Locus 4937

Sequence ID	3L_DroMel_CAF1
Location	13,694,474 – 13,694,733
Length	259
Max. P	0.812005

overview

Window 6

Location	13,694,474 – 13,694,584
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.01
Mean single sequence MFE	-24.72
Consensus MFE	-15.88
Energy contribution	-15.88
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-1.57
Structure conservation index	0.64
SVM decision value	0.42
SVM RNA-class probability	0.728266
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13694474 110 + 23771897
-----ACACAUACAC----CACCCUGUGCACUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAAAUGUGCCCUGGGUUCAU-
-----..........----.((((.(.((((..(((((......)))))............((((((((((((((((....)))))))...)))))))))....)))).).))))....- ( -26.00)
>DroPse_CAF1 91020 98 + 1
-----A-----------------CCGAGCAUUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAAAUGUUCUAGGGGUGGGUG
-----(-----------------((..(((....))).((((((((..((((....)))).((((((((((((((((....)))))))...)))))))))........))))))))))). ( -22.50)
>DroEre_CAF1 107834 107 + 1
-----ACACAU-------ACACCCUGUGCACUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAAAUGUGCCAGGGGUUCAU-
-----......-------...(((((.((((..(((((......)))))............((((((((((((((((....)))))))...)))))))))....)))))))))......- ( -30.30)
>DroYak_CAF1 111204 119 + 1
AACUCACACAUACGGCGUACACCCUGUGCACUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAGAUGUGCCAGGGGUUCAU-
................(.((.(((((.((((..(((((......)))))............((((((((((((((((....)))))))...)))))))))....))))))))))).)..- ( -31.10)
>DroAna_CAF1 159282 93 + 1
-----GCAC----CC----UCCGCUGUGCAUUGUUGCGUGUCCUUGCAGUCU-ACAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUUGUACUCAAGCAAAUAGAUGUG-------------
-----....----..----...((((((((...((((((.(((.........-(((((....))))).....)))))))))....)))))...)))...........------------- ( -15.94)
>DroPer_CAF1 92464 98 + 1
-----A-----------------CCGAGCAUUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAAAUGUCCUAGGGGUGGGUG
-----(-----------------((..(((....))).((((((((..((((....)))).((((((((((((((((....)))))))...)))))))))........))))))))))). ( -22.50)
>consensus
_____ACAC__________CACCCUGUGCACUGUUGCGUAUCCUUGCAGUUUGAGAAAAUAAUUUGUUUAAUGGAAUGUAAAUUUCAUACUUAAGCAAAUAAAUGUGCCAGGGGUUCAU_
.........................(((((...(((((......)))))............((((((((((((((((....)))))))...)))))))))...)))))............ (-15.88 = -15.88 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	13,694,545 – 13,694,639
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	95.32
Mean single sequence MFE	-29.26
Consensus MFE	-22.82
Energy contribution	-23.26
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.78
SVM decision value	0.08
SVM RNA-class probability	0.575974
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13694545 94 + 23771897
AAUUUCAUACUUAAGCAAAUAAAUGUGCCCUGGGUUCAUUUGCUUGGGUUCGGUUGGGUUGAGCGACUGGAUCUUAGUUUAUUCCGGCUCUGGC
........((((((((((((.(((.(.....).))).))))))))))))..((((((..(((((............)))))..))))))..... ( -23.60)
>DroSec_CAF1 101898 94 + 1
AAUUUCAUACUUAAGCAAAUAAAUGUGCCCGGGGUUCAUUUGCUUGGGUUCGGUUGGGUGGACCGACUGGAUCUUAGUUUAUUCCGGCUCUGGC
..............(((........)))((((((((.((..(((.((((((((((((.....)))))))))))).)))..))...)))))))). ( -30.40)
>DroSim_CAF1 112300 94 + 1
AAUUUCAUACUUAAGCAAAUAAAUGUGCCCGGGGUUCAUUUGCUUGGGUUCGGUUGGGUGGACCGACUGGAUCUUAGUUUAUUCCGGCUCUGGC
..............(((........)))((((((((.((..(((.((((((((((((.....)))))))))))).)))..))...)))))))). ( -30.40)
>DroEre_CAF1 107902 94 + 1
AAUUUCAUACUUAAGCAAAUAAAUGUGCCAGGGGUUCAUUUGGUUGGGUUCGGUUGGGUGGACCGACUGGCUCUUAGUUUAUUCCGGCUCUGGC
.........((..(((.(((((((..(((((.((((((((..(..(....)..)..))))))))..))))).....)))))))...)))..)). ( -31.10)
>DroYak_CAF1 111284 94 + 1
AAUUUCAUACUUAAGCAAAUAGAUGUGCCAGGGGUUCAUUUGGCUGGGUUCGGUUGGGUGGACCGACUGGAUCUUAGUUUAUUCCGGCUCUGUU
.............(((.(((((((...((((.((((((((..((((....))))..))))))))..))))......)))))))...)))..... ( -30.80)
>consensus
AAUUUCAUACUUAAGCAAAUAAAUGUGCCCGGGGUUCAUUUGCUUGGGUUCGGUUGGGUGGACCGACUGGAUCUUAGUUUAUUCCGGCUCUGGC
.........((..(((...((((((.(((...))).))))))...((((((((((((.....))))))))))))............)))..)). (-22.82 = -23.26 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	13,694,639 – 13,694,733
Length	94
Sequences	4
Columns	98
Reading direction	reverse
Mean pairwise identity	81.91
Mean single sequence MFE	-14.25
Consensus MFE	-9.44
Energy contribution	-9.75
Covariance contribution	0.31
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.66
SVM decision value	0.65
SVM RNA-class probability	0.812005
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13694639 94 - 23771897
CAUCCUUUUAACUUUGUCCCAUCACCACAACAAUCAUUGUCAGCAUCUGCCACGCAGGGCAAAAUAAAACUAUUC----UUUCGAACCGACAAAGGAA
...........(((((((...((...((((......))))..((.(((((...)))))))...............----....))...)))))))... ( -16.30)
>DroSec_CAF1 101992 89 - 1
CACCCUUCUAACUUUGU-----UACCACAACCAUCAUUGUCAGCAUCUGCCACACAGAGCCAAAUAUAACUAUUC----UUUCGAACCGACAAAGGAA
...........((((((-----(...((((......))))..((.((((.....))))))...............----.........)))))))... ( -11.80)
>DroEre_CAF1 107996 94 - 1
CACCCUUCUAACUUUGUCCCAUCGCCACAACCAUCAGUGUCAGCAUCUGCCACACAGGGCAAAAUAGAACUAUUC----UUUCGAACCGACAAAGAAA
...........(((((((...(((((((........)))...))...((((......))))..............----....))...)))))))... ( -16.90)
>DroYak_CAF1 111378 86 - 1
CACCCUUCCAACUUUGUCCCA------------UCAUUGUCAGCAUCUGCCACACAGGACCAAAUAGAACUAUUCUUUCUUUCGAAGCGACAAAGAAA
...........(((((((.(.------------((..(((..((....)).))).((((...((((....))))...))))..)).).)))))))... ( -12.00)
>consensus
CACCCUUCUAACUUUGUCCCA_CACCACAACCAUCAUUGUCAGCAUCUGCCACACAGGGCAAAAUAGAACUAUUC____UUUCGAACCGACAAAGAAA
...........(((((((........................((.((((.....))))))............(((........)))..)))))))... ( -9.44 =  -9.75 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:29 2006