Locus 316

Sequence ID	3R_DroMel_CAF1
Location	1,222,092 – 1,222,195
Length	103
Max. P	0.940501

overview

Window 5

Location	1,222,092 – 1,222,195
Length	103
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-28.42
Consensus MFE	-20.03
Energy contribution	-20.45
Covariance contribution	0.42
Combinations/Pair	1.24
Mean z-score	-3.14
Structure conservation index	0.70
SVM decision value	1.31
SVM RNA-class probability	0.940501
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1222092 103 + 27905053
AACGAGUACAACAGCAACAGCAUACUCAUAGCAUUUAUCAAAACAAGCAACAAUUGCAAAUUGUUGCCCUGUCUGCCUUGUUGCUGUUGCUUUUGUUG------UGGCU
....((((((((((((((((((....((..(((.........(((.((((((((.....))))))))..))).)))..)).)))))))))...)))))------).))) ( -32.30)
>DroPse_CAF1 2337 100 + 1
AAAGGCU---ACAGCAACAGCAAACAUAUUGCAUUUAUCAAAAUCCGCAGCAAUUACAAAUUGUUGCUCUCUCUGCCUUGUUGUUAUUGUUGUUUAUA------UGGCU
...((((---(.(((((((((((.....))))..............((((((((.....))))))))....................)))))))....------))))) ( -21.90)
>DroSim_CAF1 2038 103 + 1
AACGGGUACAACAGCAACAGCAUACUCAUAGCAUUUAUCAAAACAAGCAACAAUUGCAAAUUGUUGCCCUGUCUGCCUUGUUGCUGUUGCUUUUGUUG------UGGCU
...((.((((((((((((((((....((..(((.........(((.((((((((.....))))))))..))).)))..)).)))))))))...)))))------)).)) ( -34.50)
>DroYak_CAF1 2064 103 + 1
AACAGGCACAACAGCAACCGCAUACUCAUAGCAUUUAUCGAAACAAGCAACAAUUGCAAAUUGUUGCCCUGUCUGCCUUGUUGCUGUUGCUUUUGUUG------UGGCU
...((.((((((((((((.(((....((..(((......((.....((((((((.....))))))))....)))))..)).))).)))))...)))))------)).)) ( -32.20)
>DroAna_CAF1 2052 106 + 1
AACA---UCAACAGCAACAACUCACUCAUUGCAUUUAUCAAAAUCGGCAACAAUUGCAAAUUAUUGCCCUGUCUGCCUUGAUGUUGUUGGUUUUGCUGUUGUCUUGGCU
..((---.(((((((((.(((.((......(((..((((((....(((((((...((((....))))..))).)))))))))).)))))))))))))))))...))... ( -27.70)
>DroPer_CAF1 4212 100 + 1
AAAGGCU---ACAGCAACAGCAAACAUAUUGCAUUUAUCAAAAUCCGCAGCAAUUACAAAUUGUUGCUCUCUCUGCCUUGUUGUUAUUGUUGUUUAUA------UGGCU
...((((---(.(((((((((((.....))))..............((((((((.....))))))))....................)))))))....------))))) ( -21.90)
>consensus
AACGGGUACAACAGCAACAGCAUACUCAUAGCAUUUAUCAAAACAAGCAACAAUUGCAAAUUGUUGCCCUGUCUGCCUUGUUGCUGUUGCUUUUGUUG______UGGCU
..((((..(((((((((((((.........))..............((((((((.....))))))))...........)))))))))))..)))).............. (-20.03 = -20.45 +   0.42)

alignment

secondary structure

dotplot

Window 6

Location	1,222,092 – 1,222,195
Length	103
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-30.12
Consensus MFE	-15.03
Energy contribution	-16.17
Covariance contribution	1.14
Combinations/Pair	1.21
Mean z-score	-2.94
Structure conservation index	0.50
SVM decision value	0.64
SVM RNA-class probability	0.807738
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1222092 103 - 27905053
AGCCA------CAACAAAAGCAACAGCAACAAGGCAGACAGGGCAACAAUUUGCAAUUGUUGCUUGUUUUGAUAAAUGCUAUGAGUAUGCUGUUGCUGUUGUACUCGUU
....(------(((((...((((((((..(((((((.....(((((((((.....))))))))))))))))....((((.....))))))))))))))))))....... ( -35.60)
>DroPse_CAF1 2337 100 - 1
AGCCA------UAUAAACAACAAUAACAACAAGGCAGAGAGAGCAACAAUUUGUAAUUGCUGCGGAUUUUGAUAAAUGCAAUAUGUUUGCUGUUGCUGU---AGCCUUU
.....------...................(((((....(.((((((((((((((.....)))))))).........((((.....)))).)))))).)---.))))). ( -21.50)
>DroSim_CAF1 2038 103 - 1
AGCCA------CAACAAAAGCAACAGCAACAAGGCAGACAGGGCAACAAUUUGCAAUUGUUGCUUGUUUUGAUAAAUGCUAUGAGUAUGCUGUUGCUGUUGUACCCGUU
....(------(((((...((((((((..(((((((.....(((((((((.....))))))))))))))))....((((.....))))))))))))))))))....... ( -35.60)
>DroYak_CAF1 2064 103 - 1
AGCCA------CAACAAAAGCAACAGCAACAAGGCAGACAGGGCAACAAUUUGCAAUUGUUGCUUGUUUCGAUAAAUGCUAUGAGUAUGCGGUUGCUGUUGUGCCUGUU
.....------.((((...(((((((((((...(((((((((.(((((((.....))))))))))))))......((((.....)))))).)))))))))))...)))) ( -35.70)
>DroAna_CAF1 2052 106 - 1
AGCCAAGACAACAGCAAAACCAACAACAUCAAGGCAGACAGGGCAAUAAUUUGCAAUUGUUGCCGAUUUUGAUAAAUGCAAUGAGUGAGUUGUUGCUGUUGA---UGUU
........(((((((((...((((.((.(((..((......(((((((((.....))))))))).((((....))))))..)))))..))))))))))))).---.... ( -30.80)
>DroPer_CAF1 4212 100 - 1
AGCCA------UAUAAACAACAAUAACAACAAGGCAGAGAGAGCAACAAUUUGUAAUUGCUGCGGAUUUUGAUAAAUGCAAUAUGUUUGCUGUUGCUGU---AGCCUUU
.....------...................(((((....(.((((((((((((((.....)))))))).........((((.....)))).)))))).)---.))))). ( -21.50)
>consensus
AGCCA______CAACAAAAGCAACAACAACAAGGCAGACAGGGCAACAAUUUGCAAUUGUUGCUGAUUUUGAUAAAUGCAAUGAGUAUGCUGUUGCUGUUGUACCCGUU
....................(((((((.......((((...(((((((((.....)))))))))...))))....((((.....))))))))))).............. (-15.03 = -16.17 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:17 2006