Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12047.1
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: 2434
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Found at i:2171 original size:27 final size:27
Alignment explanation
Indices: 2127--2216 Score: 63
Period size: 27 Copynumber: 3.3 Consensus size: 27
2117 TTAGTTTACC
* * * *
2127 AAATTACTAAAATGCCCTTAATTTGTA
1 AAATTACCAAAATACCCTCAATTTATA
* *
2154 AAATTACCAAAGTACCCTCAGTTTATA
1 AAATTACCAAAATACCCTCAATTTATA
* *** * *
2181 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCAATTTATA
*
2208 GAATTACCA
1 AAATTACCA
2217 TCAGTTTACA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCAATTTATA
Found at i:2213 original size:54 final size:54
Alignment explanation
Indices: 2166--2353 Score: 203
Period size: 54 Copynumber: 3.6 Consensus size: 54
2156 ATTACCAAAG
* * *
2166 TACCCTCAGTTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACC----
1 TACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACCATTT
* * * * *
2216 -A---TCAGTTTACAAAATTACCATTTTTCCCTCGATTTGCAGACTCACCATTT
1 TACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACCATTT
* * * * *
2266 TACCCTCAATTTATAGAATTACCGTTTTACGCTCGATTTACAAAATTACCATTT
1 TACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACCATTT
2320 TACCCTCAATTTACAAAATTACCATTTTACCCTC
1 TACCCTCAATTTACAAAATTACCATTTTACCCTC
2354 TGTTGTGAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 12
0.77 0.14 0.08
Matches are distributed among these distances:
46 39 0.35
49 1 0.01
51 1 0.01
54 69 0.63
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.37
Consensus pattern (54 bp):
TACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACCATTT
Found at i:2217 original size:27 final size:27
Alignment explanation
Indices: 2166--2217 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2156 ATTACCAAAG
*
2166 TACCCTCAGTTTATAGAATTACCATTT
1 TACCCTCAGTTTACAGAATTACCATTT
2193 TACCCTC-GATTTACAGAATTACCAT
1 TACCCTCAG-TTTACAGAATTACCAT
2218 CAGTTTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCAGTTTACAGAATTACCATTT
Found at i:2233 original size:73 final size:73
Alignment explanation
Indices: 2153--2288 Score: 166
Period size: 73 Copynumber: 1.9 Consensus size: 73
2143 CTTAATTTGT
* * *
2153 AAAATTACCAAAGTACCCTC-AGTTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCA
1 AAAATTACCAAAGTACCCTCGA-TTTACAGAATCACCATTTTACCCTCAATTTACAGAATTACCA
2217 TCAGTTTAC
65 TCAGTTTAC
*** * * * *
2226 AAAATTACCATTTTTCCCTCGATTTGCAGACTCACCATTTTACCCTCAATTTATAGAATTACC
1 AAAATTACCAAAGTACCCTCGATTTACAGAATCACCATTTTACCCTCAATTTACAGAATTACC
2289 GTTTTACGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 51 0.98
74 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (73 bp):
AAAATTACCAAAGTACCCTCGATTTACAGAATCACCATTTTACCCTCAATTTACAGAATTACCAT
CAGTTTAC
Found at i:2238 original size:46 final size:46
Alignment explanation
Indices: 2166--2255 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
2156 ATTACCAAAG
* * *
2166 TACCCTCAGTTTATAGAATTACCATTTTACCCTCGATTTACAGAAT
1 TACCATCAGTTTACAAAATTACCATTTTACCCTCGATTTACAGAAT
* *
2212 TACCATCAGTTTACAAAATTACCATTTTTCCCTCGATTTGCAGA
1 TACCATCAGTTTACAAAATTACCATTTTACCCTCGATTTACAGA
2256 CTCACCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
TACCATCAGTTTACAAAATTACCATTTTACCCTCGATTTACAGAAT
Found at i:2271 original size:27 final size:27
Alignment explanation
Indices: 2211--2353 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
2201 ATTTACAGAA
* *
2211 TTACCATCAGTTTACAAAATTACCATT
1 TTACCCTCAATTTACAAAATTACCATT
* * * * * *
2238 TTTCCCTCGATTTGCAGACTCACCATT
1 TTACCCTCAATTTACAAAATTACCATT
* * *
2265 TTACCCTCAATTTATAGAATTACCGTT
1 TTACCCTCAATTTACAAAATTACCATT
* *
2292 TTACGCTCGATTTACAAAATTACCATT
1 TTACCCTCAATTTACAAAATTACCATT
2319 TTACCCTCAATTTACAAAATTACCATT
1 TTACCCTCAATTTACAAAATTACCATT
2346 TTACCCTC
1 TTACCCTC
2354 TGTTGTGAAA
Statistics
Matches: 94, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.38
Consensus pattern (27 bp):
TTACCCTCAATTTACAAAATTACCATT
Done.