Locus 6614

Sequence ID	2L_DroMel_CAF1
Location	18,598,346 – 18,598,506
Length	160
Max. P	0.803655

overview

Window 5

Location	18,598,346 – 18,598,466
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-41.95
Consensus MFE	-26.29
Energy contribution	-27.10
Covariance contribution	0.81
Combinations/Pair	1.29
Mean z-score	-1.96
Structure conservation index	0.63
SVM decision value	0.62
SVM RNA-class probability	0.803655
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18598346 120 + 22407834
AGACAAUGCCUCCAGAAUCCUGCUGGAUCCAAUCAGAUUGCUCAGACUUGUUGAAAAGGUGGCGGUCAAAAUGCCGAUCGCCGUAAAUGGAGGCCAAAGAUUCACGGGCAUCAGGAACAG
.....((((((...(((((....(((.((((..............((((.......))))(((((((........))))))).....))))..)))..)))))..))))))......... ( -33.00)
>DroVir_CAF1 116721 120 + 1
GCUGAGAGCUUCCAGAAUGCGACUGGAGCCAAUCAGAUUGCUCAGACCCGUCGAGAAGGUGGCCGUCAAAAUGCCAAUGGCGGUAAAUGGCGGCCACAAGUUGACGGGCAUCAGGAACAG
.((((((((((((((.......))))))...........)))).(.((((((((....((((((((((...((((......))))..))))))))))...))))))))).))))...... ( -51.60)
>DroGri_CAF1 90612 120 + 1
GCUGAGAGCCUCCAAAAUACGACUGGAGCCAAUCAGAUUGCUCAAGCCCGUUGAAAAGGUGGCCGUCAAAAUGCCAAUAGCGGUAAAUGGUGGCCAGAGAUUGACGGGCAUCAGGAAUAG
.(((((((((((((.........)))))...........))))..((((((..(.....(((((..((...((((......))))..))..)))))....)..)))))).))))...... ( -43.80)
>DroWil_CAF1 155843 120 + 1
GGAUAAUGCUUCCAGAAUGCGACUAGAGCCAAUCAAAUUGCUAAGACCCGUCGAGAAGGUGGCGGUAAGUAUGCCAAUUGCGGUAAAUGGUGGCCACAAGUUAAUGGGCAUCAGGAAUAA
.........((((.((..((((...((.....))...))))...(.(((((..(....(((((.(...((.((((......)))).))..).)))))...)..)))))).)).))))... ( -27.70)
>DroMoj_CAF1 110480 120 + 1
GCUGAGCGCCUCCAAAAUACGGCUGGAACCAAUCAAAUUGCUCAGCCCUGUCGAAAAGGUGGCCGUCAGAAUGCCAAUGGCUGUGAAUGGGGGCCACAGGUUGACGGGCAUCAGGAACAG
((((((((((..........)))((....))........)))))))((((((((....((((((.(((....(((...)))......))).))))))...))))))))............ ( -47.40)
>DroAna_CAF1 69484 120 + 1
CGACAAGGCCUCCAAGACCCUACUGGAGCCGAUCAGAUUGCUCAGGCUGGUGGAGAAGGUGGCCGUCAGGAUUCCGAUGGCGGUGAAUGGCGGCCAGACGUUCACCGGCAGCAGGAACAG
.((...(((.((((.........)))))))..))....((.((..((((.(((.(((.((((((((((.....(((....)))....))))))))..)).))).))).))))..)).)). ( -48.20)
>consensus
GCAGAAAGCCUCCAAAAUACGACUGGAGCCAAUCAGAUUGCUCAGACCCGUCGAAAAGGUGGCCGUCAAAAUGCCAAUGGCGGUAAAUGGCGGCCACAGGUUGACGGGCAUCAGGAACAG
..........(((............((((..........))))...((((((((.....(((((((((...((((......))))..)))))))))....)))))))).....))).... (-26.29 = -27.10 +   0.81)

alignment

secondary structure

dotplot

Window 6

Location	18,598,386 – 18,598,506
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.67
Mean single sequence MFE	-43.70
Consensus MFE	-30.64
Energy contribution	-30.98
Covariance contribution	0.34
Combinations/Pair	1.41
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	0.62
SVM RNA-class probability	0.800921
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18598386 120 + 22407834
CUCAGACUUGUUGAAAAGGUGGCGGUCAAAAUGCCGAUCGCCGUAAAUGGAGGCCAAAGAUUCACGGGCAUCAGGAACAGGUAAUUGUUCUGCAUGGUAAAGUACGGAGUCGUGCAGCUC
(((..((((.......))))(((((((........))))))).......))).............(((((((((((((((....)))))))...))))...(((((....))))).)))) ( -33.00)
>DroVir_CAF1 116761 120 + 1
CUCAGACCCGUCGAGAAGGUGGCCGUCAAAAUGCCAAUGGCGGUAAAUGGCGGCCACAAGUUGACGGGCAUCAGGAACAGAUAAUUGUUCUGCAUUGUCUGGUACGGUGUGGUGCAGCUC
.......(((((((....((((((((((...((((......))))..))))))))))...)))))))(((((.(((((((....)))))))(((((((.....))))))))))))..... ( -51.40)
>DroGri_CAF1 90652 120 + 1
CUCAAGCCCGUUGAAAAGGUGGCCGUCAAAAUGCCAAUAGCGGUAAAUGGUGGCCAGAGAUUGACGGGCAUCAGGAAUAGAUAACUAUUGCGCAUCGUCACCGACGGCGUCGUGCAGCUC
.....((((((..(.....(((((..((...((((......))))..))..)))))....)..))))))......(((((....)))))((((..((((......))))..))))..... ( -43.90)
>DroWil_CAF1 155883 120 + 1
CUAAGACCCGUCGAGAAGGUGGCGGUAAGUAUGCCAAUUGCGGUAAAUGGUGGCCACAAGUUAAUGGGCAUCAGGAAUAAGUAAUUCUUCUGCAUGGUGGCAAACGGAGUCGUGCAGCUC
....(((((((((......))))))...((.(((((..(((((....(((((.(((........))).)))))(((((.....))))).)))))...))))).))...)))......... ( -37.30)
>DroMoj_CAF1 110520 120 + 1
CUCAGCCCUGUCGAAAAGGUGGCCGUCAGAAUGCCAAUGGCUGUGAAUGGGGGCCACAGGUUGACGGGCAUCAGGAACAGAUAGUUGUUCUGCAUGGUCACAUACGGCGUGGUGCAGCUC
...(((.(((((((....((((((.(((....(((...)))......))).))))))...)))))))(((((((((((((....))))))).....(((......))).)))))).))). ( -45.90)
>DroAna_CAF1 69524 120 + 1
CUCAGGCUGGUGGAGAAGGUGGCCGUCAGGAUUCCGAUGGCGGUGAAUGGCGGCCAGACGUUCACCGGCAGCAGGAACAGGUAGUUGUUCUGCAUCGUGAAGUAGGGCGUGGUGCAGCAC
.....(((((((((...(.(((((((((.....(((....)))....)))))))))..).))))))))).((.(((((((....)))))))((((((((........)))))))).)).. ( -50.70)
>consensus
CUCAGACCCGUCGAAAAGGUGGCCGUCAAAAUGCCAAUGGCGGUAAAUGGCGGCCACAGGUUGACGGGCAUCAGGAACAGAUAAUUGUUCUGCAUGGUCACGUACGGCGUCGUGCAGCUC
......((((((((.....(((((((((...((((......))))..)))))))))....)))))))).....(((((((....)))))))((((((............))))))..... (-30.64 = -30.98 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:37 2006