Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2405
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: 15584
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:994 original size:50 final size:51
Alignment explanation
Indices: 881--1007 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 51
871 TTTTACTATT
* * * *
881 TGTATCGATACAATATTCATTGTATCAATACATTCTGGGTTTTTATCGAGA
1 TGTATCGATACATTATTCAGTGTATCAATACATTCTGGGATTTTACCGAGA
* * * * *
932 TGTATCAATACATTCTTCGGTGTATCGATACATTCT-GGATTTTACCTAGA
1 TGTATCGATACATTATTCAGTGTATCAATACATTCTGGGATTTTACCGAGA
*
982 TGTATCGATACATTATTCAATGTATC
1 TGTATCGATACATTATTCAGTGTATC
1008 CATATATGCA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 33 0.52
51 30 0.48
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (51 bp):
TGTATCGATACATTATTCAGTGTATCAATACATTCTGGGATTTTACCGAGA
Found at i:8197 original size:13 final size:13
Alignment explanation
Indices: 8179--8205 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8169 TTTTACTATA
8179 TATCGATACAATG
1 TATCGATACAATG
8192 TATCGATACAATG
1 TATCGATACAATG
8205 T
1 T
8206 CTCATGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:8216 original size:33 final size:33
Alignment explanation
Indices: 8153--8222 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
8143 GCCATTGGGC
** *
8153 ACAATGTATCGATACTTTTTACTATATATCGAT
1 ACAATGTATCGATACAATGTACTATATATCGAT
*
8186 ACAATGTATCGATACAATGT-CTCATGTATCGAT
1 ACAATGTATCGATACAATGTACT-ATATATCGAT
8219 ACAA
1 ACAA
8223 ACAGTGGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACTATATATCGAT
Found at i:8316 original size:32 final size:33
Alignment explanation
Indices: 8275--8340 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8265 ATTCTTTATG
*
8275 TATCGATACAATG-AACATGTATCGATACATTA
1 TATCGATACAAAGCAACATGTATCGATACATTA
* *
8307 TATCGATACAAAGCAATATGTATCGATACTTTA
1 TATCGATACAAAGCAACATGTATCGATACATTA
8340 T
1 T
8341 GGCTTGTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
TATCGATACAAAGCAACATGTATCGATACATTA
Found at i:14897 original size:33 final size:33
Alignment explanation
Indices: 14860--14926 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14850 TTCAACGATT
14860 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
14893 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
14926 T
1 T
14927 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:14898 original size:13 final size:13
Alignment explanation
Indices: 14880--14904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14870 CATAAAATGT
14880 TGTATCGATACAA
1 TGTATCGATACAA
14893 TGTATCGATACA
1 TGTATCGATACA
14905 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14987 original size:13 final size:13
Alignment explanation
Indices: 14969--14993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14959 ATTACTCACA
14969 TGTATCGATACAT
1 TGTATCGATACAT
14982 TGTATCGATACA
1 TGTATCGATACA
14994 CTGATCTTTG
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:15058 original size:52 final size:52
Alignment explanation
Indices: 15002--15126 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
14992 CACTGATCTT
*
15002 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
15054 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
15106 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
15127 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.