Locus 4237

Sequence ID	3R_DroMel_CAF1
Location	11,375,579 – 11,375,739
Length	160
Max. P	0.953588

overview

Window 9

Location	11,375,579 – 11,375,699
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.33
Mean single sequence MFE	-37.53
Consensus MFE	-35.28
Energy contribution	-35.16
Covariance contribution	-0.12
Combinations/Pair	1.11
Mean z-score	-1.43
Structure conservation index	0.94
SVM decision value	1.37
SVM RNA-class probability	0.947104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11375579 120 - 27905053
UACGAGGACGCUGGCUGGAACACGAACGAGAGUCCUGUGCAAGGACACUCCACUUUCACAGCAGCCAACUGCUAUGAAUUCACCGAUAGCAACUUCAAGCUGAGUGGUCAUGCUGUUCUU
...((((((((((((............(((.(((((.....))))).)))((((((((.(((((....))))).))))........((((........)))))))))))).)).)))))) ( -37.80)
>DroSec_CAF1 123217 120 - 1
UACGAGGACGCUGGCUGGAACACUAACGAGAGUCCUGUGCAAGGACACUCCACUUUCACAGCAGCCAACUGCUAUGAAUUCACCGAUAGCAACUUCAAGCUGAGUGGUCAUGCUGUGCUU
...((((..((((..(((.........(((.(((((.....))))).)))....((((.(((((....))))).))))....))).))))..))))((((..(((......)))..)))) ( -37.40)
>DroSim_CAF1 114221 120 - 1
UAUGAGGACGCUGGCUGGAACACGAAUGAGAGUCCUGUGCAAGGACACUCCACUUUCACAGCUGCCAACUGCUAUGAAUUCACCGAUAGCAACUUCAAGCUAAGUGGUCAUGCUGUUCUU
...((((((((((((............(((.(((((.....))))).)))(((((....((((......((((((..........))))))......))))))))))))).)).)))))) ( -34.90)
>DroEre_CAF1 110774 120 - 1
UACGAGGACGCUGGCUGGAACGCGAACGAGAGUCCUGUGCAAGGACACUCCACGUUCACAGCAGCCAACUGUUAUGAAUUCACCGAUAGUAACUUCAAGCUGAGUGGUCAUGCUGUUCUU
...((((((((((.((((((((.(...(((.(((((.....))))).)))).))))).)))))))..((((((.((....))..)))))).......((((((....))).))))))))) ( -39.20)
>DroYak_CAF1 113316 120 - 1
UACGAGGACGCUGGCUGGAACACGAACGAGAGUCCUGUGCAAGGACACUCCACGUUCACAGCAGCCAACUGCUACGAAUUCACCGAUAGUAACUUCAAGCUGAGUGGCCAUGCAGUUCUU
...(((((((((((((.......(((((((.(((((.....))))).)))...)))).((((.......(((((((.......)).))))).......))))...))))).)).)))))) ( -38.34)
>consensus
UACGAGGACGCUGGCUGGAACACGAACGAGAGUCCUGUGCAAGGACACUCCACUUUCACAGCAGCCAACUGCUAUGAAUUCACCGAUAGCAACUUCAAGCUGAGUGGUCAUGCUGUUCUU
...(((((((((((((((.........(((.(((((.....))))).)))....((((.(((((....))))).))))....))..((((........))))...))))).)).)))))) (-35.28 = -35.16 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	11,375,619 – 11,375,739
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.92
Mean single sequence MFE	-43.26
Consensus MFE	-37.90
Energy contribution	-38.74
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.88
SVM decision value	1.43
SVM RNA-class probability	0.953588
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11375619 120 + 27905053
AAUUCAUAGCAGUUGGCUGCUGUGAAAGUGGAGUGUCCUUGCACAGGACUCUCGUUCGUGUUCCAGCCAGCGUCCUCGUAAAAAUCGUUGGACAGCCCGACGAUCCUGCCACUGGUCUUC
..((((((((((....))))))))))(((((.((((....))))(((((.((.(((.(....).))).)).))))).......((((((((.....))))))))....)))))....... ( -43.00)
>DroSec_CAF1 123257 120 + 1
AAUUCAUAGCAGUUGGCUGCUGUGAAAGUGGAGUGUCCUUGCACAGGACUCUCGUUAGUGUUCCAGCCAGCGUCCUCGUAGAAGUCGUUGGACAGCCCGACGAUCCUGCCACUGGUCUUC
..((((((((((....))))))))))(((((((.(((((.....))))).)))(((.((......)).)))......((((..((((((((.....)))))))).))))))))....... ( -45.00)
>DroSim_CAF1 114261 120 + 1
AAUUCAUAGCAGUUGGCAGCUGUGAAAGUGGAGUGUCCUUGCACAGGACUCUCAUUCGUGUUCCAGCCAGCGUCCUCAUAGAAGUCGUUGGACAGCCCGACGAUCCUGCCACUGGUCUUC
.........((((.(((((((((((.....(((.(((((.....))))).)))...(((..........)))...))))))..((((((((.....)))))))).)))))))))...... ( -40.40)
>DroEre_CAF1 110814 120 + 1
AAUUCAUAACAGUUGGCUGCUGUGAACGUGGAGUGUCCUUGCACAGGACUCUCGUUCGCGUUCCAGCCAGCGUCCUCGUAGAAGUCGUUGGACAGCCCGACGAUCCUGCCACUGGUCUUC
...........((((((((....((((((((((.(((((.....))))).)))...)))))))))))))))(.((..((((..((((((((.....)))))))).))))....)).)... ( -48.30)
>DroYak_CAF1 113356 120 + 1
AAUUCGUAGCAGUUGGCUGCUGUGAACGUGGAGUGUCCUUGCACAGGACUCUCGUUCGUGUUCCAGCCAGCGUCCUCGUAGAAUUCGUUGGACAGCCCGACAAUCCUGCCACUGGUCUUC
...........((((((((....((((((((((.(((((.....))))).)))...)))))))))))))))(.((..((((.(((.(((((.....)))))))).))))....)).)... ( -39.60)
>consensus
AAUUCAUAGCAGUUGGCUGCUGUGAAAGUGGAGUGUCCUUGCACAGGACUCUCGUUCGUGUUCCAGCCAGCGUCCUCGUAGAAGUCGUUGGACAGCCCGACGAUCCUGCCACUGGUCUUC
..((((((((((....))))))))))....(((.(((((.....))))).)))............(((((.(.....((((...(((((((.....)))))))..))))).))))).... (-37.90 = -38.74 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:03 2006