Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_46 ID=scaffold_46-JGI_221_v2.0
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: 41990
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.18
Warning! 17179 characters in sequence are not A, C, G, or T
Found at i:1931 original size:21 final size:21
Alignment explanation
Indices: 1907--1964 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1897 TTTATTTCGG
1907 CTCATTCTCTTGTTCAACGGC
1 CTCATTCTCTTGTTCAACGGC
*
1928 CTCATCCTCTTGTTCAACGGC
1 CTCATTCTCTTGTTCAACGGC
1949 CTCATTCTCTTGTTCA
1 CTCATTCTCTTGTTCA
1965 CTTTCAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.34, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCATTCTCTTGTTCAACGGC
Found at i:2133 original size:255 final size:255
Alignment explanation
Indices: 1682--2164 Score: 912
Period size: 255 Copynumber: 1.9 Consensus size: 255
1672 CATCTTCGGG
*
1682 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCTATCATCTCAGACAAACA
1 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
*
1747 TCACATTCCGGTTTGGAGATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
66 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
1812 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
131 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
1877 TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
196 TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
*
1937 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCGGACAAACA
1 TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
2002 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
66 TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
* *
2067 TCTTGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
131 CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
*
2132 TTGGTTGCACCACTCACTTCTTTATTTTGGCTC
196 TTGGTTGCACCACTCACTTCTTTATTTCGGCTC
2165 GGCATGTCAC
Statistics
Matches: 222, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
255 222 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (255 bp):
TTGTTCAACGGCCTCATTCTCTTGTTCACTTTCAGATTCAATCTCTCCATCATCTCAGACAAACA
TCACATTCCGGTTTGGACATTGGCTTGTGATGTGGCCCCTTCTAAGACATTTGAAACACTTTATG
CCTCGGGATCTATTTGGTTGGGCATCCATCTTCCTTTACTCGTTTCAACAATCGGTTTGTTGAAC
TTGGTTGCACCACTCACTTCTTTATTTCGGCTCATTCTCTTGTTCAACGGCCTCATCCTC
Found at i:33844 original size:17 final size:19
Alignment explanation
Indices: 33812--33851 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
33802 CTCATTTCTT
33812 TTTCTTTTGAATCACTC-TC
1 TTTCTTTT-AATCACTCATC
33831 TTTCTTTT-ATCACTCATC
1 TTTCTTTTAATCACTCATC
33849 TTT
1 TTT
33852 TTGTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 5 0.25
19 8 0.40
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTCTTTTAATCACTCATC
Found at i:36146 original size:13 final size:13
Alignment explanation
Indices: 36128--36163 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
36118 CCGTATACAA
36128 TTTTTTTTC-AAT
1 TTTTTTTTCGAAT
36140 TTTTTTTTCGAA-
1 TTTTTTTTCGAAT
36152 TTTTTTTTCGAA
1 TTTTTTTTCGAA
36164 ACTACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Done.