Locus 2973

Sequence ID	3R_DroMel_CAF1
Location	7,931,797 – 7,931,912
Length	115
Max. P	0.772958

overview

Window 7

Location	7,931,797 – 7,931,912
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.67
Mean single sequence MFE	-30.51
Consensus MFE	-17.50
Energy contribution	-19.75
Covariance contribution	2.25
Combinations/Pair	1.00
Mean z-score	-3.04
Structure conservation index	0.57
SVM decision value	0.49
SVM RNA-class probability	0.756486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931797 115 + 27905053
----ACAAAUAAAAGCAAAUUAAAUGCAGGACUCUGCAAAUGUUAAAUAUUUACAUAAGCACUUUUUGCAACUUGGUUGCAUUUUAUUUGAUUAACCAGGGCCACUUGGU-ACCUGGCGC
----.(((((((((((((......(((((((...(((..((((.........))))..)))..)))))))......)))).))))))))).....((((((((....)))-.)))))... ( -33.30)
>DroSim_CAF1 65448 116 + 1
----ACAAAUAAAAGCAAAUUAAAUGCAGGACAUUGCAAAUGGUAAAUAUUUGCAUAAGCACUUUUUGCAACUUGGUUGCAUUUUAUUUGAUUAACCAGAGCCACUUGGUUAGCUGGCGC
----.(((((((((((((......(((((((...((((((((.....))))))))........)))))))......)))).))))))))).....((((.(((....)))...))))... ( -31.40)
>DroEre_CAF1 64298 115 + 1
----GCAAAUAAAAGCAAAUUUAAUGCAGUACUCCACAAAUGUUGCAUGUUUACACUAACACUUUUUGCAACUCGGCUGCAUUUUAUUUGAUUAAACAUAGCCACUUGGU-GCCAGGCGC
----((.........(((((..((((((((...........((((((((((......)))).....))))))...))))))))..)))))..........(((...((..-..))))))) ( -26.04)
>DroYak_CAF1 65712 119 + 1
AAAUACAAAUAAAAGCAAAUUUAAUGCAGGACUCUGCAAAUGUUGUAUAUUUACAUAAACACUUUUUGCCACUUGGUUGCAUUUUAUUUGAUUAAACGCAGCCACUUGGU-GGCAGGCGC
..............((........(((((....)))))..(((((((....))))...)))....(((((((((((((((..((((......)))).)))))))...)))-))))))).. ( -31.30)
>consensus
____ACAAAUAAAAGCAAAUUAAAUGCAGGACUCUGCAAAUGUUAAAUAUUUACAUAAACACUUUUUGCAACUUGGUUGCAUUUUAUUUGAUUAAACAGAGCCACUUGGU_ACCAGGCGC
.....(((((((((((((......(((((((...(((..((((.........))))..)))..)))))))......)))).)))))))))..........(((............))).. (-17.50 = -19.75 +   2.25)

alignment

secondary structure

dotplot

Window 8

Location	7,931,797 – 7,931,912
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.67
Mean single sequence MFE	-28.30
Consensus MFE	-18.95
Energy contribution	-18.45
Covariance contribution	-0.50
Combinations/Pair	1.19
Mean z-score	-2.05
Structure conservation index	0.67
SVM decision value	0.53
SVM RNA-class probability	0.772958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7931797 115 - 27905053
GCGCCAGGU-ACCAAGUGGCCCUGGUUAAUCAAAUAAAAUGCAACCAAGUUGCAAAAAGUGCUUAUGUAAAUAUUUAACAUUUGCAGAGUCCUGCAUUUAAUUUGCUUUUAUUUGU----
..((((((.-.((....)).))))))....(((((((((((((((...))))))...((..(((.(((((((.......))))))))))..))(((.......)))))))))))).---- ( -30.20)
>DroSim_CAF1 65448 116 - 1
GCGCCAGCUAACCAAGUGGCUCUGGUUAAUCAAAUAAAAUGCAACCAAGUUGCAAAAAGUGCUUAUGCAAAUAUUUACCAUUUGCAAUGUCCUGCAUUUAAUUUGCUUUUAUUUGU----
..(((((....((....))..)))))....(((((.(((((((.....((((((((..(((..(((....)))..)))..))))))))....))))))).)))))...........---- ( -27.30)
>DroEre_CAF1 64298 115 - 1
GCGCCUGGC-ACCAAGUGGCUAUGUUUAAUCAAAUAAAAUGCAGCCGAGUUGCAAAAAGUGUUAGUGUAAACAUGCAACAUUUGUGGAGUACUGCAUUAAAUUUGCUUUUAUUUGC----
.(((.((..-..)).)))((...((..((.(((((..(((((((.....(..(((...(((((.(((....)))..))))))))..)....)))))))..))))).))..))..))---- ( -24.00)
>DroYak_CAF1 65712 119 - 1
GCGCCUGCC-ACCAAGUGGCUGCGUUUAAUCAAAUAAAAUGCAACCAAGUGGCAAAAAGUGUUUAUGUAAAUAUACAACAUUUGCAGAGUCCUGCAUUAAAUUUGCUUUUAUUUGUAUUU
((((..(((-((...))))).))))...........((((((((......(((((((((((((((((....)))).)))))))((((....))))......)))))).....)))))))) ( -31.70)
>consensus
GCGCCAGCC_ACCAAGUGGCUCUGGUUAAUCAAAUAAAAUGCAACCAAGUUGCAAAAAGUGCUUAUGUAAAUAUUCAACAUUUGCAGAGUCCUGCAUUAAAUUUGCUUUUAUUUGU____
..(((............)))..........(((((((((.((((......((((.....(((..((((.........))))..)))......))))......)))))))))))))..... (-18.95 = -18.45 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:12 2006