Locus 3986

Sequence ID	2R_DroMel_CAF1
Location	13,183,816 – 13,183,908
Length	92
Max. P	0.984189

overview

Window 4

Location	13,183,816 – 13,183,908
Length	92
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	76.68
Mean single sequence MFE	-39.28
Consensus MFE	-29.14
Energy contribution	-28.32
Covariance contribution	-0.83
Combinations/Pair	1.41
Mean z-score	-3.86
Structure conservation index	0.74
SVM decision value	1.97
SVM RNA-class probability	0.984189
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13183816 92 + 20766785
UUAA-AAUGGAAUGGCCAUGGACAACACGUUGGGUCACAUGCUUUCAGGCCUCCGAUUC-----GGUUUCAGGC-----UGGGUCGGAGGUCUGUUUUUAUCA--
....-.(((((((((((...(((.....))).)))))........((((((((((((((-----(((.....))-----))))))))))))))).))))))..-- ( -36.40)
>DroPse_CAF1 80454 104 + 1
UUAA-AAUGGAAUGGUCAUGGACAACUCUUGGUGUUAGCUGCAGCCAGGCCUCCGACUCAGCUCAGUUCCCGACAGAGCAGAGUCGGAGGUCUGCUUUAAUCCGC
....-...(((...((....((((.(....).))))....))(((.(((((((((((((.((((.(((...))).)))).))))))))))))))))....))).. ( -41.30)
>DroEre_CAF1 78931 94 + 1
UUAA-AAUGGAAUGGCCAUGGACAACACGUUGGGUCAAAUGCUGUCAGGCCUCCGAUUC-----GGUUUCCGAC-----UGGGUCGGAGGUCUAUUUUUAUCAUU
....-(((((..(((((...(((.....))).))))).........(((((((((((((-----((((...)))-----)))))))))))))).......))))) ( -35.20)
>DroYak_CAF1 79909 94 + 1
UUAA-AAUGGAAUGGCCAUGGACAACAAGUUGGGUCAAAUGCUGUCAGGCCUCCGAUUC-----GGUUCCCGAC-----UGGGUCGGAGGUCUGUUUUUAUCAUC
....-.((((..(((((...(((.....))).)))))........((((((((((((((-----((((...)))-----)))))))))))))))......)))). ( -36.70)
>DroAna_CAF1 76557 95 + 1
UUAAAAAUGGGAAGGCCAUGGACAAUUGCAGGGGUUACGUGUAGUCAGACCUCCGAUUU-----GGUUCCUGAC-----UGGAUCGGAGGUCUGGUUCCAUUAUC
.....(((((((............((((((.(.....).))))))(((((((((((((.-----.(((...)))-----..))))))))))))).)))))))... ( -41.20)
>DroPer_CAF1 74519 104 + 1
UUAA-AAUGGAAUGGUCAUGGACAACUCUUGGUGUUAGCUGCAGCCAGGCCUCCGACUCAGUUCAGUUCCCGACAGAGCUGAGUCGGAGGUCUGCUUUAAUCCAC
....-..((((...((....((((.(....).))))....))(((.((((((((((((((((((.(((...))).)))))))))))))))))))))....)))). ( -44.90)
>consensus
UUAA_AAUGGAAUGGCCAUGGACAACACGUGGGGUCAAAUGCAGUCAGGCCUCCGAUUC_____GGUUCCCGAC_____UGGGUCGGAGGUCUGUUUUUAUCAUC
......((((((..((....(((..........)))....))...((((((((((((((.((((.(((...))).)))).)))))))))))))).)))))).... (-29.14 = -28.32 +  -0.83)

alignment

secondary structure

dotplot

Window 5

Location	13,183,816 – 13,183,908
Length	92
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.68
Mean single sequence MFE	-30.65
Consensus MFE	-14.10
Energy contribution	-15.13
Covariance contribution	1.03
Combinations/Pair	1.06
Mean z-score	-2.57
Structure conservation index	0.46
SVM decision value	1.47
SVM RNA-class probability	0.956550
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13183816 92 - 20766785
--UGAUAAAAACAGACCUCCGACCCA-----GCCUGAAACC-----GAAUCGGAGGCCUGAAAGCAUGUGACCCAACGUGUUGUCCAUGGCCAUUCCAUU-UUAA
--.(((.....(((.(((((((..(.-----..........-----)..))))))).)))..(((((((......)))))))))).((((.....)))).-.... ( -23.00)
>DroPse_CAF1 80454 104 - 1
GCGGAUUAAAGCAGACCUCCGACUCUGCUCUGUCGGGAACUGAGCUGAGUCGGAGGCCUGGCUGCAGCUAACACCAAGAGUUGUCCAUGACCAUUCCAUU-UUAA
..(((....(((((.((((((((((.((((.((.....)).)))).)))))))))).)).)))((((((.........))))))..........)))...-.... ( -39.70)
>DroEre_CAF1 78931 94 - 1
AAUGAUAAAAAUAGACCUCCGACCCA-----GUCGGAAACC-----GAAUCGGAGGCCUGACAGCAUUUGACCCAACGUGUUGUCCAUGGCCAUUCCAUU-UUAA
.....(((((.......((((((...-----))))))....-----.....(((((((.((((((((.(......).))))))))...))))..))).))-))). ( -28.00)
>DroYak_CAF1 79909 94 - 1
GAUGAUAAAAACAGACCUCCGACCCA-----GUCGGGAACC-----GAAUCGGAGGCCUGACAGCAUUUGACCCAACUUGUUGUCCAUGGCCAUUCCAUU-UUAA
((((.............(((((....-----.((((...))-----)).)))))((((.(((((((..(......)..)))))))...))))....))))-.... ( -26.30)
>DroAna_CAF1 76557 95 - 1
GAUAAUGGAACCAGACCUCCGAUCCA-----GUCAGGAACC-----AAAUCGGAGGUCUGACUACACGUAACCCCUGCAAUUGUCCAUGGCCUUCCCAUUUUUAA
....(((((..((((((((((((((.-----....)))...-----...))))))))))).......(((.....))).....)))))((.....))........ ( -28.10)
>DroPer_CAF1 74519 104 - 1
GUGGAUUAAAGCAGACCUCCGACUCAGCUCUGUCGGGAACUGAACUGAGUCGGAGGCCUGGCUGCAGCUAACACCAAGAGUUGUCCAUGACCAUUCCAUU-UUAA
(((((....(((((.((((((((((((.((.((.....)).)).)))))))))))).)).)))((((((.........))))))..........))))).-.... ( -38.80)
>consensus
GAUGAUAAAAACAGACCUCCGACCCA_____GUCGGGAACC_____GAAUCGGAGGCCUGACAGCAUCUAACCCAACGAGUUGUCCAUGGCCAUUCCAUU_UUAA
...........(((.(((((((..(.((((.((.....)).)))).)..))))))).)))............................................. (-14.10 = -15.13 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:01 2006