Locus 1346

Sequence ID	3R_DroMel_CAF1
Location	3,966,662 – 3,966,780
Length	118
Max. P	0.610810

overview

Window 4

Location	3,966,662 – 3,966,780
Length	118
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	84.62
Mean single sequence MFE	-27.83
Consensus MFE	-25.57
Energy contribution	-25.57
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-0.96
Structure conservation index	0.92
SVM decision value	0.16
SVM RNA-class probability	0.610810
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3966662 118 + 27905053
AACCCAAAAAUUGUAAAAAGGUAUAGUUCCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGCGCCACAGGACCGAUGAGUUUACGAAAG
..........(((((((..((.......))(.((((((((((.......))))).....((((((.....)))))).((((........))))..))))).)......)))))))... ( -29.10)
>DroSim_CAF1 14852 115 + 1
AUC-C-AAAAUUGUAAAAAA-UUCAAUUCCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGCGCCACAGGACCGAUGAAAUUACAAAAG
...-.-....((((((....-((((....((.((((((((((.......))))).....((((((.....)))))).((((........))))..))))).)).)))).))))))... ( -28.90)
>DroEre_CAF1 13511 103 + 1
-------------AAAAAAA-U-UUUUUGCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGCGCCACAGGACCGAUGAGCUUACGAAAA
-------------.......-.-......((.((((((((((.......))))).....((((((.....)))))).((((........))))..))))).))............... ( -25.50)
>consensus
A_C_C_AAAAUUGUAAAAAA_U_UAAUUCCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGCGCCACAGGACCGAUGAGAUUACGAAAG
.............................((.((((((((((.......))))).....((((((.....)))))).((((........))))..))))).))............... (-25.57 = -25.57 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	3,966,662 – 3,966,780
Length	118
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	84.62
Mean single sequence MFE	-31.13
Consensus MFE	-28.40
Energy contribution	-28.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-0.90
Structure conservation index	0.91
SVM decision value	0.00
SVM RNA-class probability	0.534875
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3966662 118 - 27905053
CUUUCGUAAACUCAUCGGUCCUGUGGCGCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGGAACUAUACCUUUUUACAAUUUUUGGGUU
........((((((..(((((((((((((..........))))).......(((((....)))))((((.......))))))))))))((.......)).............)))))) ( -31.20)
>DroSim_CAF1 14852 115 - 1
CUUUUGUAAUUUCAUCGGUCCUGUGGCGCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGGAAUUGAA-UUUUUUACAAUUUU-G-GAU
...((((((.(((((((((((((((((((..........))))).......(((((....)))))((((.......))))))))))))))...))))-....))))))....-.-... ( -34.40)
>DroEre_CAF1 13511 103 - 1
UUUUCGUAAGCUCAUCGGUCCUGUGGCGCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGCAAAAA-A-UUUUUUU-------------
...............((((((((((((((..........))))).......(((((....)))))((((.......)))))))))))))......-.-.......------------- ( -27.80)
>consensus
CUUUCGUAAACUCAUCGGUCCUGUGGCGCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGGAAAUA_A_UUUUUUACAAUUUU_G_G_U
...............((((((((((((((..........))))).......(((((....)))))((((.......)))))))))))))............................. (-28.40 = -28.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:22 2006