Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2038
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: 4600
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:1109 original size:11 final size:11
Alignment explanation
Indices: 1093--1121 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1083 AAGGAATATG
1093 GAGTTTTTGGA
1 GAGTTTTTGGA
1104 GAGTTTTTGGA
1 GAGTTTTTGGA
1115 G-GTTTTT
1 GAGTTTTT
1122 TGGTGGTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (11 bp):
GAGTTTTTGGA
Found at i:1750 original size:13 final size:13
Alignment explanation
Indices: 1732--1757 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1722 ACAAAGATCC
1732 ATGTATCGATACA
1 ATGTATCGATACA
1745 ATGTATCGATACA
1 ATGTATCGATACA
1758 CAGAAAAATG
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:1753 original size:33 final size:33
Alignment explanation
Indices: 1711--1777 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1701 AAAATTTCCA
***
1711 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1744 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1777 A
1 A
1778 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1837 original size:13 final size:13
Alignment explanation
Indices: 1819--1843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1809 ACAATACTTA
1819 TGTATCGATACAT
1 TGTATCGATACAT
1832 TGTATCGATACA
1 TGTATCGATACA
1844 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1920 original size:21 final size:21
Alignment explanation
Indices: 1894--1991 Score: 187
Period size: 21 Copynumber: 4.7 Consensus size: 21
1884 GTTAGGACCC
1894 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
1915 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
*
1936 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
1957 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
1978 TGTATCGATACATT
1 TGTATCGATACATT
1992 TGGAATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:2831 original size:55 final size:54
Alignment explanation
Indices: 2744--2916 Score: 256
Period size: 55 Copynumber: 3.1 Consensus size: 54
2734 TATTCTACTT
* * * * * *
2744 TTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGGTT
1 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTC
*
2799 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCGTTAAGAGGTGTCCTGCTC
1 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTC
2854 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTC
1 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTC
2909 TTTGAGGA
1 TTTGAGGA
2917 TGCCACCAAC
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 2 0.02
55 104 0.96
56 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (54 bp):
TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTC
Found at i:3901 original size:17 final size:17
Alignment explanation
Indices: 3879--3915 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3869 TTCCAAACAC
*
3879 AAAAAAAAGAAAAAAGA
1 AAAAAAAACAAAAAAGA
*
3896 AAAAAAAACAAAACAGA
1 AAAAAAAACAAAAAAGA
3913 AAA
1 AAA
3916 TCTCGGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAAGA
Found at i:3993 original size:1 final size:1
Alignment explanation
Indices: 3957--3985 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3947 TACTCTTCAC
3957 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3986 GGGAAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.