Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10790.1
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: 3294
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2145 original size:30 final size:30
Alignment explanation
Indices: 2074--2156 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
2064 CTTTTGTTTC
* *
2074 AATTTCTTTTTCAGCTTCTTTTTCACTCTCA
1 AATTTCTTTTTC-GTTTCTTTTTCAATCTCA
2105 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCGTT-TCTTTTTCAATCTCA
* *
2134 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-GTTTCTTTTT
2157 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 7 0.16
30 30 0.67
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTTCGTTTCTTTTTCAATCTCA
Found at i:2156 original size:18 final size:18
Alignment explanation
Indices: 2107--2162 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2097 CACTCTCAAA
* *
2107 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
2124 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
2142 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
2161 TT
1 TT
2163 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:2163 original size:12 final size:12
Alignment explanation
Indices: 2132--2156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2122 TTTTTCAATC
2132 TCATTTTCTTTT
1 TCATTTTCTTTT
2144 TCATTTTCTTTT
1 TCATTTTCTTTT
2156 T
1 T
2157 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:2235 original size:5 final size:5
Alignment explanation
Indices: 2225--2281 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
2215 CTCTTGCCTC
* * *
2225 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
2272 TCTTT TCTTT
1 TCTTT TCTTT
2282 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:2257 original size:25 final size:25
Alignment explanation
Indices: 2229--2277 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2219 TGCCTCTCTT
*
2229 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
2254 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
2278 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:2282 original size:21 final size:20
Alignment explanation
Indices: 2238--2292 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
2228 TTTCTTTTTA
2238 TTTTG-TTTTCTTTTTCTTC
1 TTTTGTTTTTCTTTTTCTTC
*
2257 TTTTGCTTTTTC-TTTTCTTT
1 TTTTG-TTTTTCTTTTTCTTC
2277 TCTTTGTTTTCTCTTT
1 T-TTTGTTTT-TCTTT
2293 ACAAAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 11 0.37
22 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTTCTTC
Done.