Locus 5706

Sequence ID	2L_DroMel_CAF1
Location	16,235,715 – 16,235,913
Length	198
Max. P	0.913770

overview

Window 1

Location	16,235,715 – 16,235,818
Length	103
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.43
Mean single sequence MFE	-30.02
Consensus MFE	-24.79
Energy contribution	-24.65
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.83
SVM decision value	1.09
SVM RNA-class probability	0.913770
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16235715 103 - 22407834
AAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAAACCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAA----GAAG-UAAAUAUUAGUAU--U
....((((..((.((((((...((....))..........(((....)))..))))))..((((.(........).)))).....----)).)-)))..........--. ( -26.30)
>DroVir_CAF1 219197 98 - 1
AAAAGUAUGGUCAGCGGCAGCAGCUGAAGCGUCAGGCCCAGCCGUGAGGCGUUGCCGCAAUAGGUGAACAGUUCCUCCUAAAAAA---AACA--------UUUAUGA-AU
..........(((((((((((..((((....)))).....(((....)))))))))))..((((.(........).)))).....---....--------....)))-.. ( -32.50)
>DroGri_CAF1 166454 105 - 1
AAAAUAAUGGUCAGCGGCAGCAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGAACAGUUCCUCCUACAACA---AAAAGGGUGUC-AUUAUCA-UU
...(((((((.(((((((((..((....))..........(((....))).)))))))..((((.(........).)))).....---.......))))-)))))..-.. ( -29.70)
>DroEre_CAF1 156815 102 - 1
AAAAUUAUGGUCAGCGGCAUUAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAAUAA----AAAU-GAAUCGA-GUUAA--U
..((((....(((((((((...((....))..........(((....)))..))))))..((((.(........).)))).....----...)-))....)-)))..--. ( -26.70)
>DroMoj_CAF1 251255 102 - 1
AAAAUUAUGGUCAGCGGCAGCAGCUGAAGCGUCAGACCCAGCCGCGAGGCAUUGCCGCAGUAGGUGAAAAGUUCCUCCUGAAAAAACAAACA--------UUCGUAAGAU
....((((((...(((((((...((((....)))).....(((....))).)))))))..((((.(........).))))............--------.))))))... ( -29.00)
>DroPer_CAF1 231332 103 - 1
AAAAUUAUGGUCAGCGGCAGCAGCUGGAGCGUCAGACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGUACAGUUCCUCCUAAGGAC----GAGG-GACAGAUGAGUAU--C
......(((.((((((((((....(((..(....)..)))(((....))).)))))))............(((((((........----))))-)))...))).)))--. ( -35.90)
>consensus
AAAAUUAUGGUCAGCGGCAGCAGCUGAAGCGUCAAACCCAGCCGCGAGGCAUUGCCGCAAUAGGUGAACAGUUCCUCCUAAAAAA____AAAG_GA____UUAGUAA__U
.............((((((...((....))..........(((....)))..))))))..((((.(........).)))).............................. (-24.79 = -24.65 +  -0.14)

alignment

secondary structure

dotplot

Window 2

Location	16,235,778 – 16,235,883
Length	105
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	83.48
Mean single sequence MFE	-27.13
Consensus MFE	-17.95
Energy contribution	-18.57
Covariance contribution	0.61
Combinations/Pair	1.19
Mean z-score	-2.34
Structure conservation index	0.66
SVM decision value	0.20
SVM RNA-class probability	0.631833
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16235778 105 + 22407834
UGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU------ACAAUGUACACAGAACUAUACAUUAUACA
((((((((((((((((((.......)))))..........)))))..(((((((((((........))))))))))------).........))))))))........... ( -31.10)
>DroPse_CAF1 222404 104 + 1
UGGGUCUGACGCUCCAGCUGCUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGAUUAUACUAGUAUAUACACACAACUAUAU-----A--
..((((((((((...(((.((.((.......((......))..(((......))))))).)))....)))))))))).......((((((........)))))-----)-- ( -21.80)
>DroSec_CAF1 153110 105 + 1
UGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU------ACAAUGUACACAGAACUAUACAUUAUACA
((((((((((((((((((.......)))))..........)))))..(((((((((((........))))))))))------).........))))))))........... ( -31.10)
>DroSim_CAF1 155180 105 + 1
UGGUUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU------ACAAUGUACACAGAACUAUACAUUAUACA
((((((((((((((((((.......)))))..........)))))..(((((((((((........))))))))))------).........))))))))........... ( -31.10)
>DroYak_CAF1 165753 104 + 1
UGGGUUUGACGCUUCAGCUGAUGCCGCUGACCAUAAUUUUAGUGUUUCACCUGACGUACACCUUUAUGCGUUAGGU------AUAAUGCACA-AAAACUAUACAUUAUAAA
.(..((((.....(((((.......)))))...........(((((..((((((((((........))))))))))------..))))).))-))..)............. ( -25.90)
>DroPer_CAF1 231395 104 + 1
UGGGUCUGACGCUCCAGCUGCUGCCGCUGACCAUAAUUUUGAUGUUUUACUUGACGCGCUGCUUUAUGCGUUAGAUUAUACUAGUAUAUACACACAACUAUAU-----A--
..((((((((((...(((.((.((.......((......))..(((......))))))).)))....)))))))))).......((((((........)))))-----)-- ( -21.80)
>consensus
UGGGUUUGACGCUUCAGCUAAUGCCGCUGACCAUAAUUUUAGUGUUUUACCUGACGCACAGCUUUAUGCGUUAGGU______ACAAUGUACACAGAACUAUACAUUAUACA
(((.((((((((((((((.......)))))..........)))))...((((((((((........))))))))))................)))).)))........... (-17.95 = -18.57 +   0.61)

alignment

secondary structure

dotplot

Window 3

Location	16,235,818 – 16,235,913
Length	95
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.32
Mean single sequence MFE	-22.75
Consensus MFE	-12.35
Energy contribution	-12.77
Covariance contribution	0.42
Combinations/Pair	1.16
Mean z-score	-1.68
Structure conservation index	0.54
SVM decision value	0.07
SVM RNA-class probability	0.569791
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16235818 95 - 22407834
CGAUCGUAGUCG----------CGUAUAGUACAUAAUAGUUGUAUAAUGUAUAGUUCUGUGUACAUUGU------ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACU
((((....))))----------......(((((.......)))))((((((((......)))))))).(------((((.(((((((....))))))).)))))....... ( -24.20)
>DroPse_CAF1 222444 103 - 1
CCAUCAACGUCGUUCGCAUACUCGUAUAGUACAUAAUUG---U-----AUAUAGUUGUGUGUAUAUACUAGUAUAAUCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUC
......(((.((((.(((((((.(((((..(((((((((---.-----...)))))))))...))))).)))))...(....)......)))))))))............. ( -21.60)
>DroSec_CAF1 153150 95 - 1
CGAUCGUAGUCG----------CGUAUAGUACAUAAUAGUUGUAUAAUGUAUAGUUCUGUGUACAUUGU------ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACU
((((....))))----------......(((((.......)))))((((((((......)))))))).(------((((.(((((((....))))))).)))))....... ( -24.20)
>DroSim_CAF1 155220 95 - 1
CGAUCGUAGUCG----------CGUAUAGUACAUAAUAGUUGUAUAAUGUAUAGUUCUGUGUACAUUGU------ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACU
((((....))))----------......(((((.......)))))((((((((......)))))))).(------((((.(((((((....))))))).)))))....... ( -24.20)
>DroYak_CAF1 165793 94 - 1
CGAUCGUAGUCG----------CGUAUAGUACAUAAUAGUUUUAUAAUGUAUAGUUUU-UGUGCAUUAU------ACCUAACGCAUAAAGGUGUACGUCAGGUGAAACACU
((((....))))----------................(((((((.(((((((.((((-(((((.(((.------...))).))))))))))))))))...)))))))... ( -20.70)
>DroPer_CAF1 231435 103 - 1
CCAUCAACGUCGUUCGCAUACUCGUAUAGUACAUAAUUG---U-----AUAUAGUUGUGUGUAUAUACUAGUAUAAUCUAACGCAUAAAGCAGCGCGUCAAGUAAAACAUC
......(((.((((.(((((((.(((((..(((((((((---.-----...)))))))))...))))).)))))...(....)......)))))))))............. ( -21.60)
>consensus
CGAUCGUAGUCG__________CGUAUAGUACAUAAUAGUUGUAUAAUGUAUAGUUCUGUGUACAUUGU______ACCUAACGCAUAAAGCUGUGCGUCAGGUAAAACACU
.......................((...(((((((......................)))))))...........((((.((((((......)))))).))))...))... (-12.35 = -12.77 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:42 2006