Locus 4660

Sequence ID	2R_DroMel_CAF1
Location	15,221,906 – 15,221,997
Length	91
Max. P	0.655929

overview

Window 3

Location	15,221,906 – 15,221,997
Length	91
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.25
Mean single sequence MFE	-16.00
Consensus MFE	-8.72
Energy contribution	-8.42
Covariance contribution	-0.30
Combinations/Pair	1.31
Mean z-score	-2.08
Structure conservation index	0.54
SVM decision value	0.26
SVM RNA-class probability	0.655929
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15221906 91 + 20766785
-----------AAA--AACAAAACAAUUAGGCAAUUAAAUGUCU-UGGUAUUACCAAAAAUUUUCGUUUUGGUAACAAAACGCGUCAUAAAAUAAGCCAAAAUGU--
-----------...--......(((.((.(((...........(-(((.....)))).......(((((((....))))))).............))).)).)))-- ( -15.90)
>DroVir_CAF1 77938 89 + 1
-----------AAA--AACAAAACAAUUAGGCAAUUAAAUGUGC-UCAUAUUACCAAAAAUUUUCGUUUUGGUAACAAAACGCGUCAUAAAAUACGGCCAA--GG--
-----------...--.............(((.(((..((((((-.....(((((((((.......)))))))))......))).)))..)))...)))..--..-- ( -15.30)
>DroGri_CAF1 61738 84 + 1
-----------AAGGAAACAAAACAAUUAGGCAAUUAAAUUCGC-UCAUAUUACCAAAAAUUUUCGUUUUGGUAACAAAACGCGUCGUAAAAGGCC-----------
-----------..(....)..........(((..(((....(((-.....(((((((((.......)))))))))......)))...)))...)))----------- ( -16.20)
>DroWil_CAF1 132734 105 + 1
CAAACGAAAAACAA--AACAAAACAAUUAGGCAAUUAAAUGUGACUCUUAUUACCAAAAAUUUUCGCUUUGGUAACAAAAUGCGCCAUAAAAUAGGCCAAAAAGUGU
..............--......(((.((((....)))).))).((.(((.((((((((.........)))))))).....((.(((........)))))..))).)) ( -13.30)
>DroMoj_CAF1 74774 89 + 1
-----------AAG--AACAAAACAAUUAGGCAAUUAAAUGUGC-GCAUAUUACCGAAAAUUUUUGUUUUGGUAACAAAACGCGUCAUAAAAUGCCGCCAA--GG--
-----------...--.............((((.....((((((-(....(((((((((.......))))))))).....)))).)))....)))).....--..-- ( -18.50)
>DroPer_CAF1 56636 92 + 1
-----------AAA--AACAAAACAAUUAGGCAAUUAAAUGUCUUUGGUAUUACCAAAAAUUUUCGUUUUGGUAACAAAACGCGUCAUAAAAUAAGCCAAAAUGU--
-----------...--......(((.((.(((...........(((((.....)))))......(((((((....))))))).............))).)).)))-- ( -16.80)
>consensus
___________AAA__AACAAAACAAUUAGGCAAUUAAAUGUGC_UCAUAUUACCAAAAAUUUUCGUUUUGGUAACAAAACGCGUCAUAAAAUACGCCAAA__GU__
.............................(((.....((((((...))))))............(((((((....))))))).)))..................... ( -8.72 =  -8.42 +  -0.30)

alignment

secondary structure

dotplot

Window 4

Location	15,221,906 – 15,221,997
Length	91
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.25
Mean single sequence MFE	-19.62
Consensus MFE	-9.63
Energy contribution	-9.86
Covariance contribution	0.22
Combinations/Pair	1.09
Mean z-score	-2.15
Structure conservation index	0.49
SVM decision value	-0.05
SVM RNA-class probability	0.507438
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15221906 91 - 20766785
--ACAUUUUGGCUUAUUUUAUGACGCGUUUUGUUACCAAAACGAAAAUUUUUGGUAAUACCA-AGACAUUUAAUUGCCUAAUUGUUUUGUU--UUU-----------
--(((.((.(((..(((..(((...(((((((....))))))).....((((((.....)))-))))))..))).))).)).)))......--...----------- ( -19.10)
>DroVir_CAF1 77938 89 - 1
--CC--UUGGCCGUAUUUUAUGACGCGUUUUGUUACCAAAACGAAAAUUUUUGGUAAUAUGA-GCACAUUUAAUUGCCUAAUUGUUUUGUU--UUU-----------
--..--..(((...(((..(((..((....(((((((((((.......)))))))))))...-)).)))..))).))).............--...----------- ( -18.10)
>DroGri_CAF1 61738 84 - 1
-----------GGCCUUUUACGACGCGUUUUGUUACCAAAACGAAAAUUUUUGGUAAUAUGA-GCGAAUUUAAUUGCCUAAUUGUUUUGUUUCCUU-----------
-----------(((..((.....(((....(((((((((((.......)))))))))))...-))).....))..)))..................----------- ( -18.70)
>DroWil_CAF1 132734 105 - 1
ACACUUUUUGGCCUAUUUUAUGGCGCAUUUUGUUACCAAAGCGAAAAUUUUUGGUAAUAAGAGUCACAUUUAAUUGCCUAAUUGUUUUGUU--UUGUUUUUCGUUUG
..((..((.(((..(((..(((..((.((((((((((((((.......))))))))))))))))..)))..))).))).))..))......--.............. ( -21.90)
>DroMoj_CAF1 74774 89 - 1
--CC--UUGGCGGCAUUUUAUGACGCGUUUUGUUACCAAAACAAAAAUUUUCGGUAAUAUGC-GCACAUUUAAUUGCCUAAUUGUUUUGUU--CUU-----------
--..--.....((((((..(((..((((..(((((((((((......)))).))))))).))-)).)))..)).)))).............--...----------- ( -19.80)
>DroPer_CAF1 56636 92 - 1
--ACAUUUUGGCUUAUUUUAUGACGCGUUUUGUUACCAAAACGAAAAUUUUUGGUAAUACCAAAGACAUUUAAUUGCCUAAUUGUUUUGUU--UUU-----------
--(((.((.(((..(((..(((...(((((((....)))))))....(((((((.....))))))))))..))).))).)).)))......--...----------- ( -20.10)
>consensus
__AC__UUUGGCGUAUUUUAUGACGCGUUUUGUUACCAAAACGAAAAUUUUUGGUAAUAUGA_GCACAUUUAAUUGCCUAAUUGUUUUGUU__UUU___________
.....................(((.(((((((....)))))))(((((..((((((((..............)))))).))..))))))))................ ( -9.63 =  -9.86 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:59 2006