Locus 3593

Sequence ID	X_DroMel_CAF1
Location	9,629,409 – 9,629,597
Length	188
Max. P	0.982410

overview

Window 3

Location	9,629,409 – 9,629,502
Length	93
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.47
Mean single sequence MFE	-35.22
Consensus MFE	-17.62
Energy contribution	-18.23
Covariance contribution	0.61
Combinations/Pair	1.26
Mean z-score	-2.85
Structure conservation index	0.50
SVM decision value	1.91
SVM RNA-class probability	0.982410
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9629409 93 - 22224390
GGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAUUAAGUUAAAUGCCGGCGUAGACGACAGGAACAAUGAUGAUGG----GU----CCUGCCCAUG----------
(((((((.((((((...(.((((((.(..((((.((((((......)))))).)))).).)))))))...))))))..)))----))----))........---------- ( -37.90)
>DroGri_CAF1 7424 95 - 1
AGAUUCAAAACGUUUUACGCUGUCGCCGCAUGA-UGCAUUACGUUAAAUGGCAACGUUGAUGUCG---ACGCUGACGAUG------------ACACCGAUGACACCGACUC
.................((.((((((((..(((-((.....)))))..))))...((((.(((((---.((....)).))------------))).)))))))).)).... ( -23.30)
>DroSec_CAF1 5002 93 - 1
GGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAUUAAGUUAAAUGCCGGCGUAGACGACAGGAACAAUGAUGAUGG----GU----CCUGCCCAUG----------
(((((((.((((((...(.((((((.(..((((.((((((......)))))).)))).).)))))))...))))))..)))----))----))........---------- ( -37.90)
>DroSim_CAF1 5172 93 - 1
GGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAUUAAGUUAAAUGCCGGCGUAGACGACAGGAACAAUGAUGAUGG----GU----CCUGCCCAUG----------
(((((((.((((((...(.((((((.(..((((.((((((......)))))).)))).).)))))))...))))))..)))----))----))........---------- ( -37.90)
>DroWil_CAF1 54029 106 - 1
GGACUCAAAACGUUUUACGUUGUCGCCGCAUGUG-GCAUUAAGUUAAAUGGCAACGUAGACGAUGAUGUCGAUGUCGAUGUCGUUGUCGUUGUCGUCGAGGAUGAGG----
...(((..(((....(((((((((((((....))-))(((......))))))))))))(((((((((((((....))))))))))))))))(((......)))))).---- ( -39.30)
>DroYak_CAF1 5856 93 - 1
GGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAUUAAGUUAAAUGCCGGCGUAGACGACAGGAACAAUGAUGAUGG----GU----UCUGCCCAUG----------
(((((((.((((((...(.((((((.(..((((.((((((......)))))).)))).).)))))))...))))))..)))----))----))........---------- ( -35.00)
>consensus
GGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAUUAAGUUAAAUGCCGGCGUAGACGACAGGAACAAUGAUGAUGG____GU____CCUGCCCAUG__________
........((((((.....((((((.(..((((.((((((......)))))).)))).).)))))).......))))))................................ (-17.62 = -18.23 +   0.61)

alignment

secondary structure

dotplot

Window 4

Location	9,629,463 – 9,629,565
Length	102
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-28.82
Consensus MFE	-18.92
Energy contribution	-20.53
Covariance contribution	1.61
Combinations/Pair	1.12
Mean z-score	-1.67
Structure conservation index	0.66
SVM decision value	0.14
SVM RNA-class probability	0.604189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9629463 102 - 22224390
ACCGUUACACAUUCCCACACCCACUAUGAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
...................(((((.((((((....)))((.(((((.((((......))))(....)..............))))).))..))))))))... ( -27.10)
>DroSec_CAF1 5056 102 - 1
ACCCAUUCCCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
.............((((((......(....)...(((.((.(((((.((((......))))(....)..............))))).)).)))))))))... ( -30.10)
>DroSim_CAF1 5226 102 - 1
ACCCAUUCCCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
.............((((((......(....)...(((.((.(((((.((((......))))(....)..............))))).)).)))))))))... ( -30.10)
>DroEre_CAF1 5334 94 - 1
--------CCAUUCCCACACCCACUGGGAACCCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
--------...((((((.......))))))(((((((.((.(((((.((((......))))(....)..............))))).)).))).).)))... ( -31.60)
>DroWil_CAF1 54097 79 - 1
-------------------UCCUCUGGUU-UCUCUGGUGCUCUAUACGAGUAUCUAAUCCA--GGACUCAAAACGUUUUACGUUGUCGCCGCAUGUG-GCAU
-------------------....((((..-.....(((((((.....)))))))....)))--)(((....((((.....)))))))((((....))-)).. ( -22.90)
>DroYak_CAF1 5910 96 - 1
AU------CCAGACCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
..------...(.((((((......(....)...(((.((.(((((.((((......))))(....)..............))))).)).)))))))))).. ( -31.10)
>consensus
AC______CCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGGGGACUCAAAUCGUUUUACGCUGUCGCCGCAUGUGGGCAU
...................(((((.((.....))(((.((.(((((.((((......)))).(((((.......)))))..))))).)).))).)))))... (-18.92 = -20.53 +   1.61)

alignment

secondary structure

dotplot

Window 5

Location	9,629,502 – 9,629,597
Length	95
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	80.43
Mean single sequence MFE	-21.08
Consensus MFE	-13.48
Energy contribution	-13.52
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.64
SVM decision value	0.84
SVM RNA-class probability	0.863804
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9629502 95 - 22224390
CUCCA--ACCCAUUUGAGUUGACCCCAUACCC------AUACCGUUACACAUUCCCACACCCACUAUGAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
...((--((.(....).))))...........------...(((......(((((((...........(((....)))((....))))))))).......))) ( -14.12)
>DroSec_CAF1 5095 95 - 1
CCCCA--ACCCAUCUGGGUUGACCCCAUACCC------AUACCCAUUCCCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
.((((--((((....))))))...........------......(((((((((((..........))))....((((....)))).)))))))........)) ( -22.20)
>DroSim_CAF1 5265 101 - 1
CCCCA--ACCCAUCUGGGUUGACCCCAUACCCAUACCCAUACCCAUUCCCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
.((((--((((....)))))).......................(((((((((((..........))))....((((....)))).)))))))........)) ( -22.20)
>DroEre_CAF1 5373 78 - 1
CCCCAA-GCCCAUCGGGGUUGACC------------------------CCAUUCCCACACCCACUGGGAACCCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
......-......(((((((((.(------------------------(((((((((.......))))))...((((....)))).))))..)).))))))). ( -25.30)
>DroYak_CAF1 5949 88 - 1
CCCAACCACCCAUCUGGGUUGACC---UACCC------ACAU------CCAGACCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
..............(((((.....---.))))------)..(------((((...........))))).....((((....))))((((((......)))))) ( -21.60)
>consensus
CCCCA__ACCCAUCUGGGUUGACCCCAUACCC______AUACC__U_CCCAUUCCCACACCCACUGGAAACUCCUGUUGCUGCAGCUGGGAAUCUAAUCCCGG
.......((((....))))......................................................((((....))))((((((......)))))) (-13.48 = -13.52 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:19 2006