Locus 3154

Sequence ID	2L_DroMel_CAF1
Location	9,020,044 – 9,020,162
Length	118
Max. P	0.688831

overview

Window 3

Location	9,020,044 – 9,020,136
Length	92
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	79.41
Mean single sequence MFE	-24.98
Consensus MFE	-15.39
Energy contribution	-15.12
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-1.66
Structure conservation index	0.62
SVM decision value	0.32
SVM RNA-class probability	0.688831
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9020044 92 + 22407834
UAUG---GGUUU---------CCCCCGCAGGGCCCCAAACAUUUUAUUUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGCUGCACGUGCGCAGCAUGU
...(---((...---------..)))(((((((....((((((((((((((........)))).)))))))))).......))).))))((((((...)))))) ( -29.90)
>DroPse_CAF1 15994 88 + 1
--UG---G--CU---------CCCCAGUCGUCUCCUAUGCAUUUUAUAUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGUUGCACGUGCGCAGCAUGU
--.(---(--((---------.....((..((......(((((((((.(((........)))..))))))))).))..))))))(((((......))))).... ( -21.20)
>DroWil_CAF1 28242 87 + 1
--GC---G--CC---------CUUCUGUGCCCCCCAUUGCAUUUUAUAUG-CUUUUACUUGAGCAUAAAAUGUUGAAAGCAGCCGCUGCACGUGCGCAGCAUGU
--((---(--(.---------....(((((........((((((..((((-(((......)))))))))))))....(((....)))))))).))))....... ( -23.60)
>DroYak_CAF1 13779 92 + 1
CCUG---GAUUU---------CCCCCGCUGGGCCCCAAACAUUUUAUUUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGCUGCACGUGCGCAGCAUGU
.(((---..(((---------((((....))).....((((((((((((((........)))).)))))))))))))).)))..(((((......))))).... ( -25.30)
>DroAna_CAF1 19164 104 + 1
UCUCCCUGCCCUCAUUCAAAAUCCCCCUAGGGCUCCCUGCAUUUUAUUUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGCUGCACGUGCGCAGCAUGU
.......(((((................)))))...((((.(((((...(((((((((....))).)))))).)))))))))..(((((......))))).... ( -28.69)
>DroPer_CAF1 15858 88 + 1
--UG---G--CU---------CCCCAGUCGUCUCCUAUGCAUUUUAUAUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGUUGCACGUGCGCAGCAUGU
--.(---(--((---------.....((..((......(((((((((.(((........)))..))))))))).))..))))))(((((......))))).... ( -21.20)
>consensus
__UG___G__CU_________CCCCCGUAGGCCCCCAUGCAUUUUAUAUCAUUUUUGCUUGAGCAUAAAAUGUUGAAAGCAGCCGCUGCACGUGCGCAGCAUGU
......................................((((............((((((.(((((...)))))..))))))..(((((......))))))))) (-15.39 = -15.12 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	9,020,044 – 9,020,136
Length	92
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	79.41
Mean single sequence MFE	-28.28
Consensus MFE	-13.64
Energy contribution	-13.80
Covariance contribution	0.17
Combinations/Pair	1.17
Mean z-score	-2.18
Structure conservation index	0.48
SVM decision value	0.13
SVM RNA-class probability	0.598196
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9020044 92 - 22407834
ACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAAAUAAAAUGUUUGGGGCCCUGCGGGGG---------AAACC---CAUA
...(((((((....)))))))((.((((..((((((((((..(((........))).))))))))))..))))...)).(((.---------...))---)... ( -35.00)
>DroPse_CAF1 15994 88 - 1
ACAUGCUGCGCACGUGCAACGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAUAUAAAAUGCAUAGGAGACGACUGGGG---------AG--C---CA--
....(.((((....)))).)((((.(((((..(((((((((.(((........))))))))))))....(....)))..))).---------))--)---).-- ( -22.50)
>DroWil_CAF1 28242 87 - 1
ACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCAAGUAAAAG-CAUAUAAAAUGCAAUGGGGGGCACAGAAG---------GG--C---GC--
...(((((((....)))))))((((((..(..(((((((((((........))-))))..))))).....)..))).(....)---------))--)---..-- ( -25.10)
>DroYak_CAF1 13779 92 - 1
ACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAAAUAAAAUGUUUGGGGCCCAGCGGGGG---------AAAUC---CAGG
...(((((((....)))))))(((((((..((((((((((..(((........))).))))))))))..))))..)))(((..---------...))---)... ( -29.80)
>DroAna_CAF1 19164 104 - 1
ACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAAAUAAAAUGCAGGGAGCCCUAGGGGGAUUUUGAAUGAGGGCAGGGAGA
...(((((((....))))))).(((((((((.((((((((..(((........))).))))))))(((((..(((....))).)))))..)))))))))..... ( -34.80)
>DroPer_CAF1 15858 88 - 1
ACAUGCUGCGCACGUGCAACGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAUAUAAAAUGCAUAGGAGACGACUGGGG---------AG--C---CA--
....(.((((....)))).)((((.(((((..(((((((((.(((........))))))))))))....(....)))..))).---------))--)---).-- ( -22.50)
>consensus
ACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCAAGCAAAAAUGAAAUAAAAUGCAUGGGGCCCGACGGGGG_________AG__C___CA__
...(((((((....)))))))((.........((((((.(((....))))))))).........))...................................... (-13.64 = -13.80 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	9,020,071 – 9,020,162
Length	91
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.51
Mean single sequence MFE	-21.35
Consensus MFE	-12.23
Energy contribution	-12.39
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.57
SVM decision value	0.03
SVM RNA-class probability	0.549871
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9020071 91 - 22407834
CAG--------GCAUCCACAUU-----C-GAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCU--------CAAGCAAAAAUGAAAUAAAAUG
.((--------(((.((.(...-----.-..)............((((((....)))))))).)))))....((((((.(((.--------...))))))))).......... ( -21.60)
>DroVir_CAF1 23937 97 - 1
CA--------AACGUCU-UGAU-----A-CAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCUCUGAUAUUUGAGUAAAAA-CAAAUAAAAUG
..--------......(-(((.-----.-(((...........(((((((....))))))).)))...))))((((((((((((........)))).....-...)))))))) ( -19.40)
>DroGri_CAF1 22528 100 - 1
CAG------AGGCAUCUAUGAU-----A-CAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUACGUCCCGAUGUUGAAGCAAAGA-CGAAUAAAAUG
...------.(((((((.....-----.-.)))).........(((((((....))))))))))((((.(((((((.........))))))))))).....-........... ( -24.00)
>DroEre_CAF1 13228 99 - 1
CAGGCAUCCAGGCAUCCACAUU-----C-GAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCU--------CAAGCAAAAAUGAAAUAAAAUG
.(((((.((....((((.....-----.-).)))..........((((((....)))))))).)))))....((((((.(((.--------...))))))))).......... ( -23.50)
>DroWil_CAF1 28265 94 - 1
CA---------CCACCCUCAUAUCAACG-GACAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCU--------CAAGUAAAAG-CAUAUAAAAUG
..---------((..((..........)-)..............((((((....))))))))..........(((((((((((--------........))-))))..))))) ( -17.50)
>DroAna_CAF1 19203 90 - 1
C----------GCAUCCACAUU-----UGGAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCU--------CAAGCAAAAAUGAAAUAAAAUG
.----------(((((((....-----))))............(((((((....)))))))..)))......((((((.(((.--------...))))))))).......... ( -22.10)
>consensus
CA_________GCAUCCACAUU_____A_GAGAUAAUUAAACAUGCUGCGCACGUGCAGCGGCUGCUUUCAACAUUUUAUGCU________CAAGCAAAAA_CAAAUAAAAUG
...........................................(((((((....)))))))...........((((((((.........................)))))))) (-12.23 = -12.39 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:39 2006