Locus 4709

Sequence ID	2R_DroMel_CAF1
Location	15,417,810 – 15,417,906
Length	96
Max. P	0.938091

overview

Window 7

Location	15,417,810 – 15,417,906
Length	96
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	78.87
Mean single sequence MFE	-27.53
Consensus MFE	-12.94
Energy contribution	-13.30
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.82
Structure conservation index	0.47
SVM decision value	1.27
SVM RNA-class probability	0.938091
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15417810 96 + 20766785
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGACUUG--------GCAUUGGAACGAUUCGCGACGAUCCUGUCGCGU
...(((((((((((((.....((....(((((((((((......)))))).)))))))...))--------)))...))))))))(((((((....))))))). ( -28.10)
>DroVir_CAF1 302824 100 + 1
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGAUCUGACGAUCUGGCAUUAG--CGA--CGCGUCGCUCCUGGCGCGU
...(((((((.((((.......)))).(((((((((((......)))))).)))))......)))))))..((....)--).(--(((((((....)))))))) ( -29.30)
>DroPse_CAF1 261135 91 + 1
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGACUUC--------GCAUUGGGAC-----GCGACGAUCCUGGCGCGU
...(((((((.((((.((((((((...(((((((((((......)))))).))))).....))--------)))))).)))-----).)))))))......... ( -31.40)
>DroGri_CAF1 266114 92 + 1
AGCGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGAUCUCUGAAUC-GACGUUGC--UGA--CGCUUCGAUCCU-------
...(((((...(((((....(((((..(((((((((((......)))))).)))))((((......)))-)..)))))--)))--))...)))))..------- ( -26.30)
>DroMoj_CAF1 336454 89 + 1
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUCUCUAUAUGAAUUCACUUAACGAUCUGACGAUCUG-----------A--CGCGUUGCUCCUC--GGUU
...(((((....((...((((((....(((((((((.((.....)))))).))))).((((....))))..-----------.--))))))))....)--)))) ( -18.70)
>DroPer_CAF1 221875 91 + 1
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGACUUC--------GCAUUGGGAC-----GCGACGAUCCUGGCGCGU
...(((((((.((((.((((((((...(((((((((((......)))))).))))).....))--------)))))).)))-----).)))))))......... ( -31.40)
>consensus
AACGAUCGUUUUGUCAUAAUGCGACAUUUAAGGAAUUUUUAUAUGAAUUCACUUAACGACCUC________GCAUUGG__C_A__CGCGACGAUCCUGGCGCGU
...(((((...((((.......)))).(((((((((((......)))))).)))))..................................)))))......... (-12.94 = -13.30 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	15,417,810 – 15,417,906
Length	96
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	78.87
Mean single sequence MFE	-24.18
Consensus MFE	-12.84
Energy contribution	-13.20
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.25
Structure conservation index	0.53
SVM decision value	0.76
SVM RNA-class probability	0.843152
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15417810 96 - 20766785
ACGCGACAGGAUCGUCGCGAAUCGUUCCAAUGC--------CAAGUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
.((((((......)))))).((((((.......--------.......(((((.(((((........)))))))))).(((((.....))))).)))))).... ( -23.00)
>DroVir_CAF1 302824 100 - 1
ACGCGCCAGGAGCGACGCG--UCG--CUAAUGCCAGAUCGUCAGAUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
....(.((..(((((....--)))--))..)).).((((((.......(((((.(((((........)))))))))).(((((.....)))))..))))))... ( -25.40)
>DroPse_CAF1 261135 91 - 1
ACGCGCCAGGAUCGUCGC-----GUCCCAAUGC--------GAAGUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
.........((((((...-----(((..(((((--------((.....(((((.(((((........))))))))))...)))))))..)))...))))))... ( -26.40)
>DroGri_CAF1 266114 92 - 1
-------AGGAUCGAAGCG--UCA--GCAACGUC-GAUUCAGAGAUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGCU
-------.(((((((.((.--...--))....))-)))))((.((((((((((.(((((........))))))))...(((((.....))))).))))))).)) ( -25.40)
>DroMoj_CAF1 336454 89 - 1
AACC--GAGGAGCAACGCG--U-----------CAGAUCGUCAGAUCGUUAAGUGAAUUCAUAUAGAGAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
...(--((.((((...)).--)-----------)...)))...((((((((((.(((((........))))))))...(((((.....))))).)))))))... ( -18.50)
>DroPer_CAF1 221875 91 - 1
ACGCGCCAGGAUCGUCGC-----GUCCCAAUGC--------GAAGUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
.........((((((...-----(((..(((((--------((.....(((((.(((((........))))))))))...)))))))..)))...))))))... ( -26.40)
>consensus
ACGCGCCAGGAUCGACGCG__U_G__CCAAUGC________CAAAUCGUUAAGUGAAUUCAUAUAAAAAUUCCUUAAAUGUCGCAUUAUGACAAAACGAUCGUU
.........(((((..................................(((((.(((((........)))))))))).(((((.....)))))...)))))... (-12.84 = -13.20 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:21 2006