Locus 6075

Sequence ID	2L_DroMel_CAF1
Location	17,070,452 – 17,070,675
Length	223
Max. P	0.891376

overview

Window 2

Location	17,070,452 – 17,070,556
Length	104
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	91.04
Mean single sequence MFE	-22.36
Consensus MFE	-18.22
Energy contribution	-18.30
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.76
Structure conservation index	0.81
SVM decision value	0.97
SVM RNA-class probability	0.891376
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17070452 104 + 22407834
CCAU------AUACAAACUCUGCGAAAUACCCAUCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC-CGCA-CAUGGCACAAAAGGUUGG
((..------..........(((((........))))).....((((.((((((((.........))))))))..)))).......((-((..-..))))......)).... ( -19.20)
>DroSec_CAF1 34430 104 + 1
CCAU------AUACCAACUCGGCGAAAUACCCAUCGCACACAUUUUACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC-CGCA-CAUGGCACAAAAGGUUGG
....------...((((((..((((........))))...........((((((((.........)))))))).............((-((..-..))))......)))))) ( -23.20)
>DroSim_CAF1 29725 106 + 1
CCAU------AUACCAACUCGGCGAAAUACCCAUCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGCCCGCAUCAUGGCACAAAAGGUUGG
....------...((((((..((((........))))......((((.((((((((.........))))))))..)))).......(((........)))......)))))) ( -23.20)
>DroEre_CAF1 33929 110 + 1
ACAUACUCGUAUACCAACUCUGCGAUGGGUAUUUCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGAAGC-CGCA-CAUGGCACAAAAGGUUGG
.............((((((.(((((........))))).....((((.((((((((.........))))))))..)))).......((-((..-..))))......)))))) ( -25.20)
>DroYak_CAF1 33332 104 + 1
ACAU------AUACCAACUCUGCGGAAUACCCAUCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC-CGCA-CAUGGCACAAAAGGUUGC
....------....(((((.(((((.....))...........((((.((((((((.........))))))))..))))....)))((-((..-..))))......))))). ( -21.00)
>consensus
CCAU______AUACCAACUCUGCGAAAUACCCAUCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC_CGCA_CAUGGCACAAAAGGUUGG
.............((((((..((((........))))......((((.((((((((.........))))))))..))))...........((......))......)))))) (-18.22 = -18.30 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	17,070,479 – 17,070,596
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.82
Mean single sequence MFE	-22.27
Consensus MFE	-15.02
Energy contribution	-15.93
Covariance contribution	0.92
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.67
SVM decision value	0.10
SVM RNA-class probability	0.583978
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17070479 117 + 22407834
-UCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC-CGCA-CAUGGCACAAAAGGUUGGCCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGG
-...(((.((((((((((((((((.........))))))))..........((...-.)).-..((((.(((....)))))))...............))))))))..........))). ( -25.60)
>DroPse_CAF1 22167 90 + 1
CUUGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUA--------------------CAAAAGGUUGGCCAACAAAAACGCAAAUGG--AAAAGCAAAA-A-------
.((((...((((((..((((((((.........))))))))........--------------------.....((....)).........).))))).--....))))..-.------- ( -15.50)
>DroSec_CAF1 34457 117 + 1
-UCGCACACAUUUUACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC-CGCA-CAUGGCACAAAAGGUUGGCCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGG
-.....(((.......((((((((.........)))))))).(((......(((..-..((-(.((((.(((....))))))).......(......))))...)))......)))))). ( -25.30)
>DroSim_CAF1 29752 119 + 1
-UCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGCCCGCAUCAUGGCACAAAAGGUUGGCCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGG
-...(((.((((((((((((((((.........))))))))..........((.....))....((((.(((....)))))))...............))))))))..........))). ( -25.60)
>DroEre_CAF1 33962 116 + 1
-UCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGAAGC-CGCA-CAUGGCACAAAAGGUUGGCCAACAAAAACUCCACUGGUGAAAUGCAAA-AGCAGGUGG
-.....((((((((((((((((((.........))))))))...............-....-..((((.(((....)))))))...............)))))))((...-.))..))). ( -26.10)
>DroPer_CAF1 20130 90 + 1
CUUGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUA--------------------CAAAAGGUUGGCCAACAAAAACGCAAAUGG--AAAAGCAAAA-A-------
.((((...((((((..((((((((.........))))))))........--------------------.....((....)).........).))))).--....))))..-.------- ( -15.50)
>consensus
_UCGCACACAUUUCACGCAUUUUGAUAUGCAAACAAAAUGCACUGAAUAAAGCAGC_CGCA_CAUGGCACAAAAGGUUGGCCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGG
........((((((((((((((((.........)))))))).................................((....))................)))))))).............. (-15.02 = -15.93 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	17,070,556 – 17,070,675
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	99.58
Mean single sequence MFE	-21.12
Consensus MFE	-21.10
Energy contribution	-21.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	1.00
SVM decision value	0.34
SVM RNA-class probability	0.694037
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17070556 119 + 22407834
CCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGGGGUAGGUAACAAAAUAAAAAACGUAUAGAACGAAUGGUAAAAACCGUCGAAAUUUGCACGUGAACACAAAGAAGCAAUU
.........((((((((.((............)).)))))))).................((((.((((.(((.((((....)))))))...)))).)))).................. ( -21.10)
>DroSec_CAF1 34534 119 + 1
CCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGGGGUAGGUAACAAAAUAAAAAACGUAUAGAACGAAUGGUAAAAACCGUCGAAAUUUGCACGUGAACACAAAGAAGCAAUU
.........((((((((.((............)).)))))))).................((((.((((.(((.((((....)))))))...)))).)))).................. ( -21.10)
>DroSim_CAF1 29831 119 + 1
CCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGGGGUAGGUAACAAAAUAAAAAACGUAUAGAACGAAUGGUAAAAACCGUCGAAAUUUGCACGUGAACACAAAGAAGCAAUU
.........((((((((.((............)).)))))))).................((((.((((.(((.((((....)))))))...)))).)))).................. ( -21.10)
>DroYak_CAF1 33436 118 + 1
CCAACAAAAACUCCACUGGUGAAAUGCAAA-AACAGGUGGGGUAGGUAACAAAAUAAAAAACGUAUAGAACGAAUGGUAAAAACCGUCGAAAUUUGCACGUGAACACAAAGAAGCAAUU
.........((((((((.((..........-.)).)))))))).................((((.((((.(((.((((....)))))))...)))).)))).................. ( -21.20)
>consensus
CCAACAAAAACUCCACUGGUGAAAUGCAAAAAACAGGUGGGGUAGGUAACAAAAUAAAAAACGUAUAGAACGAAUGGUAAAAACCGUCGAAAUUUGCACGUGAACACAAAGAAGCAAUU
.........((((((((.((............)).)))))))).................((((.((((.(((.((((....)))))))...)))).)))).................. (-21.10 = -21.10 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:42 2006