Locus 1493

Sequence ID	X_DroMel_CAF1
Location	4,423,730 – 4,423,874
Length	144
Max. P	0.842564

overview

Window 8

Location	4,423,730 – 4,423,834
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.79
Mean single sequence MFE	-35.88
Consensus MFE	-27.50
Energy contribution	-27.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.77
SVM decision value	0.76
SVM RNA-class probability	0.842564
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423730 104 - 22224390
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCAGACUGUAACCGAUCACGUUCCCACUGGG---GGAUGUGGGAUA--------CAGGGACAUGGGAU-----
..........(((((((((.....))))).))))...........((((...(((((.((...(((((((((....))---))))))))).))--------))).).))).....----- ( -35.50)
>DroSec_CAF1 26133 113 - 1
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCAGACUGUAACCGAUCACGUUCCCACUGGG--GGGAUGUGGGAUACAGGGAUACAGGGACAUGGGAU-----
..........(((((((((.....))))).))))...........((((...(((((.((..((((((((((.....)--)))))))))......))..))))).).))).....----- ( -36.70)
>DroSim_CAF1 27459 113 - 1
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCAGACUGUAACCGAUCACGUUCCCACUGGG--GGGAUGUGGGAUACAGGGAUACAGGGACAUGGGAU-----
..........(((((((((.....))))).))))...........((((...(((((.((..((((((((((.....)--)))))))))......))..))))).).))).....----- ( -36.70)
>DroEre_CAF1 27081 117 - 1
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCGGACUGUAACCGAUCACUUUCCCACUGG---GGGAUGUGGGACACAGGGAUACAGGGAUGUGGGAUGAACG
..........(((((((((.....))))).)))).......((...((((..(((((.((..((((.(((((....)---)))).))))......))..)))))...))))...)).... ( -34.50)
>DroYak_CAF1 26718 101 - 1
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCAGACUGUAACCGAUCACGUUCCCACCUGGGUGGGAUGUGGGAUACAGGAAUA-------------------
..........(((((((((.....))))).))))..................(((((.((...(((((.(((((....)))))))))))).))))).....------------------- ( -36.00)
>consensus
GAAACAAUUAGGCACCUGACUUCCUCAGGAUGCCAAAUAAACGGGAUGCAGACUGUAACCGAUCACGUUCCCACUGGG__GGGAUGUGGGAUACAGGGAUACAGGGACAUGGGAU_____
((........(((((((((.....))))).)))).......(((..(((.....))).))).))....((((((...........))))))............................. (-27.50 = -27.50 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	4,423,756 – 4,423,874
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.43
Mean single sequence MFE	-31.98
Consensus MFE	-27.52
Energy contribution	-27.56
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.31
Structure conservation index	0.86
SVM decision value	0.25
SVM RNA-class probability	0.653718
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423756 118 + 22224390
--CCCAGUGGGAACGUGAUCGGUUACAGUCUGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCUGCAACCCCUGCUCCUAUUGAUUUCUUCCC
--..((((((((..((((((((..(((((..((.....))......((((.(((((.....)))))))))..)))))..)))..)))))..(((.....))))))))))).......... ( -33.40)
>DroSec_CAF1 26168 116 + 1
--CCCAGUGGGAACGUGAUCGGUUACAGUCUGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCCGCAACCCCUGCUCCUAUUGAUUUCUUC--
--..((((((((..((((((((..(((((..((.....))......((((.(((((.....)))))))))..)))))..)))..)))))..(((.....)))))))))))........-- ( -33.70)
>DroSim_CAF1 27494 116 + 1
--CCCAGUGGGAACGUGAUCGGUUACAGUCUGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCUGCAACCCCUGCUCCUAUUGAUUUCUUC--
--..((((((((..((((((((..(((((..((.....))......((((.(((((.....)))))))))..)))))..)))..)))))..(((.....)))))))))))........-- ( -33.40)
>DroEre_CAF1 27121 115 + 1
---CCAGUGGGAAAGUGAUCGGUUACAGUCCGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCUCCAACCCCUGCU--UAUUGAUUUCUUCCC
---.(((.(((..(((((((((..(((((.((.....)).......((((.(((((.....)))))))))..)))))..)))..)))).))....))))))..--............... ( -28.40)
>DroYak_CAF1 26739 118 + 1
ACCCAGGUGGGAACGUGAUCGGUUACAGUCUGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCUCCAACCCCUGCU--UAUUGAUUUCUUUCC
.....((((((((((.((((((.......))).))).)........((((.(((((.....))))))))).....)))))))))...................--............... ( -31.00)
>consensus
__CCCAGUGGGAACGUGAUCGGUUACAGUCUGCAUCCCGUUUAUUUGGCAUCCUGAGGAAGUCAGGUGCCUAAUUGUUUCCGCCAUCAUCUGCAACCCCUGCUCCUAUUGAUUUCUUCCC
....(((.(((...((((((((..(((((..((.....))......((((.(((((.....)))))))))..)))))..)))..)))))......))))))................... (-27.52 = -27.56 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:00 2006