Locus 980

Sequence ID	X_DroMel_CAF1
Location	2,828,551 – 2,828,709
Length	158
Max. P	0.928196

overview

Window 3

Location	2,828,551 – 2,828,669
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.80
Mean single sequence MFE	-23.50
Consensus MFE	-15.31
Energy contribution	-15.25
Covariance contribution	-0.06
Combinations/Pair	1.13
Mean z-score	-2.01
Structure conservation index	0.65
SVM decision value	0.74
SVM RNA-class probability	0.838525
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2828551 118 - 22224390
AUAGGCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUUAAUGCGUAUAUUUAUUUAUAACAUUCGAAUGGUAUACCUAUUUCAAUGGUUUAUUUCUGACAUUUAUGGAUUAA--UU
((((((..((((...(((((((((((.((((.(.....).)))).)))))))))))..)))).((((.((((((.....)))))).))))))))))....................--.. ( -22.70)
>DroSec_CAF1 216783 118 - 1
AUAGCGAAUGUAUAUUAGAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAUUUGAAUUGUAUGCCUAUUUCAAUGGUUUAUUUCUGACAUUUAUGGAUUAA--UU
....((((((((((.((((((((((((((((........))))).)))))))))))..))).)))))))....(((.(((.........))).)))....................--.. ( -24.00)
>DroSim_CAF1 189362 101 - 1
AUAGCCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAU-----------------UUCAAUGGUUUAUUUCUGACAUUUAUGGAUUAA--UU
..((((((((((((.((((((((((((((((........))))).)))))))))))..))).))))-----------------.....))))).......................--.. ( -20.10)
>DroEre_CAF1 236525 109 - 1
AUAGGCAAUGUAUAUUAAAUGUGCGCUUUGCCGUUAUUCUUAAAUGCGCAUGUUUAUUUAUAACAU-----------ACUUAUACUUAUGUUUUAUGUGUGUCGUUUACGGAUUAACAUA
...((((((((((((...)))))))..)))))((((.((((((((((((((((........(((((-----------(........))))))..))))))).)))))).))).))))... ( -27.20)
>consensus
AUAGCCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAU___________ACCUAUUUCAAUGGUUUAUUUCUGACAUUUAUGGAUUAA__UU
.......(((((((.((((((((((((((((........))))).)))))))))))..))).))))...................................................... (-15.31 = -15.25 +  -0.06)

alignment

secondary structure

dotplot

Window 4

Location	2,828,589 – 2,828,709
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.46
Mean single sequence MFE	-23.03
Consensus MFE	-17.61
Energy contribution	-17.18
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-2.27
Structure conservation index	0.76
SVM decision value	1.19
SVM RNA-class probability	0.928196
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2828589 120 - 22224390
UAAUGAGUAUAACAUUCAACUUCAAGUUUUAAUCUACAUAAUAGGCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUUAAUGCGUAUAUUUAUUUAUAACAUUCGAAUGGUAUACC
......(((((.(((((........((........)).......(.((((((((.(((((((((((.((((.(.....).)))).)))))))))))..))).))))))))))).))))). ( -24.80)
>DroSec_CAF1 216821 120 - 1
UAAUGAGUAUAACAUUCAACUUCAAGUUUUAAUCUACAUAAUAGCGAAUGUAUAUUAGAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAUUUGAAUUGUAUGCC
...(((((.....)))))..................((((....((((((((((.((((((((((((((((........))))).)))))))))))..))).))))))).....)))).. ( -26.30)
>DroSim_CAF1 189397 106 - 1
UAAUGAGUAUAACAUUCAACUUCAAGUUAUAAUCUACAUAAUAGCCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAU--------------
...(((((.....))))).......(((((((..(((((........)))))...((((((((((((((((........))))).))))))))))).)))))))..-------------- ( -23.40)
>DroEre_CAF1 236565 109 - 1
UAAUAAAUAUAACAUUCAACUUCAAGUUUUAAUCUACAUAAUAGGCAAUGUAUAUUAAAUGUGCGCUUUGCCGUUAUUCUUAAAUGCGCAUGUUUAUUUAUAACAU-----------ACU
..(((((((.(((..............((((((.(((((........))))).)))))).((((((...................)))))))))))))))).....-----------... ( -17.61)
>consensus
UAAUGAGUAUAACAUUCAACUUCAAGUUUUAAUCUACAUAAUAGCCAAUGUAUAUUAAAUGUGCGCUUUGGUGUAAUUCUUAAAUGCGCAUAUUUAUUUAUAACAU___________ACC
..(((((((....................((((.(((((........))))).))))((((((((((((((........))))).))))))))))))))))................... (-17.61 = -17.18 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:33 2006