Locus 7315

Sequence ID	3R_DroMel_CAF1
Location	19,322,134 – 19,322,275
Length	141
Max. P	0.999543

overview

Window 3

Location	19,322,134 – 19,322,236
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	77.56
Mean single sequence MFE	-39.56
Consensus MFE	-26.18
Energy contribution	-28.98
Covariance contribution	2.80
Combinations/Pair	1.17
Mean z-score	-5.82
Structure conservation index	0.66
SVM decision value	2.89
SVM RNA-class probability	0.997602
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19322134 102 + 27905053
CAUCCACAUACCCGGUAUUAACAACUGCAGCAGCAACAACAAGGCCAGGCCGAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCU
..........................(((((((((((((((((((..(((((.(((((((.....))))))---).))))))).))))))))...))))))))). ( -43.60)
>DroPse_CAF1 136689 84 + 1
----AAGA---UC---AGCAGCAGCAGCAACAACAACAACAAGGCCAGGCCAAAAUAUGCAACAUGCAUGUUAUUGUGGC-----------UUGUUGCUGUUGCU
----....---..---...((((((((((((((..((((...(((...)))..(((((((.....))))))).))))...-----------)))))))))))))) ( -34.10)
>DroSec_CAF1 117855 102 + 1
CAUCCACAUGCCCGGUAUUAACAACUGCAGCAGCAACAACAAGGCCAGCCCAAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCU
..........................(((((((((((((((((..(((((...(((((((.....))))))---)..)))))..))))))))...))))))))). ( -43.40)
>DroSim_CAF1 119212 102 + 1
CAUCCACAUCCCCGGUAUUAACAACUGCAGCAGCAACAACAAGGCCAGGCCAAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCU
..........................(((((((((((((((((((..((((..(((((((.....))))))---)..)))))).))))))))...))))))))). ( -41.00)
>DroAna_CAF1 122216 95 + 1
-AACAACA---CC---AGUAACAUUGGUAACAGCAACAACAAGGCCAAGCCAAAAUAUGCAACAUGCAUGU---UAUUGCGGCCGAUGUUGUUGUUGCUGCUGCU
-......(---((---(((...))))))..((((((((((((((((..((...(((((((.....))))))---)...))))))....))))))))))))..... ( -35.70)
>consensus
CAUCCACAU_CCCGGUAUUAACAACUGCAGCAGCAACAACAAGGCCAGGCCAAAAUAUGCAACAUGCAUGU___UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCU
..........................((((((((((((((((((...(((((..((((((.....)))))).....)))))..)))))))))...))))))))). (-26.18 = -28.98 +   2.80)

alignment

secondary structure

dotplot

Window 4

Location	19,322,134 – 19,322,236
Length	102
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	77.56
Mean single sequence MFE	-34.92
Consensus MFE	-21.22
Energy contribution	-20.62
Covariance contribution	-0.60
Combinations/Pair	1.17
Mean z-score	-3.36
Structure conservation index	0.61
SVM decision value	3.70
SVM RNA-class probability	0.999543
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19322134 102 - 27905053
AGCAGCAACAAAAACAACAAGAGCAGCCGCA---ACAUGCAUGUUGCAUAUUUCGGCCUGGCCUUGUUGUUGCUGCUGCAGUUGUUAAUACCGGGUAUGUGGAUG
.((((((.....(((((((((.((.((((.(---(.((((.....)))).)).))))...)))))))))))..))))))...........(((......)))... ( -36.90)
>DroPse_CAF1 136689 84 - 1
AGCAACAGCAACAA-----------GCCACAAUAACAUGCAUGUUGCAUAUUUUGGCCUGGCCUUGUUGUUGUUGUUGCUGCUGCUGCU---GA---UCUU----
((((.((((((((.-----------...((((((((((((.....)))).....(((...)))..)))))))))))))))).))))...---..---....---- ( -30.30)
>DroSec_CAF1 117855 102 - 1
AGCAGCAACAAAAACAACAAGAGCAGCCGCA---ACAUGCAUGUUGCAUAUUUUGGGCUGGCCUUGUUGUUGCUGCUGCAGUUGUUAAUACCGGGCAUGUGGAUG
.((((((.....(((((((((..(((((.((---(.((((.....))))...))))))))..)))))))))..))))))...........(((......)))... ( -36.90)
>DroSim_CAF1 119212 102 - 1
AGCAGCAACAAAAACAACAAGAGCAGCCGCA---ACAUGCAUGUUGCAUAUUUUGGCCUGGCCUUGUUGUUGCUGCUGCAGUUGUUAAUACCGGGGAUGUGGAUG
.((((((.....(((((((((.((.((((.(---(.((((.....)))).)).))))...)))))))))))..))))))...........(((......)))... ( -35.30)
>DroAna_CAF1 122216 95 - 1
AGCAGCAGCAACAACAACAUCGGCCGCAAUA---ACAUGCAUGUUGCAUAUUUUGGCUUGGCCUUGUUGUUGCUGUUACCAAUGUUACU---GG---UGUUGUU-
(((((((((((((((((....((((((...(---(.((((.....)))).))...))..))))))))))))))))))((((.......)---))---))))...- ( -35.20)
>consensus
AGCAGCAACAAAAACAACAAGAGCAGCCGCA___ACAUGCAUGUUGCAUAUUUUGGCCUGGCCUUGUUGUUGCUGCUGCAGUUGUUAAUACCGGG_AUGUGGAUG
(((((((((((.........................((((.....)))).....(((...)))...)))))))))))............................ (-21.22 = -20.62 +  -0.60)

alignment

secondary structure

dotplot

Window 5

Location	19,322,171 – 19,322,275
Length	104
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	77.18
Mean single sequence MFE	-34.38
Consensus MFE	-16.00
Energy contribution	-16.36
Covariance contribution	0.36
Combinations/Pair	1.28
Mean z-score	-2.30
Structure conservation index	0.47
SVM decision value	1.39
SVM RNA-class probability	0.949356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19322171 104 + 27905053
AACAAGGCCA-GGCCGAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCUGUGGUAGCCACUGCAAACCCAAGGGGGGAAACUGCAUUC
((((((((..-(((((.(((((((.....))))))---).))))))).))))))......((.(((((....))))).))(((...((....))((....)))))... ( -39.40)
>DroVir_CAF1 133708 88 + 1
AACAAGGCCGCAACAAAAAUAUGCAGCAUGCAUGUUGUU---UUUGUAACUGUUGUUGUUACUGAUGUUGUGGUCGCCAAAGCAAAGCAAA-----------------
.....((((((((((..(((((((.....)))))))...---...(((((.......)))))...))))))))))((....))........----------------- ( -27.70)
>DroSec_CAF1 117892 104 + 1
AACAAGGCCA-GCCCAAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCUGUGGUUGCCACUGCAAACCCAAGGGGGGAAACUGCAUCC
((((((..((-(((...(((((((.....))))))---)..)))))..))))))........((((((.((((...)))).)))..((....))((....)))))... ( -38.30)
>DroSim_CAF1 119249 104 + 1
AACAAGGCCA-GGCCAAAAUAUGCAACAUGCAUGU---UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCUGUGGUUGCCACUGCAAACCCAAGGGGGGAAACUGCAUCC
((((((((..-((((..(((((((.....))))))---)..)))))).))))))........((((((.((((...)))).)))..((....))((....)))))... ( -35.90)
>DroAna_CAF1 122246 104 + 1
AACAAGGCCA-AGCCAAAAUAUGCAACAUGCAUGU---UAUUGCGGCCGAUGUUGUUGUUGCUGCUGCUGCGGUCGCCAAAGCCAACCGAAGGGGGGAAAAUGCAUUC
((((.((((.-.((...(((((((.....))))))---)...))))))..))))......(((((....))))).((.....((..((....)).)).....)).... ( -30.60)
>consensus
AACAAGGCCA_GGCCAAAAUAUGCAACAUGCAUGU___UGCGGCUGCUCUUGUUGUUUUUGUUGCUGCUGUGGUCGCCACUGCAAACCCAAGGGGGGAAACUGCAUCC
.....(((((.(((...((((.((((((.(((............)))...))))))...))))...))).)))))((....))...((....)).............. (-16.00 = -16.36 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:57 2006