Locus 5375

Sequence ID	3L_DroMel_CAF1
Location	14,784,016 – 14,784,214
Length	198
Max. P	0.999849

overview

Window 9

Location	14,784,016 – 14,784,134
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.56
Mean single sequence MFE	-30.23
Consensus MFE	-26.77
Energy contribution	-26.66
Covariance contribution	-0.11
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.89
SVM decision value	0.36
SVM RNA-class probability	0.705016
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14784016 118 - 23771897
CUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGAUUUAUAUUGCUCACAAACAUAUGGAAAAUAUAUA--UACU
.((((.((((((((.(((....)))))))))))..))))..((((((((...............))))).))).........((((((..((.((......)))).))))))..--.... ( -30.76)
>DroEre_CAF1 26298 113 - 1
CUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGAUUUAUAUAGCUCACAAACUUAUGGAAACUAUAU-------
.((((.((((((((.(((....)))))))))))..))))....((((((...............))))))(((.(((((.....))))).))).........(....).....------- ( -31.06)
>DroYak_CAF1 27234 119 - 1
CUGGCAGGCGCAAGUGUUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGAUUUAUAUUGCUCACAAACAUAUGGAAAAUAUAUACG-AGU
.((((.((((((((.((.....)).))))))))..)))).(((((((((...............))))))............((((((..((.((......)))).))))))...)-)). ( -28.86)
>consensus
CUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGAUUUAUAUUGCUCACAAACAUAUGGAAAAUAUAUA___A_U
.((((.((((((((.(((....)))))))))))..))))..((((((((...............))))).))).......((((((.((........))))))))............... (-26.77 = -26.66 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	14,784,054 – 14,784,174
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.15
Mean single sequence MFE	-31.14
Consensus MFE	-29.72
Energy contribution	-29.92
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.95
SVM decision value	3.88
SVM RNA-class probability	0.999684
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14784054 120 - 23771897
CACUUAUAUAUAUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
....................................(((((.(((.((((((((.(((....))))))))))).((((......))))((....))..........)))..))))).... ( -32.00)
>DroSec_CAF1 27063 118 - 1
CACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCAGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
.........--.........................(((((.(((.((((((((.(((....)))))))))))..(((......))).((....))..........)))..))))).... ( -31.50)
>DroSim_CAF1 19270 118 - 1
CACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCAGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
.........--.........................(((((.(((.((((((((.(((....)))))))))))..(((......))).((....))..........)))..))))).... ( -31.50)
>DroEre_CAF1 26331 118 - 1
CACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
.........--.........................(((((.(((.((((((((.(((....))))))))))).((((......))))((....))..........)))..))))).... ( -32.00)
>DroYak_CAF1 27273 118 - 1
CACUUAUAU--AUAUGAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGUUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
.........--.........................(((((.(((.((((((((.((.....)).)))))))).((((......))))((....))..........)))..))))).... ( -28.70)
>consensus
CACUUAUAU__AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAUCUCAGGCUGCAAAUGCAUUAAAUCCAGCCUUGAACUAUGA
....................................(((((.(((.((((((((.(((....)))))))))))..(((......))).((....))..........)))..))))).... (-29.72 = -29.92 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	14,784,094 – 14,784,214
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.54
Mean single sequence MFE	-27.29
Consensus MFE	-23.46
Energy contribution	-23.18
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-2.71
Structure conservation index	0.86
SVM decision value	3.15
SVM RNA-class probability	0.998596
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14784094 120 + 23771897
AUGGCUUAGCACAAGGGCGAAAACCACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUUAUAUAUAUAUAAGUGUAUCCACAAACAAACGUGUAUAAAAUGCGCAUAUAUAACA
.((((...((.((((((......)).)))).))..))))..............((((...(((((((((((.......(((....))).......)))))))))))..))))........ ( -26.74)
>DroSec_CAF1 27103 118 + 1
AUGGCUUAGCACAAGGGCGAAAACCACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUUAUAU--AUAUAAGUGCAUCCACAAACAAACGUGUAAUAAAUGCGCAUAUAUAACA
.((((...((.((((((......)).)))).))..))))........((((((........)))))).(--(((((.((((((.(((........)))......)))))).))))))... ( -26.40)
>DroSim_CAF1 19310 118 + 1
AUGGCUUAGCACAAGGGCGAAAACCACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUUAUAU--AUAUAAGUGCAUCCACAAACAAACGUGUAUAAAAUGCGCAUAUAUAACA
.((((...((.((((((......)).)))).))..))))........((((((........)))))).(--(((((.((((((.(((........)))......)))))).))))))... ( -26.40)
>DroEre_CAF1 26371 118 + 1
AUGGCUUAGCACAAGGGCGAAAACCACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUUAUAU--AUAUAAGUGCAUUCGCAAGCAAACGUAUAUAAAAUGCGCAUAUAUAACA
.((((...((.((((((......)).)))).))..))))..............((((...(((((((((--((.....(((........)))...)))))))))))..))))........ ( -28.70)
>DroYak_CAF1 27313 118 + 1
AUGGCUUAGCACAAGGGCGAAAAACACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUCAUAU--AUAUAAGUGCAUCCACAAACAAAUGUAUAUGAAAUGCGCAUAUAUAACA
.((((...((.(((((........).)))).))..))))..............((((...(((((((((--((((..((..........))..)))))))))))))..))))........ ( -28.20)
>consensus
AUGGCUUAGCACAAGGGCGAAAACCACUUGCGCCUGCCAGAACUGGAAUAAAAAUGCAAUGUUUUAUAU__AUAUAAGUGCAUCCACAAACAAACGUGUAUAAAAUGCGCAUAUAUAACA
.((((...((.((((((......)).)))).))..))))....(((((((.........))))))).....(((((.((((((......((....)).......)))))).))))).... (-23.46 = -23.18 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	14,784,094 – 14,784,214
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.54
Mean single sequence MFE	-32.46
Consensus MFE	-29.06
Energy contribution	-28.94
Covariance contribution	-0.12
Combinations/Pair	1.11
Mean z-score	-3.09
Structure conservation index	0.90
SVM decision value	4.25
SVM RNA-class probability	0.999849
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14784094 120 - 23771897
UGUUAUAUAUGCGCAUUUUAUACACGUUUGUUUGUGGAUACACUUAUAUAUAUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAU
((..(((.(((((..(((((((...((.(((..(((....)))..))).)).)))))))...)))))...)))..))....((((.((((((((.(((....)))))))))))..)))). ( -31.90)
>DroSec_CAF1 27103 118 - 1
UGUUAUAUAUGCGCAUUUAUUACACGUUUGUUUGUGGAUGCACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAU
((..(((.((((((((((((.(((....)))..))))))))..((((..--..))))......))))...)))..))....((((.((((((((.(((....)))))))))))..)))). ( -33.50)
>DroSim_CAF1 19310 118 - 1
UGUUAUAUAUGCGCAUUUUAUACACGUUUGUUUGUGGAUGCACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAU
((..(((.(((((((((.....((((......)))))))))..((((..--..))))......))))...)))..))....((((.((((((((.(((....)))))))))))..)))). ( -31.30)
>DroEre_CAF1 26371 118 - 1
UGUUAUAUAUGCGCAUUUUAUAUACGUUUGCUUGCGAAUGCACUUAUAU--AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAU
((..(((.(((((..(((((((((..(.(((........)))...)..)--))))))))...)))))...)))..))....((((.((((((((.(((....)))))))))))..)))). ( -33.70)
>DroYak_CAF1 27313 118 - 1
UGUUAUAUAUGCGCAUUUCAUAUACAUUUGUUUGUGGAUGCACUUAUAU--AUAUGAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGUUUUUCGCCCUUGUGCUAAGCCAU
((..(((.(((((..(((((((((....(((..(((....)))..))))--))))))))...)))))...)))..))....((((.((((((((.((.....)).))))))))..)))). ( -31.90)
>consensus
UGUUAUAUAUGCGCAUUUUAUACACGUUUGUUUGUGGAUGCACUUAUAU__AUAUAAAACAUUGCAUUUUUAUUCCAGUUCUGGCAGGCGCAAGUGGUUUUCGCCCUUGUGCUAAGCCAU
((..(((.(((((((((.....((((......)))))))))..(((((....)))))......))))...)))..))....((((.((((((((.(((....)))))))))))..)))). (-29.06 = -28.94 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:42 2006