Locus 3347

Sequence ID	3R_DroMel_CAF1
Location	9,016,081 – 9,016,174
Length	93
Max. P	0.993468

overview

Window 1

Location	9,016,081 – 9,016,174
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	91.07
Mean single sequence MFE	-29.89
Consensus MFE	-22.18
Energy contribution	-22.98
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.74
SVM decision value	0.53
SVM RNA-class probability	0.773052
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9016081 93 + 27905053
UCGGCUUUACCACUUUUUAUUGCGUAUACGCUGGGGCACCCCCAUUACGUAUACGCAGUGUAUUACGCCCCUCCACUCACAGCAGGCAAAUGG
.........(((.....(((((((((((((.(((((...)))))...)))))))))))))......(((.((........))..)))...))) ( -29.30)
>DroSec_CAF1 130095 93 + 1
UCGGCGUUACCACUUUUUAUUGCGUAUACGCCGUGGCGGCCCCAUCGCGUAUACGCAGUGUAUUACGCCCCUCCAGUCACAGCAGGCAAAUGG
..(((((..........((((((((((((((.((((.....)))).))))))))))))))....)))))((....(((......)))....)) ( -34.24)
>DroSim_CAF1 133319 93 + 1
UCGGCGUUACCACUUUUUAUUGCGUACACGCCGGGGCGGACCCAUCGCGUAUACGCAGUGUAUUACGCCCCUCCAGUCACAGCAGACAAAUGG
..((((((((((........)).))).)))))((((((((..(((.(((....))).)))..)).))))))....(((......)))...... ( -32.80)
>DroEre_CAF1 136145 92 + 1
UUGGCCUUACCACUUUUUAUUGCGUAUACGCAGGG-AGGCCCCAUCGCGUAUACGCAGUGUAUUACGCCCCUCCAGUCACAGCAUGCAAAUGG
((((.............((((((((((((((.(((-....)))...))))))))))))))............))))......(((....))). ( -27.21)
>DroYak_CAF1 141563 91 + 1
UCGGCCUUACCACUUUUUAUUGCGUAUACGCAGUG-AGGGCCCAUCGCGUAUACGCAGUGUAUUACGCCCC-CCAGUCACAGCAUGCAAAUGG
..(((..(((........(((((((((((((.(((-......))).))))))))))))))))....)))..-..........(((....))). ( -25.90)
>consensus
UCGGCCUUACCACUUUUUAUUGCGUAUACGCAGGGGCGGCCCCAUCGCGUAUACGCAGUGUAUUACGCCCCUCCAGUCACAGCAGGCAAAUGG
..(((.............(((((((((((((.(((.....)))...)))))))))))))(.....))))........................ (-22.18 = -22.98 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	9,016,081 – 9,016,174
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	91.07
Mean single sequence MFE	-35.11
Consensus MFE	-28.61
Energy contribution	-28.53
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.54
Structure conservation index	0.81
SVM decision value	2.40
SVM RNA-class probability	0.993468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9016081 93 - 27905053
CCAUUUGCCUGCUGUGAGUGGAGGGGCGUAAUACACUGCGUAUACGUAAUGGGGGUGCCCCAGCGUAUACGCAAUAAAAAGUGGUAAAGCCGA
(((((..(.....)..)))))...(((......((((((((((((((..(((((...))))))))))))))).......)))).....))).. ( -37.71)
>DroSec_CAF1 130095 93 - 1
CCAUUUGCCUGCUGUGACUGGAGGGGCGUAAUACACUGCGUAUACGCGAUGGGGCCGCCACGGCGUAUACGCAAUAAAAAGUGGUAACGCCGA
.......(((.(.......).)))(((((....((((((((((((((..(((.....)))..)))))))))).......))))...))))).. ( -35.41)
>DroSim_CAF1 133319 93 - 1
CCAUUUGUCUGCUGUGACUGGAGGGGCGUAAUACACUGCGUAUACGCGAUGGGUCCGCCCCGGCGUGUACGCAAUAAAAAGUGGUAACGCCGA
((.(..(((......)))..).))(((((....((((((((((((((...(((....)))..)))))))))).......))))...))))).. ( -37.11)
>DroEre_CAF1 136145 92 - 1
CCAUUUGCAUGCUGUGACUGGAGGGGCGUAAUACACUGCGUAUACGCGAUGGGGCCU-CCCUGCGUAUACGCAAUAAAAAGUGGUAAGGCCAA
(((.(..(.....)..).)))...(((.(....(((((((((((((((..(((....-)))))))))))))).......))))...).))).. ( -33.31)
>DroYak_CAF1 141563 91 - 1
CCAUUUGCAUGCUGUGACUGG-GGGGCGUAAUACACUGCGUAUACGCGAUGGGCCCU-CACUGCGUAUACGCAAUAAAAAGUGGUAAGGCCGA
(((.(..(.....)..).)))-..(((.(....(((((((((((((((.(((....)-)).))))))))))).......))))...).))).. ( -32.01)
>consensus
CCAUUUGCCUGCUGUGACUGGAGGGGCGUAAUACACUGCGUAUACGCGAUGGGGCCGCCCCGGCGUAUACGCAAUAAAAAGUGGUAACGCCGA
(((.(..(.....)..).)))...(((......((((((((((((((...(((.....))).)))))))))).......)))).....))).. (-28.61 = -28.53 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:58 2006