Locus 472

Sequence ID	3R_DroMel_CAF1
Location	1,763,258 – 1,763,362
Length	104
Max. P	0.964268

overview

Window 4

Location	1,763,258 – 1,763,362
Length	104
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	74.56
Mean single sequence MFE	-28.00
Consensus MFE	-10.59
Energy contribution	-10.45
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-2.61
Structure conservation index	0.38
SVM decision value	1.56
SVM RNA-class probability	0.964268
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1763258 104 + 27905053
CUU-UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUGUUGGU-GGGGCAAAGAGGAAUGCUCCUUGUUUAUAGC--CUCA--GCCACAUUGGCGUG
...-.(((((.((((((((((....)))))))))).))))).....((((((.(((-(((((...(((((....))))).......))--))))--.))))))))..... ( -33.00)
>DroPse_CAF1 62517 91 + 1
CUU-UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUGUUGGC-CGGGGGCCGGGGA--GCCACUUGUUUAUGAC--CCAG--GCC-----------
...-.(((((.((((((((((....)))))))))).)))))............(((-(..(((.((..((--((.....)))).)).)--)).)--)))----------- ( -25.40)
>DroGri_CAF1 73467 102 + 1
CUU-UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUUUUUGGUUG--CAGA---GA--GUCAGUUGUUUAUGACAUCCGGCAUCCCCCAUAACGUG
...-.(((((.((((((((((....)))))))))).))))).......(((..(((.((--(.(.---((--((((........)))).))).)))....))).)))... ( -22.40)
>DroMoj_CAF1 77611 100 + 1
GUUUUUUAUGUAAUCGUAAAGAUAUUUUUAUGAUUUCAUAAUUUUACAGUUUUGGUUUG--CGUA---GA--GGCAGAAGUUUAUGGC--CCUGCAUACCC-AUGGCUGG
.....(((((.((((((((((....)))))))))).))))).....((((..(((....--.(((---(.--(((...........))--)))))....))-)..)))). ( -27.10)
>DroAna_CAF1 67385 104 + 1
CUU-UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUGUUGGC-GGGGCCGAGAAGAGUGUCGGUUGUUUAUGGC--CAUA--GCCACAUUGCCCUC
...-.(((((.((((((((((....)))))))))).))))).....((((((.(((-..(((((.(((.((......)).))).))))--)...--)))))))))..... ( -32.60)
>DroPer_CAF1 69001 102 + 1
CUU-UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUGUUCGC-CGGGGGCCGGGGA--GCCACUUGUUUAUGAC--CCAG--GGCCCAGUACCUUG
...-.(((((.((((((((((....)))))))))).)))))....(((((((((.(-(((...)))).))--).))).))).......--.(((--((.......))))) ( -27.50)
>consensus
CUU_UUUAUGUAAUCGUAAAAAUAUUUUUAUGAUUUCAUAAUUUUACAGUGUUGGC_CGGGCGCAG_GGA__GCCACUUGUUUAUGAC__CCAG__GCCCCAAUGCCGUG
.....(((((.((((((((((....)))))))))).)))))..................................................................... (-10.59 = -10.45 +  -0.14)

alignment

secondary structure

dotplot

Window 5

Location	1,763,258 – 1,763,362
Length	104
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	74.56
Mean single sequence MFE	-21.77
Consensus MFE	-6.53
Energy contribution	-6.70
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.30
SVM decision value	0.73
SVM RNA-class probability	0.834356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1763258 104 - 27905053
CACGCCAAUGUGGC--UGAG--GCUAUAAACAAGGAGCAUUCCUCUUUGCCCC-ACCAACACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA-AAG
.....((.(((((.--((.(--((.......((((((.....))))))))).)-))).))).)).....(((((.((((.(((((....))))).)))).))))).-... ( -19.11)
>DroPse_CAF1 62517 91 - 1
-----------GGC--CUGG--GUCAUAAACAAGUGGC--UCCCCGGCCCCCG-GCCAACACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA-AAG
-----------(((--(.((--(((((......)))))--))...((...)))-)))............(((((.((((.(((((....))))).)))).))))).-... ( -22.10)
>DroGri_CAF1 73467 102 - 1
CACGUUAUGGGGGAUGCCGGAUGUCAUAAACAACUGAC--UC---UCUG--CAACCAAAAACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA-AAG
....((((((.((.(((.((..((((........))))--..---)).)--)).)).....))))))..(((((.((((.(((((....))))).)))).))))).-... ( -20.20)
>DroMoj_CAF1 77611 100 - 1
CCAGCCAU-GGGUAUGCAGG--GCCAUAAACUUCUGCC--UC---UACG--CAAACCAAAACUGUAAAAUUAUGAAAUCAUAAAAAUAUCUUUACGAUUACAUAAAAAAC
.(((....-.(((.((((((--((...........)))--.)---)..)--)).)))....))).....(((((.((((.((((......)))).)))).)))))..... ( -18.20)
>DroAna_CAF1 67385 104 - 1
GAGGGCAAUGUGGC--UAUG--GCCAUAAACAACCGACACUCUUCUCGGCCCC-GCCAACACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA-AAG
...(((..((((((--....--)))))).....((((........))))....-)))............(((((.((((.(((((....))))).)))).))))).-... ( -24.30)
>DroPer_CAF1 69001 102 - 1
CAAGGUACUGGGCC--CUGG--GUCAUAAACAAGUGGC--UCCCCGGCCCCCG-GCGAACACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA-AAG
....((...(((((--..((--(((((......)))))--.))..)))))...-)).............(((((.((((.(((((....))))).)))).))))).-... ( -26.70)
>consensus
CAAGCCAAUGGGGC__CAGG__GCCAUAAACAACUGGC__UCC_CUCCGCCCA_GCCAACACUGUAAAAUUAUGAAAUCAUAAAAAUAUUUUUACGAUUACAUAAA_AAG
.....................................................................(((((.((((.(((((....))))).)))).)))))..... ( -6.53 =  -6.70 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:02 2006