Locus 7363

Sequence ID	3R_DroMel_CAF1
Location	19,522,765 – 19,522,901
Length	136
Max. P	0.861108

overview

Window 2

Location	19,522,765 – 19,522,884
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.49
Mean single sequence MFE	-38.21
Consensus MFE	-24.81
Energy contribution	-25.97
Covariance contribution	1.17
Combinations/Pair	1.16
Mean z-score	-1.56
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.561844
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522765 119 + 27905053
GCAUCCACAAAGGUGGCCAAGAGUGGAACCAAUGCGGCAUCGAUUACUCCAAUACCCAGUCCCAAGGCAAAAUGGGGCAGCAAUAGUUGGGCCACCGUUGUAGCACUGGGUAUCUGCAA-
(((.((.((..(((..(((....))).)))..)).))..............(((((((((((((........))))((.(((((....((....))))))).))))))))))).)))..- ( -36.00)
>DroVir_CAF1 15524 120 + 1
GCAUCCACAAAAGUGGCCAGAAGUGGAACCAAGGCCGCAUCGAUCACACCAAUGCCUAGGCCCAGGGCAAAGUGGGGCAACAGUAGUUGAGCAACAGUCGUGGCACUGGGUAUCUGCAUA
....((((....))))......(..(((((.(((((((.(((((.((.(((.(((((.......)))))...)))(....).)).)))))((....)).))))).)).))).))..)... ( -37.70)
>DroGri_CAF1 16404 120 + 1
GCAUCCACACAACUGGCCAACAGUGGCACCAAAGCUGCAUCAAUUACACCAAUGCCCAGGCCCAGGGCAAAAUGGGGCAACAGUAACUGAGCCACAGUUGUGGCGCUGGGAAUCUGCAUU
((((((.((((((((((((....)))).........((.(((.((((.(((.(((((.......)))))...)))(....).)))).)))))..))))))))......)))...)))... ( -41.10)
>DroWil_CAF1 14099 119 + 1
GCAUCUACAAAGCUAGCCAGCAGUGGAACUAAAGCAGCAUCAAUUAUUCCUAUGCCCAAUCCCAAUGCAAAAUGGGGCAACAGAAGCUGUGCCAGUGUUGUGGCACUGGGUAUCUGCAA-
...(((((...(((....))).)))))......((((..............(((((((.(((((........)))))...........((((((......)))))))))))))))))..- ( -32.93)
>DroMoj_CAF1 14815 119 + 1
GCAUCCACAAAGGUAGCCAGGAGUGGAACCAAGGCCGCAUCAAUCACCCCAAUGCCCAAGCCCAGAGCAAAAUGGGGCAGCAAGAGCUGCGCCACAGUUGUGGCGCUGGGUAUCUGCAA-
(((........((.......((((((........)))).)).......)).(((((((.(((((.(((....(((.(((((....))))).)))..))).))).))))))))).)))..- ( -43.44)
>DroAna_CAF1 15991 119 + 1
GCAUCCACAAAGGUGGCCAGCAGGGGAACCAGAGCAGCAUCAAUAACGCCAAUGCCCAGACCCAGAGCAAAGUGGGGUAACAGCAAUUGGGCCACUGUUGUGGCACUGGGAAUCUAUAA-
....((((((.(((((((.((.((....)).((......))......))((((((....((((...((...)).))))....)).))))))))))).))))))................- ( -38.10)
>consensus
GCAUCCACAAAGGUGGCCAGCAGUGGAACCAAAGCAGCAUCAAUUACACCAAUGCCCAGGCCCAGGGCAAAAUGGGGCAACAGUAGCUGAGCCACAGUUGUGGCACUGGGUAUCUGCAA_
((((((((..............)))))........................((((((((.((((........))))..............(((((....))))).)))))))).)))... (-24.81 = -25.97 +   1.17)

alignment

secondary structure

dotplot

Window 3

Location	19,522,805 – 19,522,901
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	82.31
Mean single sequence MFE	-30.42
Consensus MFE	-19.68
Energy contribution	-20.35
Covariance contribution	0.67
Combinations/Pair	1.17
Mean z-score	-2.50
Structure conservation index	0.65
SVM decision value	0.59
SVM RNA-class probability	0.791550
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522805 96 + 27905053
CGAUUACUCCAAUACCCAGUCCCAAGGCAAAAUGGGGCAGCAAUAGUUGGGCCACCGUUGUAGCACUGGGUAUCUGCAAAG---UAAAUAA-UAUAUUUG
...(((((.(((((((((((((((........))))((.(((((....((....))))))).))))))))))).))...))---)))....-........ ( -27.50)
>DroSec_CAF1 17587 96 + 1
CGAUUACUCCAAUACCCAGUCCCAAGGCAAAAUGGGGCAGCAAUAGUUGGGCCACUGUUGUAGCACUGGGUAUCUGCAAAG---UAAAUAA-UAUAUAUG
...(((((.(((((((((((((((........))))((.((((((((......)))))))).))))))))))).))...))---)))....-........ ( -31.50)
>DroSim_CAF1 17776 96 + 1
CGAUUACUCCAAUACCCAGUCCCAAGGCAAAAUGGGGCAGCAAUAGUUGGGCCACUGUUGUAGCACUGGGUAUCUGCAAAG---UAAAUAA-UAUAUAUG
...(((((.(((((((((((((((........))))((.((((((((......)))))))).))))))))))).))...))---)))....-........ ( -31.50)
>DroEre_CAF1 17713 97 + 1
CGAUUACACCAAUGCCCAGGCCCAAGGCGAAAUGGGGCAUCAAUAGCUGGGCAACCGUCGUGGCACUGGGUAUCUGUAAAA---UUCAGAGUUAUAAUUG
((((((......((((((((((...(((.......(((.......)))((....)))))..))).)))))))((((.....---..))))....)))))) ( -31.60)
>DroYak_CAF1 17797 97 + 1
CGAUUACACCAAUGCCCAGGCCCAAGGCGAAAUGGGGCAUCAGCAGUUGGGCAACCGUUGUAGCACUCGGUAUCUGUAAGG---UUCAGAGUUAUAAUUG
((((((......(((((((.((((........))))((....))..)))))))((((..(.....).)))).((((.....---..))))....)))))) ( -24.80)
>DroMoj_CAF1 14855 98 + 1
CAAUCACCCCAAUGCCCAAGCCCAGAGCAAAAUGGGGCAGCAAGAGCUGCGCCACAGUUGUGGCGCUGGGUAUCUGCAAACACACAGAUAA-CAUACA-A
.............(((((.(((((.(((....(((.(((((....))))).)))..))).))).)))))))(((((........)))))..-......-. ( -35.60)
>consensus
CGAUUACUCCAAUACCCAGGCCCAAGGCAAAAUGGGGCAGCAAUAGUUGGGCCACCGUUGUAGCACUGGGUAUCUGCAAAG___UAAAUAA_UAUAUAUG
.........((((((((((.((((........))))((.(((((....((....))))))).)).)))))))).))........................ (-19.68 = -20.35 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	19,522,805 – 19,522,901
Length	96
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	82.31
Mean single sequence MFE	-31.32
Consensus MFE	-21.97
Energy contribution	-21.67
Covariance contribution	-0.30
Combinations/Pair	1.32
Mean z-score	-2.62
Structure conservation index	0.70
SVM decision value	0.83
SVM RNA-class probability	0.861108
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19522805 96 - 27905053
CAAAUAUA-UUAUUUA---CUUUGCAGAUACCCAGUGCUACAACGGUGGCCCAACUAUUGCUGCCCCAUUUUGCCUUGGGACUGGGUAUUGGAGUAAUCG
........-....(((---(((....((((((((((((..(((..((......))..)))..))((((........)))))))))))))).))))))... ( -31.00)
>DroSec_CAF1 17587 96 - 1
CAUAUAUA-UUAUUUA---CUUUGCAGAUACCCAGUGCUACAACAGUGGCCCAACUAUUGCUGCCCCAUUUUGCCUUGGGACUGGGUAUUGGAGUAAUCG
........-....(((---(((....((((((((((((..(((.(((......))).)))..))((((........)))))))))))))).))))))... ( -30.50)
>DroSim_CAF1 17776 96 - 1
CAUAUAUA-UUAUUUA---CUUUGCAGAUACCCAGUGCUACAACAGUGGCCCAACUAUUGCUGCCCCAUUUUGCCUUGGGACUGGGUAUUGGAGUAAUCG
........-....(((---(((....((((((((((((..(((.(((......))).)))..))((((........)))))))))))))).))))))... ( -30.50)
>DroEre_CAF1 17713 97 - 1
CAAUUAUAACUCUGAA---UUUUACAGAUACCCAGUGCCACGACGGUUGCCCAGCUAUUGAUGCCCCAUUUCGCCUUGGGCCUGGGCAUUGGUGUAAUCG
..........((((..---.....))))(((((((((((.(((..(((....)))..)))..((((...........))))...)))))))).))).... ( -27.80)
>DroYak_CAF1 17797 97 - 1
CAAUUAUAACUCUGAA---CCUUACAGAUACCGAGUGCUACAACGGUUGCCCAACUGCUGAUGCCCCAUUUCGCCUUGGGCCUGGGCAUUGGUGUAAUCG
..........((((..---.....))))...............(((((((((((.((((.(.((((...........)))).).)))))))).))))))) ( -26.40)
>DroMoj_CAF1 14855 98 - 1
U-UGUAUG-UUAUCUGUGUGUUUGCAGAUACCCAGCGCCACAACUGUGGCGCAGCUCUUGCUGCCCCAUUUUGCUCUGGGCUUGGGCAUUGGGGUGAUUG
.-......-.(((((((......)))))))....(((((((....)))))))(((....)))((((((...(((((.......))))).))))))..... ( -41.70)
>consensus
CAAAUAUA_UUAUUUA___CUUUGCAGAUACCCAGUGCUACAACGGUGGCCCAACUAUUGCUGCCCCAUUUUGCCUUGGGACUGGGCAUUGGAGUAAUCG
..........................(((((((((((((.((.((((((.....)))))).)).((((........))))....)))))))).))).)). (-21.97 = -21.67 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:04 2006