Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1357
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: 15732
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:61 original size:20 final size:20
Alignment explanation
Indices: 38--110 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
28 ACAATTCAAA
38 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
58 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
79 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
99 GTATCGATACAT
1 GTATCGATACAT
111 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:81 original size:21 final size:21
Alignment explanation
Indices: 55--131 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
45 TACATGTTGC
55 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
76 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
96 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
116 GGATGTATCGATACAT
1 -AATGTATCGATACAT
132 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:89 original size:41 final size:41
Alignment explanation
Indices: 38--131 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
28 ACAATTCAAA
38 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
79 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
120 GTATCGATACAT
1 GTATCGATACAT
132 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:188 original size:13 final size:13
Alignment explanation
Indices: 170--195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160 TACAGCAAGT
170 ATGTATCGATACA
1 ATGTATCGATACA
183 ATGTATCGATACA
1 ATGTATCGATACA
196 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4275 original size:15 final size:15
Alignment explanation
Indices: 4255--4285 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4245 TAAAAATGTC
*
4255 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4270 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4285 C
1 C
4286 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:6382 original size:13 final size:13
Alignment explanation
Indices: 6364--6402 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
6354 ACATTTTTCC
6364 TTGTATCGATACA
1 TTGTATCGATACA
6377 TTGTATCGATACA
1 TTGTATCGATACA
*
6390 CTGTATCGATACA
1 TTGTATCGATACA
6403 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8848 original size:20 final size:20
Alignment explanation
Indices: 8825--8897 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
8815 ACAATTCAAA
8825 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
8845 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
8866 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
8886 GTATCGATACAT
1 GTATCGATACAT
8898 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:8868 original size:21 final size:21
Alignment explanation
Indices: 8842--8918 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
8832 TACATGTTGC
8842 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
8863 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
8883 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
8903 GGATGTATCGATACAT
1 -AATGTATCGATACAT
8919 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:8876 original size:41 final size:41
Alignment explanation
Indices: 8825--8918 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
8815 ACAATTCAAA
8825 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
8866 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
8907 GTATCGATACAT
1 GTATCGATACAT
8919 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:8975 original size:13 final size:13
Alignment explanation
Indices: 8957--8982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8947 TACAGCAAGT
8957 ATGTATCGATACA
1 ATGTATCGATACA
8970 ATGTATCGATACA
1 ATGTATCGATACA
8983 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10162 original size:13 final size:13
Alignment explanation
Indices: 10144--10169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10134 TACAGCAAGT
10144 ATGTATCGATACA
1 ATGTATCGATACA
10157 ATGTATCGATACA
1 ATGTATCGATACA
10170 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:12412 original size:21 final size:20
Alignment explanation
Indices: 12386--12429 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12376 TTGCAAGTTG
* *
12386 AAATAAAGAAGTTGGCTATGA
1 AAATAAAG-AGTTAGCTAAGA
*
12407 AAATAATGAGTTAGCTAAGA
1 AAATAAAGAGTTAGCTAAGA
12427 AAA
1 AAA
12430 ATGAAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (20 bp):
AAATAAAGAGTTAGCTAAGA
Found at i:14251 original size:15 final size:15
Alignment explanation
Indices: 14231--14269 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
14221 TAAAATGGTC
*
14231 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
14246 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
14261 CCAAATGAA
1 CAAAATGAA
14270 TTGATGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.