Locus 456

Sequence ID	3L_DroMel_CAF1
Location	1,331,049 – 1,331,196
Length	147
Max. P	0.956167

overview

Window 3

Location	1,331,049 – 1,331,156
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.65
Mean single sequence MFE	-31.30
Consensus MFE	-22.70
Energy contribution	-23.18
Covariance contribution	0.48
Combinations/Pair	1.24
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.52
SVM RNA-class probability	0.766682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1331049 107 + 23771897
--GGUUACCCA-----------UCAGCUCGCGUUGAUUGCAGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACAAUGAAUCAGCUGCAAAUUCUGCAGCUGACCUGUUA
--((....)).-----------.(((.....(((((..(((...((((...((((.....))))....))))...))).)))))......(((((((((.....))))))))).)))... ( -29.80)
>DroSec_CAF1 3153 109 + 1
GCGAUUUAAUA-----------GCGGCUUGCGUUGAUUGCAGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACCAUGAAUCAGCUGCAAAUUCUGCAGCCGAGAUGUUA
......(((((-----------.(((((.(((..(.((((((((((((...((((.....))))....))))(((((.......)))))...)))))))).)..))))))))...))))) ( -32.40)
>DroSim_CAF1 3154 109 + 1
GCGAUUUAGUA-----------UCAGCUUGCGUUGAUUGCAGCUCGAAAAUUAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACCAUGAAUCAGCUGCAAAUUCUGCAGCCGAGAUGUUA
((((((.....-----------((((((.(((.....))))))).)).....)))))).....(((......(((((.......))))).((.((((((.....)))))).))))).... ( -25.90)
>DroEre_CAF1 3133 116 + 1
GCGAUUUAAUAUGGUCAUCAGCUAAGCUUGCGUUGAUUGCAGCUCGAAAAUCAGUUG----UUGUCAGUUCGUCAUGUUUCAAAAAUGAAUCAGCUGCACGUUCUGCAGCCGAGCUGCUU
..((((......))))((((((.........)))))).((((((((....(((.(((----....((........))...)))...)))....((((((.....)))))))))))))).. ( -32.40)
>DroYak_CAF1 3273 116 + 1
GCGAUUUAAUAUGGUUAGCCA-UCAGCUUGCGUUGAUUGCAGCUCGAGAAUCAGUUA---AAUGGCAGUUCGUCAUGUUUUAAAAAUGAAUCAGCUGCAAAUUAUGCAGUCGAGCUGCUA
...........(((....)))-(((((....)))))..(((((((((((.(((.(((---((((((.....)))))...))))...))).))..(((((.....)))))))))))))).. ( -36.00)
>consensus
GCGAUUUAAUA___________UCAGCUUGCGUUGAUUGCAGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACAAUGAAUCAGCUGCAAAUUCUGCAGCCGAGCUGUUA
.......................(((((((.(((((..(((...((((...((((.....))))....))))...))).))))).........((((((.....)))))))))))))... (-22.70 = -23.18 +   0.48)

alignment

secondary structure

dotplot

Window 4

Location	1,331,049 – 1,331,156
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.65
Mean single sequence MFE	-29.89
Consensus MFE	-20.11
Energy contribution	-20.83
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.67
SVM decision value	1.46
SVM RNA-class probability	0.956167
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1331049 107 - 23771897
UAACAGGUCAGCUGCAGAAUUUGCAGCUGAUUCAUUGUUGAAACAUGACGAACUGACAAUUAACAACUGAUUUUCGAGCUGCAAUCAACGCGAGCUGA-----------UGGGUAACC--
..((..(((((((((.....((((((((((.((((((((((..................))))))).)))...)).)))))))).....)).))))))-----------)..))....-- ( -32.47)
>DroSec_CAF1 3153 109 - 1
UAACAUCUCGGCUGCAGAAUUUGCAGCUGAUUCAUGGUUGAAACAUGACGAACUGACAAUUAACAACUGAUUUUCGAGCUGCAAUCAACGCAAGCCGC-----------UAUUAAAUCGC
........(((((((.....((((((((...(((((.......))))).....(((.(((((.....))))).))))))))))).....)).))))).-----------........... ( -29.10)
>DroSim_CAF1 3154 109 - 1
UAACAUCUCGGCUGCAGAAUUUGCAGCUGAUUCAUGGUUGAAACAUGACGAACUGACAAUUAACAACUAAUUUUCGAGCUGCAAUCAACGCAAGCUGA-----------UACUAAAUCGC
.......((((((((.....((((((((...(((((.......))))).....(((.(((((.....))))).))))))))))).....)).))))))-----------........... ( -28.90)
>DroEre_CAF1 3133 116 - 1
AAGCAGCUCGGCUGCAGAACGUGCAGCUGAUUCAUUUUUGAAACAUGACGAACUGACAA----CAACUGAUUUUCGAGCUGCAAUCAACGCAAGCUUAGCUGAUGACCAUAUUAAAUCGC
...(((((.((((((......(((((((..((((....))))......((((....((.----....))...)))))))))))......)).)))).))))).................. ( -29.90)
>DroYak_CAF1 3273 116 - 1
UAGCAGCUCGACUGCAUAAUUUGCAGCUGAUUCAUUUUUAAAACAUGACGAACUGCCAUU---UAACUGAUUCUCGAGCUGCAAUCAACGCAAGCUGA-UGGCUAACCAUAUUAAAUCGC
..((((((((((((((.....)))))..((.(((.((......((........)).....---.)).))).))))))))))).((((.(....).)))-)((....))............ ( -29.10)
>consensus
UAACAGCUCGGCUGCAGAAUUUGCAGCUGAUUCAUUGUUGAAACAUGACGAACUGACAAUUAACAACUGAUUUUCGAGCUGCAAUCAACGCAAGCUGA___________UAUUAAAUCGC
.......((((((((.....((((((((..((((....))))......((((....................)))))))))))).....))).)))))...................... (-20.11 = -20.83 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	1,331,076 – 1,331,196
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.39
Mean single sequence MFE	-26.66
Consensus MFE	-22.18
Energy contribution	-23.14
Covariance contribution	0.96
Combinations/Pair	1.13
Mean z-score	-1.74
Structure conservation index	0.83
SVM decision value	0.88
SVM RNA-class probability	0.873660
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1331076 120 + 23771897
AGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACAAUGAAUCAGCUGCAAAUUCUGCAGCUGACCUGUUAUGAAAUAACUUUAAAGAGUCAUAUUUUUACGUAAUCUCCA
.(((((((...((((.....))))....)))....(((((((..((((..(((((((((.....)))))))))..)))).)))))))........))))..................... ( -26.50)
>DroSec_CAF1 3182 120 + 1
AGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACCAUGAAUCAGCUGCAAAUUCUGCAGCCGAGAUGUUAUGAAAUAACUUCAAAGAGUCAUAUUCUUACGUAAUCUCCA
.((((.......(((((((.....(((...((((....((((....))))((.((((((.....)))))).))))))...)))))))))).....))))..................... ( -24.20)
>DroSim_CAF1 3183 120 + 1
AGCUCGAAAAUUAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACCAUGAAUCAGCUGCAAAUUCUGCAGCCGAGAUGUUAUGAAAUAACUUCAAAGAGUCAUAUUCUUACGUAAUCUCCA
.((((.......(((((((.....(((...((((....((((....))))((.((((((.....)))))).))))))...)))))))))).....))))..................... ( -24.90)
>DroEre_CAF1 3173 114 + 1
AGCUCGAAAAUCAGUUG----UUGUCAGUUCGUCAUGUUUCAAAAAUGAAUCAGCUGCACGUUCUGCAGCCGAGCUGCUUUUAAAUAACUUC--AGAGUCAUAUUCUUACGCAAUCUCCA
.((((((.....(((((----((..(((((((...((.((((....)))).))((((((.....)))))))))))))......)))))))))--.))))..................... ( -26.40)
>DroYak_CAF1 3312 117 + 1
AGCUCGAGAAUCAGUUA---AAUGGCAGUUCGUCAUGUUUUAAAAAUGAAUCAGCUGCAAAUUAUGCAGUCGAGCUGCUAUGAAAUAACAUUGAGGAGUCAUAAUCUUACGUAAUCUCCA
.....((((....((((---.(((((((((((((((.........))))....((((((.....)))))))))))))))))....))))....((((.......))))......)))).. ( -31.30)
>consensus
AGCUCGAAAAUCAGUUGUUAAUUGUCAGUUCGUCAUGUUUCAACAAUGAAUCAGCUGCAAAUUCUGCAGCCGAGCUGUUAUGAAAUAACUUCAAAGAGUCAUAUUCUUACGUAAUCUCCA
.((((.......(((((((......(((((((...((.((((....)))).))((((((.....)))))))))))))......))))))).....))))..................... (-22.18 = -23.14 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:15 2006