Locus 3831

Sequence ID	X_DroMel_CAF1
Location	10,170,761 – 10,170,995
Length	234
Max. P	0.729370

overview

Window 1

Location	10,170,761 – 10,170,875
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.16
Mean single sequence MFE	-40.95
Consensus MFE	-28.61
Energy contribution	-29.61
Covariance contribution	1.00
Combinations/Pair	1.03
Mean z-score	-4.21
Structure conservation index	0.70
SVM decision value	0.26
SVM RNA-class probability	0.656758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10170761 114 + 22224390
CUGAUGGGGGAGAGCGGGAAAAAGGAGGUGACGAA----AGAGAGAGGCAACAGAAA-AAGGGAUGAAUCUUUAGAUUUGGAUUUGAUUUUUCUGACUUCUCUUCGCUCUCCUU-UCCCA
....((((((((((((..........(....)...----.((((((((...((((((-((....(((((((........))))))).)))))))).))))))))))))))))..-.)))) ( -41.40)
>DroSim_CAF1 2294 113 + 1
CUGAUGGGGGAGAGCGGGAAAAAGGAGGUGACGAA----AGA--GAGGCAACAGAAAAAAGGGAUGAAUCUUUAGAUUUGGAUUUGAUUUUUCUGUCUUCUCUCCGCUCUCCUU-UCCCA
....(((((((((((((.........(....)...----(((--((((..(((((((((..(((((((((....)))))..))))..)))))))))))))))))))))))))..-.)))) ( -44.70)
>DroEre_CAF1 5304 113 + 1
CUGAUGG-GGAGAGUGGGAAAAAGGAGGUGACGAA----AGAGAGAGGAAACAGAAA-AAGGGAUGAAUCUUUAGAUUUGGAUUUGAUUUUUCUGCCUUCUCUUCGUUCUCCUU-UCCAC
.......-.....((((((...(((((..((((((----.((((.(((...((((((-((....(((((((........))))))).)))))))))))))))))))))))))))-))))) ( -36.00)
>DroYak_CAF1 2345 118 + 1
CUGAUAG-GAAGAGUGGGAAAAAGGAGGUGACGAAAGUAAGAGAGAGGAAACAGAAA-AAGGGAUGAAUCUUUAGAUUUGGAUUUGAUUUUUCUGUCUUCUCUCCGUUCUCCUUUUCCCC
.......-.......(((((((.(((((..((....))..(((((((((..((((((-((....(((((((........))))))).)))))))))))))))))...)))))))))))). ( -41.70)
>consensus
CUGAUGG_GGAGAGCGGGAAAAAGGAGGUGACGAA____AGAGAGAGGAAACAGAAA_AAGGGAUGAAUCUUUAGAUUUGGAUUUGAUUUUUCUGUCUUCUCUCCGCUCUCCUU_UCCCA
...............((((...((((((...((.......((((((((..(((((((..(((..((((((....))))))..)))....))))))))))))))))).))))))..)))). (-28.61 = -29.61 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	10,170,761 – 10,170,875
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.16
Mean single sequence MFE	-33.54
Consensus MFE	-24.75
Energy contribution	-25.12
Covariance contribution	0.38
Combinations/Pair	1.10
Mean z-score	-4.91
Structure conservation index	0.74
SVM decision value	0.42
SVM RNA-class probability	0.729370
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10170761 114 - 22224390
UGGGA-AAGGAGAGCGAAGAGAAGUCAGAAAAAUCAAAUCCAAAUCUAAAGAUUCAUCCCUU-UUUCUGUUGCCUCUCUCU----UUCGUCACCUCCUUUUUCCCGCUCUCCCCCAUCAG
((((.-..((((((((.(((((.((((((((((.........((((....))))......))-))))))..)).)))))..----...(......)........)))))))))))).... ( -29.56)
>DroSim_CAF1 2294 113 - 1
UGGGA-AAGGAGAGCGGAGAGAAGACAGAAAAAUCAAAUCCAAAUCUAAAGAUUCAUCCCUUUUUUCUGUUGCCUC--UCU----UUCGUCACCUCCUUUUUCCCGCUCUCCCCCAUCAG
((((.-..(((((((((((((..((((((((((.........((((....)))).......))))))))))..)))--)).----...(......)........)))))))))))).... ( -36.79)
>DroEre_CAF1 5304 113 - 1
GUGGA-AAGGAGAACGAAGAGAAGGCAGAAAAAUCAAAUCCAAAUCUAAAGAUUCAUCCCUU-UUUCUGUUUCCUCUCUCU----UUCGUCACCUCCUUUUUCCCACUCUCC-CCAUCAG
(((((-((((((.((((((((((((((((((((.........((((....))))......))-))))))...))).)))).----)))))...)))))))...)))).....-....... ( -30.66)
>DroYak_CAF1 2345 118 - 1
GGGGAAAAGGAGAACGGAGAGAAGACAGAAAAAUCAAAUCCAAAUCUAAAGAUUCAUCCCUU-UUUCUGUUUCCUCUCUCUUACUUUCGUCACCUCCUUUUUCCCACUCUUC-CUAUCAG
((((((((((((...((((((.(((((((((((.........((((....))))......))-))))))))).))))))...((....))...)))))))))))).......-....... ( -37.16)
>consensus
GGGGA_AAGGAGAACGAAGAGAAGACAGAAAAAUCAAAUCCAAAUCUAAAGAUUCAUCCCUU_UUUCUGUUGCCUCUCUCU____UUCGUCACCUCCUUUUUCCCACUCUCC_CCAUCAG
.((((..(((((.((((((((.(((((((((...........((((....)))).........))))))))).))).........)))))...)))))...))))............... (-24.75 = -25.12 +   0.38)

alignment

secondary structure

dotplot

Window 3

Location	10,170,875 – 10,170,995
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.86
Mean single sequence MFE	-37.25
Consensus MFE	-31.42
Energy contribution	-32.48
Covariance contribution	1.06
Combinations/Pair	1.15
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	0.36
SVM RNA-class probability	0.705682
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10170875 120 + 22224390
CACUAGCAUCCAUCCAGCUACCUCUAUCUCGCUUCCACCUUAGCCGCUUCUUCCAGUUGUUUUUGUUGUUACUUUCCGUUCCUGGCAGGAGGUGUGUUUGUGCGAGAGAGAGGGGAAUGC
.....((((...(((.....(((((.((((((...((....(((((((((((((((........((....)).........)))).)))))))).))))).)))))).)))))))))))) ( -35.63)
>DroSim_CAF1 2407 120 + 1
CACUAGCAUCCAUCCUGCUAACUCCAUCUCGCUUCCACCUUAGCCGCUUCUUCCAGUUGUUUUUGUUGUUACUUUCCGUUCCUGGCAGGAGGUGUGUUUGUGCGAGCGAGAGGGGAAUGA
...(((((.......))))).((((.((((((((.(((...(((((((((((((((........((....)).........)))).)))))))).))).))).))))))))))))..... ( -42.03)
>DroEre_CAF1 5417 120 + 1
CGCUGGCAUCCAUCUCGGUGUCUCCAUCUCGCUUGCACCUUAGCCGCUUCUUUCAGUUGUUUUUGUUGUUACUUUCCGUUCCUCGCAGGAGGUGUGUUUGUGCGAGCGAGAAGAGAAUAC
((((((........))))))((((..((((((((((((...(((((((((((.(((........((....)).........)).).)))))))).))).)))))))))))).)))).... ( -39.23)
>DroYak_CAF1 2463 120 + 1
CACUAGCAUCCAUCUAGGUAUCUCCAUCUCACUUGCGCCUUAGCCGCUUCUUUCAGUUGUUUUUGUUGUUGCUAUCCGUUCCUCGCAGGAGGUGUGUUUGUGCGAGCGAGACGAGAAUAC
..((((.......))))(((((((..((((.(((((((...((((((((((..(((......)))....(((............)))))))))).))).))))))).)))).))).)))) ( -32.10)
>consensus
CACUAGCAUCCAUCCAGCUAUCUCCAUCUCGCUUCCACCUUAGCCGCUUCUUCCAGUUGUUUUUGUUGUUACUUUCCGUUCCUCGCAGGAGGUGUGUUUGUGCGAGCGAGAGGAGAAUAC
.....................((((.((((((((((((...(((((((((((((((........((....)).........)))).)))))))).))).))))))))))))))))..... (-31.42 = -32.48 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:47 2006