Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014286.1 Corchorus olitorius cultivar O-4 contig14319, 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: 22499
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:3729 original size:11 final size:11
Alignment explanation
Indices: 3713--3738 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3703 CCTTTGCCTA
3713 AAAACTAGAAG
1 AAAACTAGAAG
3724 AAAACTAGAAG
1 AAAACTAGAAG
3735 AAAA
1 AAAA
3739 AAAATTATCT
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:5852 original size:14 final size:15
Alignment explanation
Indices: 5833--5862 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5823 CAATCAAAGC
5833 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
5847 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
5862 A
1 A
5863 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:6246 original size:21 final size:21
Alignment explanation
Indices: 6220--6278 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
6210 GGAATGATGA
6220 TGGCACGGGCATGGCCGGTAG
1 TGGCACGGGCATGGCCGGTAG
* ** *
6241 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATGGCCGGTAG
*
6262 TGGCACGGTGAATGGCC
1 TGGCACGG-GCATGGCC
6279 AGGCATGGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGGTAG
Found at i:8762 original size:30 final size:30
Alignment explanation
Indices: 8716--8792 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
8706 CTTTATATGA
*
8716 CACAAAAACTCCTTTTTTTTTAG--AAAAA-
1 CACAAAAACT-TTTTTTTTTTAGAAAAAAAT
*
8744 CGCAAAAACTTTTTTTTTTTAGAAAAAAAT
1 CACAAAAACTTTTTTTTTTTAGAAAAAAAT
8774 CACAAAAACTTTTTTTTTT
1 CACAAAAACTTTTTTTTTT
8793 CGACGCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 11 0.26
28 9 0.21
29 5 0.12
30 18 0.42
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (30 bp):
CACAAAAACTTTTTTTTTTTAGAAAAAAAT
Found at i:8806 original size:29 final size:28
Alignment explanation
Indices: 8715--8824 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 28
8705 TCTTTATATG
8715 ACACAAAAACTCCTTTTTTTTT--AGAAAA
1 ACACAAAAACT--TTTTTTTTTCGAGAAAA
* * *
8743 ACGCAAAAACTTTTTTTTTTTAGAAAAAA
1 ACACAAAAAC-TTTTTTTTTTCGAGAAAA
*
8772 ATCACAAAAACTTTTTTTTTTCGACGCAAA
1 A-CACAAAAACTTTTTTTTTTCGA-GAAAA
*
8802 ACACAAAACAAATTTTTTTTTTC
1 ACAC-AAA-AACTTTTTTTTTTC
8825 AAAAAGACGC
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
27 9 0.13
28 9 0.13
29 22 0.32
30 15 0.22
31 13 0.19
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (28 bp):
ACACAAAAACTTTTTTTTTTCGAGAAAA
Found at i:9191 original size:16 final size:15
Alignment explanation
Indices: 9153--9194 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
9143 ACAGAGATTG
*
9153 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
9168 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
9183 ACTAGAAAACAA
1 AC-AGAAAACAA
9195 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:9972 original size:11 final size:11
Alignment explanation
Indices: 9956--9981 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9946 CCTTTGCCTA
9956 AAAACTAGAAG
1 AAAACTAGAAG
9967 AAAACTAGAAG
1 AAAACTAGAAG
9978 AAAA
1 AAAA
9982 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:19509 original size:22 final size:23
Alignment explanation
Indices: 19481--19523 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
19471 TAGAAGGAGT
19481 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
19503 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
19524 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Done.