Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5896.1
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: 16332
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.29
Warning! 1441 characters in sequence are not A, C, G, or T
Found at i:1694 original size:13 final size:13
Alignment explanation
Indices: 1676--1708 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1666 AGCTGAAAAC
1676 TAATTAAATAATT
1 TAATTAAATAATT
1689 TAATTAAATAATT
1 TAATTAAATAATT
*
1702 TATTTAA
1 TAATTAA
1709 TTCCAGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTAAATAATT
Found at i:1778 original size:20 final size:20
Alignment explanation
Indices: 1753--1794 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1743 TGGAAATGAA
1753 CTCGTTGAGCTAGAATTGAG
1 CTCGTTGAGCTAGAATTGAG
* *
1773 CTCGTTGGGCTGGAATTGAG
1 CTCGTTGAGCTAGAATTGAG
1793 CT
1 CT
1795 AGGCCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (20 bp):
CTCGTTGAGCTAGAATTGAG
Found at i:5071 original size:18 final size:18
Alignment explanation
Indices: 5050--5143 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 18
5040 TTCAATTTTC
5050 TTTTCTTTCTCACATTCT
1 TTTTCTTTCTCACATTCT
*
5068 TTTT-TGCTCTCA-ATCTCT
1 TTTTCT-TTCTCACAT-TCT
**
5086 TTTTACTTTCTTTCATTCT
1 TTTT-CTTTCTCACATTCT
* *
5105 TTTT-TTTTTCA-ATTTTT
1 TTTTCTTTCTCACA-TTCT
* *
5122 TTTTCTTTTTCACATGCT
1 TTTTCTTTCTCACATTCT
5140 TTTT
1 TTTT
5144 TATTTCATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.02
17 14 0.24
18 29 0.50
19 11 0.19
20 3 0.05
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTCTTTCTCACATTCT
Found at i:5095 original size:37 final size:34
Alignment explanation
Indices: 5041--5144 Score: 91
Period size: 36 Copynumber: 2.9 Consensus size: 34
5031 ACTTTCTTTT
*
5041 TCAATTTTCTTTTCTTTCTCACATTCTTTTTTGCTC
1 TCAATTCT-TTTTCTTTCTCACATTCTTTTTT-CTC
** * *
5077 TCAATCTCTTTTTACTTTCTTTCATTCTTTTTTTTT
1 TCAAT-TCTTTTT-CTTTCTCACATTCTTTTTTCTC
* * *
5113 TCAATTTTTTTTTCTTTTTCACATGCTTTTTT
1 TCAA-TTCTTTTTCTTTCTCACATTCTTTTTT
5145 ATTTCATTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
35 15 0.27
36 20 0.36
37 20 0.36
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (34 bp):
TCAATTCTTTTTCTTTCTCACATTCTTTTTTCTC
Found at i:5457 original size:14 final size:14
Alignment explanation
Indices: 5410--5457 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5400 GTACGAATGG
*
5410 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
5424 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
5438 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
5452 ATTGGT
1 AATGGT
5458 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:9860 original size:21 final size:20
Alignment explanation
Indices: 9826--9875 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
9816 ACATTCTTGT
9826 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
9847 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
9868 AAAGAAAA
1 AAAGAAAA
9876 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:9868 original size:15 final size:14
Alignment explanation
Indices: 9837--9875 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9827 AAGAGAAAAC
9837 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
9853 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
9868 AAAGAAAA
1 AAAGAAAA
9876 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:9973 original size:11 final size:12
Alignment explanation
Indices: 9941--9971 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9931 TTGAGAGAAC
*
9941 TTGAAAAAACCT
1 TTGAAAAAGCCT
9953 TTGAAAAAGCCT
1 TTGAAAAAGCCT
9965 TTGAAAA
1 TTGAAAA
9972 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:10056 original size:29 final size:29
Alignment explanation
Indices: 9975--10056 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
9965 TTGAAAAGCA
* * * *
9975 AAAAGAAAAAGAAAATGAAAATGAGATTG
1 AAAAGAAGAAGAAAAAGAAATTGAGAGTG
10004 AAAAG-AGAACG-AAAAGAAATTTGAGAGTG
1 AAAAGAAGAA-GAAAAAGAAA-TTGAGAGTG
*
10033 AAAAGAAGATGAAAAAGAAATTGA
1 AAAAGAAGAAGAAAAAGAAATTGA
10057 AACAAAAGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 10 0.23
29 23 0.52
30 11 0.25
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.13
Consensus pattern (29 bp):
AAAAGAAGAAGAAAAAGAAATTGAGAGTG
Found at i:16299 original size:115 final size:115
Alignment explanation
Indices: 16097--16325 Score: 449
Period size: 115 Copynumber: 2.0 Consensus size: 115
16087 TACATGAACA
*
16097 TATAGTGTCAAAAGGAAAGCTAGCTGAAAGGTCACTTTTAATGAAGCTAATAATGAGGCCTAATG
1 TATAGTGTCAAAAGAAAAGCTAGCTGAAAGGTCACTTTTAATGAAGCTAATAATGAGGCCTAATG
16162 AAAAGTCACAACTATAGAAATTCTATTCCAAGTAACTCCAGCCTTCAATT
66 AAAAGTCACAACTATAGAAATTCTATTCCAAGTAACTCCAGCCTTCAATT
16212 TATAGTGTCAAAAGAAAAGCTAGCTGAAAGGTCACTTTTAATGAAGCTAATAATGAGGCCTAATG
1 TATAGTGTCAAAAGAAAAGCTAGCTGAAAGGTCACTTTTAATGAAGCTAATAATGAGGCCTAATG
16277 AAAAGTCACAACTATAGAAATTCTATTCCAAGTAACTCCAGCCTTCAAT
66 AAAAGTCACAACTATAGAAATTCTATTCCAAGTAACTCCAGCCTTCAAT
16326 GTGATTT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (115 bp):
TATAGTGTCAAAAGAAAAGCTAGCTGAAAGGTCACTTTTAATGAAGCTAATAATGAGGCCTAATG
AAAAGTCACAACTATAGAAATTCTATTCCAAGTAACTCCAGCCTTCAATT
Done.