Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012139.1 Corchorus olitorius cultivar O-4 contig12172, 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: 29196
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2957 original size:14 final size:15
Alignment explanation
Indices: 2938--2967 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2928 CAATTAAAGC
2938 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
2952 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
2967 A
1 A
2968 TTAAAGAGAT
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:3349 original size:21 final size:21
Alignment explanation
Indices: 3325--3374 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3315 GGAATGGCGA
*
3325 TGGCACGGGCATGGA-CGGTGG
1 TGGCACGGAC-TGGACCGGTGG
*
3346 TGGCACGGACTTGACCGGTGG
1 TGGCACGGACTGGACCGGTGG
3367 TGGCACGG
1 TGGCACGG
3375 TGAATGGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGACTGGACCGGTGG
Found at i:6970 original size:16 final size:15
Alignment explanation
Indices: 6932--6973 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
6922 ACAGAGGTTG
6932 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
6947 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
6962 ACTAGAAAACAA
1 AC-AGAAAACAA
6974 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:14100 original size:17 final size:17
Alignment explanation
Indices: 14080--14121 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
14070 TCCCTCGTCT
14080 CTCCTCAAAGCTTCTTC
1 CTCCTCAAAGCTTCTTC
*
14097 CTCCCTC-GAGCTTCTTC
1 CT-CCTCAAAGCTTCTTC
*
14114 TTCCTCAA
1 CTCCTCAA
14122 CCCGCACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (17 bp):
CTCCTCAAAGCTTCTTC
Found at i:18250 original size:54 final size:50
Alignment explanation
Indices: 18164--18279 Score: 169
Period size: 52 Copynumber: 2.2 Consensus size: 50
18154 GGAACTTTCC
*
18164 CTAAATTGAAAACTTAAAAAATTGATGGGAACTTTCCCAATTTGAAAAGAG
1 CTAAATTGAAAACTTAAAAAATTGATGAGAACTTTCCC-ATTTGAAAAGAG
* *
18215 CTTAAATTGAATACTTTGAAAAATTTGATGAGAACTTTCCCATTTGAAAAGAG
1 C-TAAATTGAAAAC-TT-AAAAAATTGATGAGAACTTTCCCATTTGAAAAGAG
18268 CTAAATTGAAAA
1 CTAAATTGAAAA
18280 AAACTTGGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
51 1 0.02
52 21 0.36
53 15 0.26
54 21 0.36
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (50 bp):
CTAAATTGAAAACTTAAAAAATTGATGAGAACTTTCCCATTTGAAAAGAG
Found at i:18264 original size:53 final size:51
Alignment explanation
Indices: 18164--18310 Score: 171
Period size: 54 Copynumber: 2.9 Consensus size: 51
18154 GGAACTTTCC
*
18164 CTAAATTGAAAACTTAAAAAATTGATGGGAACTTTCCCAATTTGAAAAGAG
1 CTAAATTGAAAACTTAAAAAATTGATGAGAACTTTCCCAATTTGAAAAGAG
* *
18215 CTTAAATTGAATACTTTGAAAAATTTGATGAGAACTTTCCC-ATTTGAAAAGAG
1 C-TAAATTGAAAAC-TT-AAAAAATTGATGAGAACTTTCCCAATTTGAAAAGAG
* * *
18268 CTAAATTG--AA---AAAAACTTGGTGGGAACTTTCCCAATTTGAAAA
1 CTAAATTGAAAACTTAAAAAATTGATGAGAACTTTCCCAATTTGAAAA
18311 CTATGAAGGA
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
45 20 0.24
46 9 0.11
50 1 0.01
51 1 0.01
52 18 0.21
53 15 0.18
54 21 0.25
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (51 bp):
CTAAATTGAAAACTTAAAAAATTGATGAGAACTTTCCCAATTTGAAAAGAG
Done.