Locus 3272

Sequence ID	3R_DroMel_CAF1
Location	8,735,884 – 8,736,044
Length	160
Max. P	0.878937

overview

Window 3

Location	8,735,884 – 8,736,004
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.57
Mean single sequence MFE	-33.33
Consensus MFE	-25.69
Energy contribution	-24.78
Covariance contribution	-0.91
Combinations/Pair	1.44
Mean z-score	-0.93
Structure conservation index	0.77
SVM decision value	0.50
SVM RNA-class probability	0.760072
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8735884 120 - 27905053
GAGAAGCAGCUGGAACCAAAGGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACAUUCGUAAGGAUGUUUCCUUGUAGUUGUCAUUAUACAUGUUU
.....(((((((((((((.......)))))))...(((((((...(((((.(....))))))......))))....((((((....)))))).)))....)))))).............. ( -36.50)
>DroSec_CAF1 162484 120 - 1
GAGAAGCAGCUGGAACCAAAAGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACACACGUAAGGAUGUUUCCUUGUAGAUAUAAUUAUACAUGUUU
......(((.((((((((.......)))))))))))..((((...(((((.(....))))))......))))(((....))).((((((....))))))..................... ( -32.10)
>DroSim_CAF1 179661 120 - 1
GAGAAGCAGCUGGAACCAAAAGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACACACGUAAGGAUGUUACCUUGUAGAUAUAAUUAUACACGUUU
......(((.((((((((.......)))))))))))..((((...(((((.(....))))))......))))(((((((..(....)..))((((...)))).........))))).... ( -30.30)
>DroEre_CAF1 178759 117 - 1
GAGCAGCAGUUGGAGCCAAUCGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGCUACGCCCUUGUUGUGGGCGUGUACACACGUAAGGAUGCUGCCUUGUAGUUAUC---UUAUAUAUAU
..(((((((((((.((......(((.(((((.....))))).)))..)))))))(((((((.......))))(((....))))))....))))))............---.......... ( -35.90)
>DroYak_CAF1 171121 120 - 1
GAGCAGCAGUUGGAACCAAUCGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGCUACGCCCUUGUUGUGGGCGUGUAUACACGUAAGGAUGCUGCUUUGUAGUUGUUAUGGUAUAUGUUU
(((((((...((((((((.......)))))))).(((.((.......))))))))((((((.......))))))((((((.(((((.(((((......))).)).))))))))))))))) ( -38.00)
>DroPer_CAF1 173764 104 - 1
AAAUACCAUCUUGAGCCUCUCCAGCUGGUCCAACUGGAUCCCUAUGUUCGUGGUAAUGCUCUGGUAGUGGGCGUUUACACUCGAUUGC---CAGUGUUAUAAUGAUC-------------
...((((((....(((.......)))(((((....))))).........))))))..((.(((((((((((.(....).))).)))))---))).))..........------------- ( -27.20)
>consensus
GAGAAGCAGCUGGAACCAAACGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGUUACGCCCUUGUUGUGGGCGUGUACACACGUAAGGAUGCUGCCUUGUAGUUAUCAUUAUACAUGUUU
..((((((..((((((((.......)))))))).......((((..........(((((((.......))))))).........)))).))))))......................... (-25.69 = -24.78 +  -0.91)

alignment

secondary structure

dotplot

Window 4

Location	8,735,924 – 8,736,044
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.39
Mean single sequence MFE	-42.30
Consensus MFE	-30.73
Energy contribution	-30.23
Covariance contribution	-0.49
Combinations/Pair	1.36
Mean z-score	-2.26
Structure conservation index	0.73
SVM decision value	0.91
SVM RNA-class probability	0.878937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8735924 120 - 27905053
UAAUAAGGAUUCCUUUGCCGCCGAGAGGAGACUUUUAAAGGAGAAGCAGCUGGAACCAAAGGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACAU
....((((...)))).(((((((((((....)))))(((((.(...(((.((((((((.......)))))))))))...))))))..)).))))(((((((.......)))))))..... ( -38.70)
>DroPse_CAF1 178865 120 - 1
CACGAAGAUGGCCCUCGAAGCCGAGAUGGAGCUGCUCAAGAAAUACCAUCUUGAGCCUCUCCAGCUGGUCCAACUGGAUCCCUAUGUUCGUGGCAAUGCUCUGGUAGUGGGCGUUUACAC
((((((.((((..((((....)))).(((((..((((((((.......))))))))..)))))...(((((....))))).)))).))))))..(((((((.......)))))))..... ( -47.20)
>DroSec_CAF1 162524 120 - 1
UAAUAAGGAUUCCUUUGCCGCCGAGAGGAGACUCUUAAAGGAGAAGCAGCUGGAACCAAAAGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACAC
....((((...)))).(((((((((((....)))))(((((.(...(((.((((((((.......)))))))))))...))))))..)).))))(((((((.......)))))))..... ( -41.30)
>DroSim_CAF1 179701 120 - 1
UAAUAAGGAUUCCUUUGCCGCCGAGAGGAGACUCUUAAAGGAGAAGCAGCUGGAACCAAAAGAAAUGGUUCUAUUGGAGCCCUUUAAGGCCGGUUACGCCUUUGUUGUGGGCGUGUACAC
....((((...)))).(((((((((((....)))))(((((.(...(((.((((((((.......)))))))))))...))))))..)).))))(((((((.......)))))))..... ( -41.30)
>DroEre_CAF1 178796 120 - 1
UAAUAAGGAUACCUUUGCCGCCGAGAGGAAACUGUUGAAGGAGCAGCAGUUGGAGCCAAUCGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGCUACGCCCUUGUUGUGGGCGUGUACAC
...(((((....)))))..((((..((....)).(((((((.((..((((.(((((((.......)))))))))))..)))))))))...))))(((((((.......)))))))..... ( -43.20)
>DroYak_CAF1 171161 120 - 1
CAAUAAGGAUACCUUUGCCGCCGAGAGGAAACUUUUGAAAGAGCAGCAGUUGGAACCAAUCGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGCUACGCCCUUGUUGUGGGCGUGUAUAC
........((((....((((.((((((....))))))((((.((..((((.(((((((.......)))))))))))..)).)))).....)))).((((((.......)))))))))).. ( -42.10)
>consensus
UAAUAAGGAUUCCUUUGCCGCCGAGAGGAAACUCUUAAAGGAGAAGCAGCUGGAACCAAACGAAAUGGUUCUAUUGGAGCCCUUUAAGCCCGGCUACGCCCUUGUUGUGGGCGUGUACAC
...................((((..((....))((((((((.(...(((.((((((((.......)))))))))))...)))))))))..))))(((((((.......)))))))..... (-30.73 = -30.23 +  -0.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:12 2006