAAACTAGAAG
1 AAAACTAGAAG
5367 AAAACTAGAAG
1 AAAACTAGAAG
5378 AAAA
1 AAAA
5382 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:5862 original size:14 final size:14
Alignment explanation
Indices: 5843--5870 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5833 AATTCCAATT
5843 AATATCTTATATGG
1 AATATCTTATATGG
5857 AATATCTTATATGG
1 AATATCTTATATGG
5871 GCTGAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
AATATCTTATATGG
Done.