Locus 4446

Sequence ID	X_DroMel_CAF1
Location	11,773,832 – 11,773,933
Length	101
Max. P	0.933144

overview

Window 6

Location	11,773,832 – 11,773,933
Length	101
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	75.80
Mean single sequence MFE	-25.97
Consensus MFE	-19.74
Energy contribution	-18.97
Covariance contribution	-0.78
Combinations/Pair	1.26
Mean z-score	-1.43
Structure conservation index	0.76
SVM decision value	1.23
SVM RNA-class probability	0.933144
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11773832 101 + 22224390
-AUUUUUUUGUUUUUAAC--GUUCUUACCUCAAGCUAGGCGAUCGCCGAUGGCCAUUCAUAUACGAAUGUCCAGGAUGUAAAUGGCCAGCAUCGGCACCGGUAA
-.................--.....((((....((...))....(((((((((((((.((((.(.........).)))).))))))))...)))))...)))). ( -25.80)
>DroVir_CAF1 4444 78 + 1
--------------------------ACCUCAAGCUAGGCGAAUGCCGAUGGCCAUUUAUAUACGAAUGUCCAGGAUGUAAAUGGCCAGCAUCGGGACCAGUCA
--------------------------.(((...(((.(((....)))...((((((((((((.(.........).)))))))))))))))...)))........ ( -26.00)
>DroGri_CAF1 3993 98 + 1
UGGUU---UG---UUUGUAAAAAUUAACCUCAAACUAGGCGAAUGCCGAUGGCCAUUCAUAUACGAAUGUCCAGGAUGUAAAUGGCCAGCAUCGGCUCCAGUCA
(((((---((---...((........))..)))))))(((....(((((((((((((.((((.(.........).)))).))))))))...)))))....))). ( -30.40)
>DroWil_CAF1 7858 87 + 1
-A------------UUGA----ACUCACCUCAAACUGGGCGAACGGCGAUGGCCAUUCAUAUACGAAUGUCCAGGAUGUAAAUGGCCAGCAUCGGCACCGGUAA
-.------------((((----.......))))(((((((((...((..((((((((.((((.(.........).)))).)))))))))).)).)).))))).. ( -24.50)
>DroYak_CAF1 3715 81 + 1
-----------------------CAUACCUCAGGCUAGGCGAUCGCCGAUGGCCAUUCAUGUACGAAUGUCCAGGAUGUAGAUGGCCAGCAUCGGCACCGGUUA
-----------------------..........(((.(((.(((.((..(((.(((((......))))).))))).....))).))))))((((....)))).. ( -25.00)
>DroAna_CAF1 3484 91 + 1
-GCCUU-------AAAG-----CCUUACCUUAAACUCGGCGAUUGUCGAUGGCCAUUCAUGUAGGAAAGUCCAGGAUGUAAAUGGCUAGCAUCGGCACCAGUGA
-.....-------...(-----((.............)))...(((((((((((((((((.(.((.....)).).)))..))))))...))))))))....... ( -24.12)
>consensus
______________U_G______CUUACCUCAAACUAGGCGAACGCCGAUGGCCAUUCAUAUACGAAUGUCCAGGAUGUAAAUGGCCAGCAUCGGCACCAGUAA
.................................(((.((.....(((((((((((((.((((..(......)...)))).))))))))...))))).))))).. (-19.74 = -18.97 +  -0.78)

alignment

secondary structure

dotplot

Window 7

Location	11,773,832 – 11,773,933
Length	101
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	75.80
Mean single sequence MFE	-25.08
Consensus MFE	-17.78
Energy contribution	-18.64
Covariance contribution	0.86
Combinations/Pair	1.10
Mean z-score	-1.12
Structure conservation index	0.71
SVM decision value	0.45
SVM RNA-class probability	0.740785
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11773832 101 - 22224390
UUACCGGUGCCGAUGCUGGCCAUUUACAUCCUGGACAUUCGUAUAUGAAUGGCCAUCGGCGAUCGCCUAGCUUGAGGUAAGAAC--GUUAAAAACAAAAAAAU-
(((((((((((((...((((((((((.((.(.........).)).))))))))))))))).)))((...))....)))))....--.................- ( -26.80)
>DroVir_CAF1 4444 78 - 1
UGACUGGUCCCGAUGCUGGCCAUUUACAUCCUGGACAUUCGUAUAUAAAUGGCCAUCGGCAUUCGCCUAGCUUGAGGU--------------------------
........(((((.((((((((((((.((.(.........).)).)))))))))...(((....))).)))))).)).-------------------------- ( -21.20)
>DroGri_CAF1 3993 98 - 1
UGACUGGAGCCGAUGCUGGCCAUUUACAUCCUGGACAUUCGUAUAUGAAUGGCCAUCGGCAUUCGCCUAGUUUGAGGUUAAUUUUUACAAA---CA---AACCA
.((((((.((.(((((((((((((((.((.(.........).)).)))))))))...)))))).))))))))...((((..(((....)))---..---)))). ( -28.40)
>DroWil_CAF1 7858 87 - 1
UUACCGGUGCCGAUGCUGGCCAUUUACAUCCUGGACAUUCGUAUAUGAAUGGCCAUCGCCGUUCGCCCAGUUUGAGGUGAGU----UCAA------------U-
(((((.(.((((....))))).....((..((((((....))....(((((((....)))))))..))))..)).)))))..----....------------.- ( -26.30)
>DroYak_CAF1 3715 81 - 1
UAACCGGUGCCGAUGCUGGCCAUCUACAUCCUGGACAUUCGUACAUGAAUGGCCAUCGGCGAUCGCCUAGCCUGAGGUAUG-----------------------
.....((((((((...(((((((.....((.((.((....)).)).)))))))))))))).)))((((......))))...----------------------- ( -24.80)
>DroAna_CAF1 3484 91 - 1
UCACUGGUGCCGAUGCUAGCCAUUUACAUCCUGGACUUUCCUACAUGAAUGGCCAUCGACAAUCGCCGAGUUUAAGGUAAGG-----CUUU-------AAGGC-
...((...(((((((...((((((((......((.....))....)))))))))))).......(((........)))..))-----)...-------.))..- ( -23.00)
>consensus
UGACCGGUGCCGAUGCUGGCCAUUUACAUCCUGGACAUUCGUAUAUGAAUGGCCAUCGGCAAUCGCCUAGCUUGAGGUAAG______C_A______________
.....((((((((...((((((((((...................))))))))))))))).)))(((........))).......................... (-17.78 = -18.64 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:16 2006