Locus 3020

Sequence ID	X_DroMel_CAF1
Location	8,066,890 – 8,066,990
Length	100
Max. P	0.886202

overview

Window 5

Location	8,066,890 – 8,066,990
Length	100
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.21
Mean single sequence MFE	-28.70
Consensus MFE	-22.76
Energy contribution	-22.88
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.79
SVM decision value	0.94
SVM RNA-class probability	0.886202
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8066890 100 + 22224390
GCGUCCCUAAUCGAACAUCUGCCAAAAGGGAGGAAACUUCAGAUAAAAGCU--CCUCAGAGGUCGACAGAUUGAUGAGGCGGAUAAAAAUAGAAAUGGG---GGC
..(((((((.((....(((((((.....((((....))))...........--..(((..((((....))))..)))))))))).......))..))))---))) ( -31.50)
>DroSec_CAF1 48841 102 + 1
GCGUUCCUAAUCGAACAUCUGCCAG-AGGGAGGAAACUUCAGAUAAAAGCU--CCUCGGAGGUCGACAGAUUGAUGAGGCGGAUAAAAAUAGGAAUGGGCUGACC
.((((((((.......(((((((..-..((((....))))...........--..(((..((((....))))..)))))))))).....))))))))........ ( -31.20)
>DroSim_CAF1 24569 104 + 1
GCGUUCCUAAUCGAACAUCUGUCAA-AGGGAGGAAACUUCAGAUUAAAGCUCUCCUUAGAGGUCGACAGAUUAAUGAGGCGGAUAAAAAUAGGAAUGGGCUGACC
.((((((((.(((...(((((((..-..((((....)))).........((((....))))...)))))))...)))............))))))))........ ( -27.22)
>DroEre_CAF1 36490 96 + 1
GCGUCCCUAAUCGAACAUCUGCCAA-AGGGAG--AACUGCUGCCAAAGGCU--CCUCAGAGGUCGACAGAUUGAUGAGGCGGAUAAAAAUAGCAAUGGACU----
..((((...........(((.((..-.)).))--)..(((((((...))).--(((((..((((....))))..)))))...........))))..)))).---- ( -26.10)
>DroYak_CAF1 43017 98 + 1
GCGUCCCUAAUCGAACAUCUGCCGA-AGGGAGGAAACUUCAGAUAAAAGCU--CCUCAGAGGUCGACAGAUUGAUGAGGCGGAUAAAAAUAGGAAUGGGCU----
.(((.((((.......(((((((..-..((((....))))...........--..(((..((((....))))..)))))))))).....)))).)))....---- ( -27.50)
>consensus
GCGUCCCUAAUCGAACAUCUGCCAA_AGGGAGGAAACUUCAGAUAAAAGCU__CCUCAGAGGUCGACAGAUUGAUGAGGCGGAUAAAAAUAGGAAUGGGCU___C
.(((.((((.......(((((((.....((((....))))...............(((..((((....))))..)))))))))).....)))).)))........ (-22.76 = -22.88 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	8,066,890 – 8,066,990
Length	100
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	88.21
Mean single sequence MFE	-24.64
Consensus MFE	-20.64
Energy contribution	-21.16
Covariance contribution	0.52
Combinations/Pair	1.12
Mean z-score	-1.40
Structure conservation index	0.84
SVM decision value	0.09
SVM RNA-class probability	0.579093
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8066890 100 - 22224390
GCC---CCCAUUUCUAUUUUUAUCCGCCUCAUCAAUCUGUCGACCUCUGAGG--AGCUUUUAUCUGAAGUUUCCUCCCUUUUGGCAGAUGUUCGAUUAGGGACGC
...---....................(((.(((.(((((((((.....((((--((((((.....)))).))))))....)))))))))....))).)))..... ( -25.60)
>DroSec_CAF1 48841 102 - 1
GGUCAGCCCAUUCCUAUUUUUAUCCGCCUCAUCAAUCUGUCGACCUCCGAGG--AGCUUUUAUCUGAAGUUUCCUCCCU-CUGGCAGAUGUUCGAUUAGGAACGC
((....))..................(((.(((.((((((((......((((--((((((.....)))).))))))...-.))))))))....))).)))..... ( -24.20)
>DroSim_CAF1 24569 104 - 1
GGUCAGCCCAUUCCUAUUUUUAUCCGCCUCAUUAAUCUGUCGACCUCUAAGGAGAGCUUUAAUCUGAAGUUUCCUCCCU-UUGACAGAUGUUCGAUUAGGAACGC
((....))..............(((...((....(((((((((......((((((.((((.....))))))))))....-)))))))))....))...))).... ( -23.30)
>DroEre_CAF1 36490 96 - 1
----AGUCCAUUGCUAUUUUUAUCCGCCUCAUCAAUCUGUCGACCUCUGAGG--AGCCUUUGGCAGCAGUU--CUCCCU-UUGGCAGAUGUUCGAUUAGGGACGC
----.((((((((((...........(((((....((....))....)))))--.(((...)))))))))(--((((..-..)).)))...........)))).. ( -22.80)
>DroYak_CAF1 43017 98 - 1
----AGCCCAUUCCUAUUUUUAUCCGCCUCAUCAAUCUGUCGACCUCUGAGG--AGCUUUUAUCUGAAGUUUCCUCCCU-UCGGCAGAUGUUCGAUUAGGGACGC
----......................(((.(((.(((((((((.....((((--((((((.....)))).))))))...-)))))))))....))).)))..... ( -27.30)
>consensus
G___AGCCCAUUCCUAUUUUUAUCCGCCUCAUCAAUCUGUCGACCUCUGAGG__AGCUUUUAUCUGAAGUUUCCUCCCU_UUGGCAGAUGUUCGAUUAGGGACGC
..........................(((.(((.(((((((((.....((((...(((((.....)))))..))))....)))))))))....))).)))..... (-20.64 = -21.16 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:06 2006