Locus 3619

Sequence ID	X_DroMel_CAF1
Location	9,675,425 – 9,675,604
Length	179
Max. P	0.986843

overview

Window 2

Location	9,675,425 – 9,675,541
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.91
Mean single sequence MFE	-31.20
Consensus MFE	-20.49
Energy contribution	-22.04
Covariance contribution	1.55
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.66
SVM decision value	2.06
SVM RNA-class probability	0.986843
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9675425 116 - 22224390
AUUCCUUCUCGGUCUCGCAUUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAGCGAGUGACAAA----GCGAGAGAGCAGGGCAAAAAGUCGC
..((((.(((..((((((....(((..((((((((.((((.....))))......))))))))..))).((..((....))...)).....----))))))))).))))........... ( -33.70)
>DroAna_CAF1 38469 103 - 1
-------------CUCG--CUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAG--AGUGACAAAGAAGGCGAGAGGGCAGGGCGAGAAGUCAG
-------------((((--((((((..((((((((.((((.....))))......))))))))..)))............--.............((......)).)))))))....... ( -27.90)
>DroSim_CAF1 22570 116 - 1
AUUCCUCCUUGGUCUCGCAUUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAGCGAGUGACAAA----GCGAGAGAGCAGGGCAAAAAGUCGC
......(((((.((((.(((((((...((((((((.((((.....))))......))))))))(((......)))....))))))).....----....)))).)))))........... ( -33.40)
>DroEre_CAF1 17934 116 - 1
AUUCCUCCUUGCUCUCGCAUUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAGCGAGUGACAAA----GCGAGAGAGCAGGGCAAAAAGUCGC
......((((((((((.(((((((...((((((((.((((.....))))......))))))))(((......)))....))))))).....----....))))))))))........... ( -37.90)
>DroYak_CAF1 22129 95 - 1
AUUCCUCCUUCGUCUCGCAUUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAGCGAGUGACAAA----GC---------------------GC
..........(((....(((((((...((((((((.((((.....))))......))))))))(((......)))....))))))).....----))---------------------). ( -23.10)
>consensus
AUUCCUCCUUGGUCUCGCAUUCGCAAUCAUAAAAGGCAACAAAAUGUUGAACAAAUUUUUAUGGCUGCACAAAGCAACAGCGAGUGACAAA____GCGAGAGAGCAGGGCAAAAAGUCGC
............((((((....(((..((((((((.((((.....))))......))))))))..))).((..((....))...)).........))))))......(((.....))).. (-20.49 = -22.04 +   1.55)

alignment

secondary structure

dotplot

Window 3

Location	9,675,501 – 9,675,604
Length	103
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	86.00
Mean single sequence MFE	-15.13
Consensus MFE	-11.44
Energy contribution	-11.50
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-1.46
Structure conservation index	0.76
SVM decision value	0.06
SVM RNA-class probability	0.562442
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9675501 103 - 22224390
CACCCCUCAUCCCCG-CCCCUUUUACACCUGAUCCUUCCGUUGGCUUCUUCUUGGCCCUCUGCCAUUCCUUCUCGGUCUCGCAUUCGCAAUCAUAAAAGGCAAC
...............-..(((((((....((((......(..((((.......))))..)(((....((.....))....)))......))))))))))).... ( -14.60)
>DroSim_CAF1 22646 91 - 1
------------CCG-CCCCUUUUACACCUGAUCCUUCCGUUGGCUUCUUCUUGGCCCUCUGCCAUUCCUCCUUGGUCUCGCAUUCGCAAUCAUAAAAGGCAAC
------------...-..(((((((....((((......(..((((.......))))..).((((........))))...((....)).))))))))))).... ( -15.50)
>DroEre_CAF1 18010 94 - 1
----------CCCCACCCCCCUUUACACCUGGUCCUGUCUUUGGCUUCUUCUUGGCCUUCUGCCAUUCCUCCUUGCUCUCGCAUUCGCAAUCAUAAAAGGCAAC
----------.........................((((((((((.......((((.....)))).........)))...((....)).......))))))).. ( -13.59)
>DroYak_CAF1 22184 101 - 1
CACUCCC---CCCCGCCCCCUUUUACACCUGAUCCUUGCGUUGGCUUCUUCUUGGCCUUCUGCCAUUCCUCCUUCGUCUCGCAUUCGCAAUCAUAAAAGGCAAC
.......---........(((((((....((.....((((..(((.......((((.....))))..........))).))))....))....))))))).... ( -16.83)
>consensus
__________CCCCG_CCCCUUUUACACCUGAUCCUUCCGUUGGCUUCUUCUUGGCCCUCUGCCAUUCCUCCUUGGUCUCGCAUUCGCAAUCAUAAAAGGCAAC
..................(((((((....((((.........((((.......)))).......................((....)).))))))))))).... (-11.44 = -11.50 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:54 2006