Locus 2070

Sequence ID	X_DroMel_CAF1
Location	5,668,536 – 5,668,776
Length	240
Max. P	0.980290

overview

Window 3

Location	5,668,536 – 5,668,656
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.52
Mean single sequence MFE	-38.37
Consensus MFE	-34.82
Energy contribution	-35.27
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.49
Structure conservation index	0.91
SVM decision value	1.09
SVM RNA-class probability	0.914121
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5668536 120 + 22224390
CCCCGACCAUUGAAAAGUUGAAAAGUGUUUGCAUUCAGCUUCAUCAGCUGAUUGCCGGCAGGUUCAAAGCAUCAAAGCGAAGAAGGCAAACUUUCAGGGGGGGGAAUGCGAAAUGGGGAA
((((..((.((((....(((((...(((..(((.((((((.....)))))).)))..)))..)))))....))))......(((((....))))).))..))))................ ( -38.20)
>DroSec_CAF1 7592 117 + 1
CCCCGACCAUUGAAAUGUUGAAAAGUGUUUGCAUUCAGCUUCAUCAGCUGAUUGCCGGCAGGUUCAAAGCUUCAAAGCGAAGAAGGCAAACUUUCCGA---GGGAAUGCGAAAUGGGGAA
(((((....(((((...(((((...(((..(((.((((((.....)))))).)))..)))..)))))...)))))..........(((...((((...---.)))))))....))))).. ( -35.90)
>DroSim_CAF1 8395 117 + 1
CCCCGACCAUUGGAAAGUUGAAAAGUGUUUGCAUUCAGCUUCAUCAGCUGAUUGCCGGCAGGUUCAAAGCUUCAAAGCGAAGAAGGCAAACUUUCCGA---GGGAAUGCGAAAUGGGGAA
((((..((.(((((((((((((...(((..(((.((((((.....)))))).)))..)))..)))....((((........))))...))))))))))---.)).((.....)))))).. ( -41.00)
>consensus
CCCCGACCAUUGAAAAGUUGAAAAGUGUUUGCAUUCAGCUUCAUCAGCUGAUUGCCGGCAGGUUCAAAGCUUCAAAGCGAAGAAGGCAAACUUUCCGA___GGGAAUGCGAAAUGGGGAA
(((((....(((((...(((((...(((..(((.((((((.....)))))).)))..)))..)))))...)))))..........(((...(((((.....))))))))....))))).. (-34.82 = -35.27 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	5,668,616 – 5,668,736
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.61
Mean single sequence MFE	-23.03
Consensus MFE	-23.51
Energy contribution	-23.40
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	1.02
SVM decision value	1.86
SVM RNA-class probability	0.980290
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5668616 120 - 22224390
CUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAACUCGACUAACUGACGCAUUUUCCCCAUUUCGCAUUCCCCCCCCUGAAAGUUUGCCUUCU
....(((.(((((((..........))))))).)))((((((((((((((.....................))))))))).......(((((............))))))))))...... ( -21.80)
>DroSec_CAF1 7672 112 - 1
CUCUGGCAGAUUUGCAACAAAACUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA-----CUAACUGACAUAUUUUCCCCAUUUCGCAUUCCC---UCGGAAAGUUUGCCUUCU
....(((((((((............((.((.(((.......(((((((((...........-----.....)))))))))....))).)).))..(((.---..)))))))))))).... ( -22.89)
>DroSim_CAF1 8475 112 - 1
CUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA-----CUAACUGACGCAUUUUCCCCAUUUCGCAUUCCC---UCGGAAAGUUUGCCUUCU
....(((((((((............((.((.(((.......(((((((((...........-----.....)))))))))....))).)).))..(((.---..)))))))))))).... ( -24.39)
>consensus
CUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA_____CUAACUGACGCAUUUUCCCCAUUUCGCAUUCCC___UCGGAAAGUUUGCCUUCU
....(((((((((............((.((.(((.......(((((((((.....................)))))))))....))).)).))..(((......)))))))))))).... (-23.51 = -23.40 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	5,668,656 – 5,668,776
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.63
Mean single sequence MFE	-26.00
Consensus MFE	-26.03
Energy contribution	-25.37
Covariance contribution	-0.66
Combinations/Pair	1.10
Mean z-score	-1.98
Structure conservation index	1.00
SVM decision value	1.50
SVM RNA-class probability	0.958912
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5668656 120 - 22224390
AAAUCAAGUUCUCAUAUGCAAGACUUUUGGAAAAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAACUCGACUAACUGACGCAUU
.......(((..........(((((((........)))))))..(((.(((((((..........))))))).)))..)))(((((((((.....................))))))))) ( -26.00)
>DroSec_CAF1 7709 113 - 1
AAAUCAAGUU--CAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAACUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA-----CUAACUGACAUAUU
........((--(((((.(..(....)..).)))))))(((...(((.(((((((..........))))))).))).....((.((((....)))).))..-----......)))..... ( -25.40)
>DroSim_CAF1 8512 113 - 1
AAAUCAAGUU--CAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA-----CUAACUGACGCAUU
........((--(((((.(..(....)..).)))))))((....(((.(((((((..........))))))).)))...))(((((((((...........-----.....))))))))) ( -26.59)
>consensus
AAAUCAAGUU__CAUAUGCUGGACUUUUGGAAUAUGAAGUCUCUGGCAGAUUUGCAACAAAAUUCGCAAAUUGGCCUAAACGAUGUGUCAACACACCUCAA_____CUAACUGACGCAUU
.......(((..........(((((((........)))))))..(((.(((((((..........))))))).)))..)))(((((((((.....................))))))))) (-26.03 = -25.37 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:30 2006