Locus 6996

Sequence ID	X_DroMel_CAF1
Location	17,513,992 – 17,514,115
Length	123
Max. P	0.998194

overview

Window 6

Location	17,513,992 – 17,514,096
Length	104
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	78.98
Mean single sequence MFE	-22.44
Consensus MFE	-13.92
Energy contribution	-14.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.62
SVM decision value	0.66
SVM RNA-class probability	0.813869
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17513992 104 - 22224390
CCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCAUCCAUUGAUUCCUAAAAACUC---AGAAU----AUUGGCAUUUCAAGAACCUAUAAAC----UA--AA--
....(.((((((.(((.(((((....))))))))...(((....(((((.....))))))))........---.....----..))).))).)..............----..--..-- ( -18.50)
>DroSec_CAF1 4860 97 - 1
CCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAUAGUCAUCCAUGGAUUCCUAAAAAC-C---A---U----ACUAUGAACUCAGAA---UAUAGAC----UA--AA--
...((.((((((.(((.(((((....))))))))....(((....))).....)))))).))......-.---.---.----.(((((.........---)))))..----..--..-- ( -21.80)
>DroSim_CAF1 3211 97 - 1
CCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAUAGUCAUCCAUGGAUUCCUAAAAAC-C---A---U----ACUAUGAACUCAGAA---UAUAGAC----UA--AA--
...((.((((((.(((.(((((....))))))))....(((....))).....)))))).))......-.---.---.----.(((((.........---)))))..----..--..-- ( -21.80)
>DroEre_CAF1 3133 109 - 1
CCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCGUCCAUUGUUUCCUGAAAAC-C---A---UAUGCAUUAUGAACUGGCGA---UAUUGGUAUUUUAAGAACC
.............(((.(((((....))))))))((((.(((((.((((.(((..((((.....))))-(---(---((.....))))...))))))---).))))).))))....... ( -25.80)
>DroYak_CAF1 3123 111 - 1
CCAAGCGAUCCACUCCACCGUGUACACA-GGGGAAAAAGGCUAAAGUCAUCCAUUGUUUCCUUACAAC-CUUAA---UGUAUAUGAUGAACUGGAAA---UAUUGGCAUUUUAAUAACU
((((....((((...((.((((((((..-((((.....(((....))).....((((......)))))-)))..---)))))))).))...))))..---..))))............. ( -24.30)
>consensus
CCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCAUCCAUUGAUUCCUAAAAAC_C___A___U____AUUAUGAACUCAAAA___UAUAGAC____UA__AA__
...((.((..(..(((.(((((....))))))))....(((....))).......)..))))......................................................... (-13.92 = -14.12 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	17,514,021 – 17,514,115
Length	94
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	91.44
Mean single sequence MFE	-29.48
Consensus MFE	-23.20
Energy contribution	-23.44
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.73
Structure conservation index	0.79
SVM decision value	0.58
SVM RNA-class probability	0.790189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17514021 94 + 22224390
-AUUCU---GAGUUUUUAGGAAUCAAUGGAUGACUUUAGCCUUUUUCCCCGUGUGUACACGGUGGAGUGGAUCGCUUGGACCCAGCGACCAAGACCAA
-.((((---((....)))))).....(((...............(((((((((....))))).))))(((.(((((.(....)))))))))...))). ( -27.60)
>DroSec_CAF1 4886 90 + 1
-A---U---G-GUUUUUAGGAAUCCAUGGAUGACUAUAGCCUUUUUCCCCGUGUGUACACGGUGGAGUGGAUCGCUUGGACCCAGCGACCAAGACCAA
-.---(---(-((((((((..(((....)))..)))........(((((((((....))))).)))).((.(((((.(....))))))))))))))). ( -33.00)
>DroSim_CAF1 3237 90 + 1
-A---U---G-GUUUUUAGGAAUCCAUGGAUGACUAUAGCCUUUUUCCCCGUGUGUACACGGUGGAGUGGAUCGCUUGGACCCAGCGACCAAGACCAA
-.---(---(-((((((((..(((....)))..)))........(((((((((....))))).)))).((.(((((.(....))))))))))))))). ( -33.00)
>DroEre_CAF1 3170 91 + 1
UA---U---G-GUUUUCAGGAAACAAUGGACGACUUUAGCCUUUUUCCCCGUGUGUACACGGUGGAGUGGAUCGCUUGGACCCAGCGACCAAGACCAA
..---(---(-((((...(....)..(((..........((...(((((((((....))))).)))).)).(((((.(....))))))))))))))). ( -31.00)
>DroYak_CAF1 3160 93 + 1
CA---UUAAG-GUUGUAAGGAAACAAUGGAUGACUUUAGCCUUUUUCCCC-UGUGUACACGGUGGAGUGGAUCGCUUGGACCCAACGACCAAGACCGA
..---....(-(((....(....)..(((..........((...((((.(-(((....)))).)))).)).(((.(((....))))))))).)))).. ( -22.80)
>consensus
_A___U___G_GUUUUUAGGAAUCAAUGGAUGACUUUAGCCUUUUUCCCCGUGUGUACACGGUGGAGUGGAUCGCUUGGACCCAGCGACCAAGACCAA
..........................(((...............(((((((((....))))).))))(((.(((((.(....)))))))))...))). (-23.20 = -23.44 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	17,514,021 – 17,514,115
Length	94
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	91.44
Mean single sequence MFE	-28.80
Consensus MFE	-25.88
Energy contribution	-26.12
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.17
Structure conservation index	0.90
SVM decision value	3.03
SVM RNA-class probability	0.998194
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17514021 94 - 22224390
UUGGUCUUGGUCGCUGGGUCCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCAUCCAUUGAUUCCUAAAAACUC---AGAAU-
((((((((((((((((....).)))))))...(((.(((((....))))))))..))))))))(((((.....)))))...........---.....- ( -30.60)
>DroSec_CAF1 4886 90 - 1
UUGGUCUUGGUCGCUGGGUCCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAUAGUCAUCCAUGGAUUCCUAAAAAC-C---A---U-
.(((((((((((((((....).)))))))...(((.(((((....))))))))..)))))))(((..(((....)))..))).....-.---.---.- ( -31.70)
>DroSim_CAF1 3237 90 - 1
UUGGUCUUGGUCGCUGGGUCCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAUAGUCAUCCAUGGAUUCCUAAAAAC-C---A---U-
.(((((((((((((((....).)))))))...(((.(((((....))))))))..)))))))(((..(((....)))..))).....-.---.---.- ( -31.70)
>DroEre_CAF1 3170 91 - 1
UUGGUCUUGGUCGCUGGGUCCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCGUCCAUUGUUUCCUGAAAAC-C---A---UA
((((((((((((((((....).)))))))...(((.(((((....))))))))..))))))))........................-.---.---.. ( -28.70)
>DroYak_CAF1 3160 93 - 1
UCGGUCUUGGUCGUUGGGUCCAAGCGAUCCACUCCACCGUGUACACA-GGGGAAAAAGGCUAAAGUCAUCCAUUGUUUCCUUACAAC-CUUAA---UG
..((..((((((..((((((.....)))))).(((.((.((....))-)))))....))))))..)).....((((......)))).-.....---.. ( -21.30)
>consensus
UUGGUCUUGGUCGCUGGGUCCAAGCGAUCCACUCCACCGUGUACACACGGGGAAAAAGGCUAAAGUCAUCCAUUGAUUCCUAAAAAC_C___A___U_
.(((((((((((((((....).)))))))...(((.(((((....))))))))..))))))).................................... (-25.88 = -26.12 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:37 2006