Locus 4185

Sequence ID	2R_DroMel_CAF1
Location	13,780,442 – 13,780,544
Length	102
Max. P	0.985997

overview

Window 9

Location	13,780,442 – 13,780,544
Length	102
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	76.62
Mean single sequence MFE	-32.64
Consensus MFE	-23.51
Energy contribution	-24.27
Covariance contribution	0.76
Combinations/Pair	1.11
Mean z-score	-1.47
Structure conservation index	0.72
SVM decision value	0.54
SVM RNA-class probability	0.773113
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13780442 102 + 20766785
UAUGGCUUCCACCUUCUGGAGUCGCAUGUGGAAGCCGCCGCC----GCCGCCUCACAAACGCCUCAGAAUGUUGCUGCUGUAUGGA-GC---AAAAGGAGCAGCAGCAGC-
...((......))(((((..(.((..(((((..((.((....----)).)).)))))..)))..))))).(((((((((((.....-..---.......)))))))))))- ( -32.54)
>DroGri_CAF1 95714 105 + 1
UAUGGCUUCCACCUUCUC--GUCGCAUGUGGAAGCCAAUGCCAGCAGCCGCCUCACAAACGCCUGA---UG-CGCUGCUGUACAGCAACGGCAUAAGAAACAACAACAACA
..((((((((((......--.......))))))))))(((((((((((.((.(((........)))---.)-)))))))((......)))))))................. ( -36.82)
>DroSec_CAF1 81280 100 + 1
UAUGGCUUCCACCUUCUGGAGUCGCAUGUGGAAGCCGCC-------GCCGCCUCACAAACGCCUCAGAAUGUUGCUGCUGUACGGA-GG---AAAAGGAGCAGCAGCCGCA
...(((((((((....((......)).)))))))))((.-------((.(((((.......((((.....((....))......))-))---.....)))..)).)).)). ( -31.30)
>DroSim_CAF1 85207 100 + 1
UAUGGCUUCCACCUUCUGGAGUCGCAUGUGGAAGCCGCC-------GCCGCCUCACAAACGCCUCAGAAUGUUGCUGCUGUACGGA-GG---AAAAGGAGCAGCAGCCGCA
...(((((((((....((......)).)))))))))((.-------((.(((((.......((((.....((....))......))-))---.....)))..)).)).)). ( -31.30)
>DroWil_CAF1 99193 81 + 1
UAUGGCUUCCACCUUCUCAAGUCUCAUGUGGAAGCC-------------GCCUCGCAAACGCCUG--AAAUUCGCUGCUGUACGGC---------------AGCAGCAGCA
...(((((((((...............)))))))))-------------((...((....))...--......(((((((.....)---------------)))))).)). ( -31.26)
>consensus
UAUGGCUUCCACCUUCUGGAGUCGCAUGUGGAAGCCGCC_______GCCGCCUCACAAACGCCUCAGAAUGUUGCUGCUGUACGGA_GC___AAAAGGAGCAGCAGCAGCA
..((((((((((...............))))))))))....................................((((((((..................)))))))).... (-23.51 = -24.27 +   0.76)

alignment

secondary structure

dotplot

Window 0

Location	13,780,442 – 13,780,544
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	76.62
Mean single sequence MFE	-39.63
Consensus MFE	-27.63
Energy contribution	-28.11
Covariance contribution	0.48
Combinations/Pair	1.09
Mean z-score	-2.21
Structure conservation index	0.70
SVM decision value	2.03
SVM RNA-class probability	0.985997
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13780442 102 - 20766785
-GCUGCUGCUGCUCCUUUU---GC-UCCAUACAGCAGCAACAUUCUGAGGCGUUUGUGAGGCGGC----GGCGGCGGCUUCCACAUGCGACUCCAGAAGGUGGAAGCCAUA
-(((((((((((..(...(---((-(......))))((..(.....)..))......)..)))))----))))))(((((((((...(.......)...)))))))))... ( -46.50)
>DroGri_CAF1 95714 105 - 1
UGUUGUUGUUGUUUCUUAUGCCGUUGCUGUACAGCAGCG-CA---UCAGGCGUUUGUGAGGCGGCUGCUGGCAUUGGCUUCCACAUGCGAC--GAGAAGGUGGAAGCCAUA
((((((.((((((((..(((((..(((((.....)))))-..---...)))))....)))))))).)).)))).((((((((((...(...--..)...)))))))))).. ( -43.00)
>DroSec_CAF1 81280 100 - 1
UGCGGCUGCUGCUCCUUUU---CC-UCCGUACAGCAGCAACAUUCUGAGGCGUUUGUGAGGCGGC-------GGCGGCUUCCACAUGCGACUCCAGAAGGUGGAAGCCAUA
....((((((((.......---.(-((((.((.((..((......))..)))).)).))))))))-------)))(((((((((...(.......)...)))))))))... ( -38.20)
>DroSim_CAF1 85207 100 - 1
UGCGGCUGCUGCUCCUUUU---CC-UCCGUACAGCAGCAACAUUCUGAGGCGUUUGUGAGGCGGC-------GGCGGCUUCCACAUGCGACUCCAGAAGGUGGAAGCCAUA
....((((((((.......---.(-((((.((.((..((......))..)))).)).))))))))-------)))(((((((((...(.......)...)))))))))... ( -38.20)
>DroWil_CAF1 99193 81 - 1
UGCUGCUGCU---------------GCCGUACAGCAGCGAAUUU--CAGGCGUUUGCGAGGC-------------GGCUUCCACAUGAGACUUGAGAAGGUGGAAGCCAUA
.(((((((((---------------(.....)))))))......--...((....))..)))-------------(((((((((...............)))))))))... ( -32.26)
>consensus
UGCUGCUGCUGCUCCUUUU___CC_UCCGUACAGCAGCAACAUUCUGAGGCGUUUGUGAGGCGGC_______GGCGGCUUCCACAUGCGACUCCAGAAGGUGGAAGCCAUA
....(((((((....................)))))))..........(.((((.....)))).)..........(((((((((...(.......)...)))))))))... (-27.63 = -28.11 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:48 2006