Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10899.1
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: 3220
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2084 original size:12 final size:12
Alignment explanation
Indices: 2069--2099 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2059 TTCTTTTTGC
2069 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2081 TTTTCAAAGGCT
1 TTTTCAAAGGCT
2093 TTTTCAA
1 TTTTCAA
2100 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:2176 original size:6 final size:6
Alignment explanation
Indices: 2160--2209 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2150 TTTCTTTTTA
*
2160 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
2209 T
1 T
2210 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:2192 original size:37 final size:37
Alignment explanation
Indices: 2149--2219 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
2139 CTTGCCTCTC
2149 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
2186 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
2220 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:2220 original size:16 final size:16
Alignment explanation
Indices: 2145--2205 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2135 GCCTCTTGCC
*
2145 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
2161 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
2177 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
2193 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
2206 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:3175 original size:12 final size:12
Alignment explanation
Indices: 3133--3192 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
3123 TTTTTTTAAC
3133 TCGATTTTTTTT
1 TCGATTTTTTTT
*
3145 GTC-ACTTTTTTT
1 -TCGATTTTTTTT
*
3157 TC--CTTTTTTT
1 TCGATTTTTTTT
3167 TCGATTTTTTTT
1 TCGATTTTTTTT
3179 T-GAATTTTTTTT
1 TCG-ATTTTTTTT
3191 TC
1 TC
3193 TGAATTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 10 0.24
11 3 0.07
12 26 0.63
13 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.07, T:0.73
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:3188 original size:14 final size:14
Alignment explanation
Indices: 3160--3199 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
3150 TTTTTTTTCC
3160 TTTTTTTTC-G-A-
1 TTTTTTTTCTGAAT
3171 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
3184 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
3198 TT
1 TT
3200 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 8 0.32
14 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Done.