Locus 8220

Sequence ID	3L_DroMel_CAF1
Location	21,602,536 – 21,602,645
Length	109
Max. P	0.998265

overview

Window 5

Location	21,602,536 – 21,602,645
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	84.53
Mean single sequence MFE	-23.66
Consensus MFE	-19.72
Energy contribution	-19.75
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	0.28
SVM RNA-class probability	0.665584
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21602536 109 + 23771897
ACCUGCAAAUCGCUGAGCAAACUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGUGGAAUUGAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAAUUUG-U
....(((((((..((((....))))((((........(((((((((((..(((.((((..........)))).))).))).))))))))........))))).)))))-) ( -24.59)
>DroVir_CAF1 38324 103 + 1
------GAUUGGUUGAACAAAUUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGCUC-AAUAAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAACUUUAU
------..((((((((...........((....))(.(((((((((((..(((.((((....-.....)))).))).))).)))))))).)...))))))))........ ( -23.90)
>DroPse_CAF1 39276 106 + 1
GGUUG---UUUGUUGGAUAAACUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGAUCGAAUAAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAAUUUU-G
(((((---((((((((......)))............(((((((((((..(((.((((..........)))).))).))).))))))))))))).)))))........-. ( -23.10)
>DroGri_CAF1 33393 103 + 1
------GGUUUGUUGAUUACAUUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGCUC-AAUAAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAACUCUGA
------((((((((((((.........((....))(.(((((((((((..(((.((((....-.....)))).))).))).)))))))).).)))))))..))))).... ( -24.30)
>DroWil_CAF1 48142 106 + 1
GAG---AAUUUGUUGAUUAAACUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUAGUUAAAUAAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAAUUUA-U
..(---((((((((((((.........((....))(.(((((((((((..(((.((((..........)))).))).))).)))))))).).)))))))..)))))).-. ( -23.20)
>DroAna_CAF1 34065 104 + 1
-----CGAAAUGUUGACCAAACUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGUUUGAAUUAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAAUUUG-A
-----............((((.((.((((........(((((((((((..(((.((((..........)))).))).))).))))))))........)))))).))))-. ( -22.89)
>consensus
______GAUUUGUUGAACAAACUCAUAGUAAAUACGCCUUUUUCCCUUUCCUGUCGUUGCUC_AAUAAAACGCCAGUAAGCGGAAAAAGACAAAUCGACUAGAAUUUU_U
...........(((((...........((....))(.(((((((((((..(((.((((..........)))).))).))).)))))))).)...)))))........... (-19.72 = -19.75 +   0.03)

alignment

secondary structure

dotplot

Window 6

Location	21,602,536 – 21,602,645
Length	109
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	84.53
Mean single sequence MFE	-31.22
Consensus MFE	-30.26
Energy contribution	-29.85
Covariance contribution	-0.41
Combinations/Pair	1.09
Mean z-score	-3.37
Structure conservation index	0.97
SVM decision value	3.05
SVM RNA-class probability	0.998265
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21602536 109 - 23771897
A-CAAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUCAAUUCCACAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUUGCUCAGCGAUUUGCAGGU
.-(((((((((((.(((.(((((((((((.(((.(((.((((..........)))).)))..)))))))))))))).))).)))).)))))))....((.....)).... ( -33.30)
>DroVir_CAF1 38324 103 - 1
AUAAAGUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUAUU-GAGCAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAAUUUGUUCAACCAAUC------
...((((((((((.(((.(((((((((((.(((.(((.((((.....-....)))).)))..)))))))))))))).))).)))).))))))............------ ( -30.10)
>DroPse_CAF1 39276 106 - 1
C-AAAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUAUUCGAUCAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUUAUCCAACAAA---CAACC
.-.((((((((((.(((.(((((((((((.(((.(((.((((..........)))).)))..)))))))))))))).))).)))).))))))..........---..... ( -30.00)
>DroGri_CAF1 33393 103 - 1
UCAGAGUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUAUU-GAGCAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAAUGUAAUCAACAAACC------
.....((((((((.(((.(((((((((((.(((.(((.((((.....-....)))).)))..)))))))))))))).))).)))).))))..............------ ( -28.60)
>DroWil_CAF1 48142 106 - 1
A-UAAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUAUUUAACUAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUUAAUCAACAAAUU---CUC
.-(((((((((((.(((.(((((((((((.(((.(((.((((..........)))).)))..)))))))))))))).))).)))).)))))))...........---... ( -32.10)
>DroAna_CAF1 34065 104 - 1
U-CAAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUAAUUCAAACAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUUGGUCAACAUUUCG-----
(-(((((((((((.(((.(((((((((((.(((.(((.((((..........)))).)))..)))))))))))))).))).)))).))))))))...........----- ( -33.20)
>consensus
A_AAAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUAUU_GAACAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUUAAUCAACAAAUC______
...((((((((((.(((.(((((((((((.(((.(((.((((..........)))).)))..)))))))))))))).))).)))).)))))).................. (-30.26 = -29.85 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:43 2006