Locus 2500

Sequence ID	3R_DroMel_CAF1
Location	6,833,157 – 6,833,340
Length	183
Max. P	0.911609

overview

Window 9

Location	6,833,157 – 6,833,271
Length	114
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	95.34
Mean single sequence MFE	-28.97
Consensus MFE	-25.27
Energy contribution	-25.71
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.40
Structure conservation index	0.87
SVM decision value	0.55
SVM RNA-class probability	0.779586
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6833157 114 - 27905053
CAAUGAUAAUGUCAUACCGAUUUCACUACAUAUCCAACCC-----AGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAAGCCAAAGGGUUGCUUCCAAAUCAGAUGGAAUGGGUAAAU
...((((...))))((((.((((((((.......((((((-----......((((((...))))))..(((((.....)))))...))))))..........)).)))))).))))... ( -29.43)
>DroSec_CAF1 92190 114 - 1
CAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC-----AGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAAGCCAAAGGGUUGCUUCCAAAUCAGAUGGAAUGGGUAAAU
...((((...))))((((.((((((((...(((.......-----))).(((..(((((((....)))(((((.....)))))...))))..))).......)).)))))).))))... ( -29.70)
>DroSim_CAF1 98504 114 - 1
CAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC-----AGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAAGCCAAAGGGUUGCUUCCAAAUCAGAUGGAAUGGGUAAAU
...((((...))))((((.((((((((...(((.......-----))).(((..(((((((....)))(((((.....)))))...))))..))).......)).)))))).))))... ( -29.70)
>DroEre_CAF1 77276 114 - 1
CAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC-----AGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAACCCAAAGGGUUGCCUUCAAAUCAGAUGGAACGGGUAAAU
..(((((...))))).(((...............((((((-----......((((((...))))))(.((((......)))))...))))))((.((......)).))..)))...... ( -25.90)
>DroYak_CAF1 90838 119 - 1
CAAUGAUAAUGUCAUACCAAUUUCACUACAUCUACGACCCAGACCAGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAACCCAAAGGGUUGCUUCCAAAUCAGAUGGAAUGGGUAAAU
..(((((...))))).....................(((((..(((......(((.(((((....))))).......((((((...))))))...))).......)))..))))).... ( -30.12)
>consensus
CAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC_____AGACAAGUGGCCUGCGGUUACGCGGUUUAAUACAAGCCAAAGGGUUGCUUCCAAAUCAGAUGGAAUGGGUAAAU
...((((...))))((((.((((((((.......((((((...........((((((...))))))..(((((.....)))))...))))))..........)).)))))).))))... (-25.27 = -25.71 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	6,833,231 – 6,833,340
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.89
Mean single sequence MFE	-27.02
Consensus MFE	-19.26
Energy contribution	-19.54
Covariance contribution	0.28
Combinations/Pair	1.17
Mean z-score	-2.34
Structure conservation index	0.71
SVM decision value	1.08
SVM RNA-class probability	0.911609
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6833231 109 - 27905053
AGAAGUCGCUCACAGGAGCAUAUAG------CACACAUACA-----UCAUGCAUUGCUGGAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCGAUUUCACUACAUAUCCAACCC
.((((((((((....))))......------...((((..(-----(((((((((((((((....)))))).....))))).))))).))))......))))))................ ( -30.50)
>DroSec_CAF1 92264 110 - 1
AGAAGUCGUUCACAGGAACAUAUAG-----AUACACAUACA-----UCAUAUAUUGCUGGAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC
.((((((((((....))))......-----....((((..(-----((((.....((((((....)))))).(((....)))))))).))))......))))))................ ( -25.60)
>DroSim_CAF1 98578 110 - 1
AGAAGUCGCUCACAGGAACAUAUAG-----AUACACACACA-----UCAUAUAUUGCUGGAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC
.(((((((((..(((....((((((-----((........)-----)).))))).((((((....)))))))))..)))...(((((...)))))...))))))................ ( -23.40)
>DroEre_CAF1 77350 120 - 1
AGAAAUCGCUCACAGGAGCAUAUAUUCGUAGCACACAUAAAUGUACAUGUACAUGGCUGAAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC
.((((((((((....))))((((..((((.((((......(((((....)))))(((((........))))).....)))).))))..))))......))))))................ ( -32.90)
>DroYak_CAF1 90917 101 - 1
AGAAGUCGCUCACAGGAACAUAUAU-------------------AGUCGUACAUGGCUGGAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCAAUUUCACUACAUCUACGACCC
.........................-------------------.((((((...(((((((....)))))))(((....)))(((((...))))).................)))))).. ( -22.70)
>consensus
AGAAGUCGCUCACAGGAACAUAUAG______CACACAUACA_____UCAUACAUUGCUGGAGAACUCCGGCCUGCAAGUGCAAUGAUAAUGUCAUACCGAUUUCACUACAUCUCCAACCC
.((((((((((....))))...........................((((.....((((((....)))))).(((....)))))))............))))))................ (-19.26 = -19.54 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:02 2006