Locus 7149

Sequence ID	X_DroMel_CAF1
Location	17,947,373 – 17,947,553
Length	180
Max. P	0.996729

overview

Window 3

Location	17,947,373 – 17,947,486
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.37
Mean single sequence MFE	-35.52
Consensus MFE	-30.13
Energy contribution	-29.38
Covariance contribution	-0.75
Combinations/Pair	1.18
Mean z-score	-2.42
Structure conservation index	0.85
SVM decision value	1.37
SVM RNA-class probability	0.947492
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17947373 113 + 22224390
-------GGAAACUUACCCUGAGUUUCUUCUUCCUCUCUGGGGUCAUGAAACCCUUCUUGGCCUUCUUGGCCUUGGAGGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
-------((((((((.....))))))))......((((..((((((.(((..((.....))..))).))))))..))))..........((((..(((..........)))..))))... ( -38.90)
>DroPse_CAF1 10220 113 + 1
-------CAGCACUUACCCUGAGUUUCUUCUUCCUUUCUGGGGUCAUGAAACCCUUUUUGGCCUUCUUGGCUUUGGAAGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
-------.(((((((.....))))...........(((..((((((.(((..((.....))..))).))))))..))))))........((((..(((..........)))..))))... ( -30.50)
>DroGri_CAF1 9988 120 + 1
UGGUUGCAGACACUUACCCGGAGUUUCUUCUUCCUCUCUGGGGUCAUGAAACCCUUCUUGGCCUUCUUGGCCUUAGAGGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
.((..(((((.((((.....)))).))).......(((((((((((.(((..((.....))..))).)))))))))))))..)).....((((..(((..........)))..))))... ( -40.10)
>DroWil_CAF1 10178 113 + 1
-------GGAAACUUACCCUGAGUUUCUUCUUCCUUUCUGGUGUCAUGAAACCCUUCUUGGCCUUCUUGGCCUUGGAGGCUUCUUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
-------((((...........(((((.....((.....))......)))))(((((..((((.....))))..)))))....))))..((((..(((..........)))..))))... ( -36.40)
>DroAna_CAF1 4334 113 + 1
-------CGUAACUCACCCUGAGUUUCUUCUUCCUCUCUGGGGUCAUGAAACCCUUCUUGGCCUUCUUGGCCUUGGAGGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
-------.(.(((((.....))))).).......((((..((((((.(((..((.....))..))).))))))..))))..........((((..(((..........)))..))))... ( -36.70)
>DroPer_CAF1 8541 113 + 1
-------CAGCACUUACCCUGAGUUUCUUCUUCCUUUCUGGGGUCAUGAAACCCUUUUUGGCCUUCUUGGCUUUGGAAGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
-------.(((((((.....))))...........(((..((((((.(((..((.....))..))).))))))..))))))........((((..(((..........)))..))))... ( -30.50)
>consensus
_______CGAAACUUACCCUGAGUUUCUUCUUCCUCUCUGGGGUCAUGAAACCCUUCUUGGCCUUCUUGGCCUUGGAGGCUUCCUCCAUGCGCUUGCGCACCUCAGCACGCUUGCGCUCG
...........((((.....))))..........((((((((((((.(((..((.....))..))).))))))))))))..........((((..(((..........)))..))))... (-30.13 = -29.38 +  -0.75)

alignment

secondary structure

dotplot

Window 4

Location	17,947,373 – 17,947,486
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.37
Mean single sequence MFE	-41.77
Consensus MFE	-36.17
Energy contribution	-36.37
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-3.15
Structure conservation index	0.87
SVM decision value	2.74
SVM RNA-class probability	0.996729
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17947373 113 - 22224390
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCCCAGAGAGGAAGAAGAAACUCAGGGUAAGUUUCC-------
...((((..(((..(....)..)))..)))).((((((...)))))).((((.....)))).....(((((....))))).............((((((.......)))))).------- ( -42.70)
>DroPse_CAF1 10220 113 - 1
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCUUCCAAAGCCAAGAAGGCCAAAAAGGGUUUCAUGACCCCAGAAAGGAAGAAGAAACUCAGGGUAAGUGCUG-------
..(((((..((...(((((((((....))))..........(((((...(((.....)))......(((((....)))))......)))))......))))).))..))))).------- ( -39.50)
>DroGri_CAF1 9988 120 - 1
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCUAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCCCAGAGAGGAAGAAGAAACUCCGGGUAAGUGUCUGCAACCA
...((((..(((..(....)..)))..)))).(((((....(((((..((((.....)))).....(((((....)))))...))))).........)))))(((...((....))))). ( -45.12)
>DroWil_CAF1 10178 113 - 1
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAAGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACACCAGAAAGGAAGAAGAAACUCAGGGUAAGUUUCC-------
...((((..(((..(....)..)))..))))..(((((..((((....((((.....)))).....(((((((......((.....)).....))))))).))))...)))))------- ( -40.30)
>DroAna_CAF1 4334 113 - 1
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCCCAGAGAGGAAGAAGAAACUCAGGGUGAGUUACG-------
...((((..(((..(....)..)))..)))).((((((...)))))).((((.....)))).....(((((....))))).............(.(((((.....))))).).------- ( -43.50)
>DroPer_CAF1 8541 113 - 1
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCUUCCAAAGCCAAGAAGGCCAAAAAGGGUUUCAUGACCCCAGAAAGGAAGAAGAAACUCAGGGUAAGUGCUG-------
..(((((..((...(((((((((....))))..........(((((...(((.....)))......(((((....)))))......)))))......))))).))..))))).------- ( -39.50)
>consensus
CGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCCCAGAAAGGAAGAAGAAACUCAGGGUAAGUGUCG_______
...((((..(((..(....)..)))..)))).((((((...)))))).((((.....)))).....(((((((......((.....)).....))))))).................... (-36.17 = -36.37 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	17,947,406 – 17,947,524
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.43
Mean single sequence MFE	-44.62
Consensus MFE	-37.83
Energy contribution	-38.83
Covariance contribution	1.00
Combinations/Pair	1.03
Mean z-score	-2.65
Structure conservation index	0.85
SVM decision value	1.68
SVM RNA-class probability	0.971792
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17947406 118 - 22224390
--UUUAAUUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCC
--...........((((.....)))).....((((((((((..((((..(((..(....)..)))..)))).((((((...)))))).((((.....))))......))))))).).)). ( -43.80)
>DroVir_CAF1 10371 118 - 1
-CUGUG-CUUACAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGCGCCGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCC
-.((((-(((....(((.....((((.....)))).......)))....((((((....)))))))))))))((((((...)))))).((((.....)))).....(((((....))))) ( -49.00)
>DroGri_CAF1 10028 118 - 1
-CACUG-CUUACAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCUAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCC
-.....-......((((.....((((....(((((....((.(((((..(((..(....)..)))..)))).).))...)))))....)))).....)))).....(((((....))))) ( -43.60)
>DroSec_CAF1 6721 118 - 1
--UUUAAUUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGGGCAAGCGGGCUGAGAUGCCCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGCUUUCAUGACCC
--.......(((..(((..((.((((.....))))....))...)))..((((((......))))..)))))((((((...)))))).((.((.(((((((.....))))))).)).)). ( -41.60)
>DroWil_CAF1 10211 118 - 1
--AUUGCGUUCCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAAGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACAC
--......(((((((((.....((((.....)))).)).))..((((..(((..(....)..)))..)))).)))))(((((((....((((.....)))).....)))))))....... ( -41.40)
>DroMoj_CAF1 10364 119 - 1
CUUCUG-UUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGCGCCGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGCUUCAUGACCC
....((-(((...((((.....)))))))))((((........((((..((((((....))))))..)))).((((((...)))))).))))..((((.((.....)).))))....... ( -48.30)
>consensus
__UUUG_UUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAAGCCUCCAAGGCCAAGAAGGCCAAGAAGGGUUUCAUGACCC
.............((((.....((((....(((((....((.(((((..((((((....))))))..)))).).))...)))))....)))).....)))).....(((((....))))) (-37.83 = -38.83 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	17,947,446 – 17,947,553
Length	107
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.68
Mean single sequence MFE	-33.73
Consensus MFE	-20.75
Energy contribution	-20.62
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.62
SVM decision value	0.87
SVM RNA-class probability	0.871034
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17947446 107 - 22224390
-----ACCAUGCUGAUACCCGGAUUGUUCGUU---CA--UUUAAUUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAA
-----.((((((....((((((..((((((((---((--(((..((((..((((.....))))...))))...)))).)))))..))))..))).)))((....))))))))..... ( -33.10)
>DroPse_CAF1 10293 100 - 1
-----ACGAUGGU-------CGAUUGUUUUUGG--UG--UUUGA-UUGCAGGCAAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAA
-----.(((((((-------(....((((((..--((--((((.-...))))))..))))))......))))...)))).((((..(((..(....)..)))..))))......... ( -33.20)
>DroWil_CAF1 10251 107 - 1
-------CAUCCUACUAAU-CGAUUCCAUUUGAAUCU--AUUGCGUUCCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAAGAA
-------............-...((((((((((.(((--...((.(....((((.....))))....).))..)))))))((((..(((..(....)..)))..))))))))))... ( -31.80)
>DroMoj_CAF1 10404 112 - 1
CGCCUACGAUGCUAAUUG-AGAUUUGUGUGUU---CGCUUCUG-UUUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGCGCCGAGGUGCGCAAGCGCAUGGAGGAA
..(((.(.((((......-.......((((((---((.(((.(-((((..((((.....))))...))))).)))..)))))))).((((((....))))))....)))).)))).. ( -41.30)
>DroAna_CAF1 4407 91 - 1
--------UUGCUGAUC-------------UC---AA--UUUGAAUUUCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAA
--------....(((((-------------((---(.--((((.......((((.....))))...)))).)))))))).((((..(((..(....)..)))..))))......... ( -29.80)
>DroPer_CAF1 8614 100 - 1
-----ACGAUGGU-------CGAUUGUUUUUGG--UG--UUUGA-UUGCAGGCAAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAA
-----.(((((((-------(....((((((..--((--((((.-...))))))..))))))......))))...)))).((((..(((..(....)..)))..))))......... ( -33.20)
>consensus
_____ACGAUGCU_AU____CGAUUGUUUUUG___CG__UUUGA_UUGCAGGCUAAGAAGGCUAAACAGGCUGAGAUCGAGCGCAAGCGUGCUGAGGUGCGCAAGCGCAUGGAGGAA
...........................................................((((.....))))....(((.((((..((((((....))))))..)))).)))..... (-20.75 = -20.62 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:20 2006