Locus 4897

Sequence ID	3R_DroMel_CAF1
Location	12,870,784 – 12,870,976
Length	192
Max. P	0.822775

overview

Window 7

Location	12,870,784 – 12,870,880
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	86.46
Mean single sequence MFE	-40.29
Consensus MFE	-31.88
Energy contribution	-31.33
Covariance contribution	-0.55
Combinations/Pair	1.39
Mean z-score	-2.71
Structure conservation index	0.79
SVM decision value	0.69
SVM RNA-class probability	0.822775
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12870784 96 - 27905053
UUGGGUAGAGGUCGCUGGUUGCCGCC---GGGCAGUGGAAAGUUGUGCGGCAUGUGCUGCUGCAUUAGAGGAUGCUG---GGGCAAUUGCGGAAUAUUCCCG
..(((...(..((((.(((((((.((---((.((..........((((((((.....)))))))).......)))))---))))))))))))..)...))). ( -38.03)
>DroSec_CAF1 1212 96 - 1
UUGGGAAGAGGUCGCUGGUUGCCGCC---GGGCAGUGGAAAGUUGGGCGGCAUGUGCUGCUGCAUUAGAGGAUGCUG---AGGCAAUUGCGGAAUAUUCCCA
.((((((....((((....(((((((---.(((........))).)))))))..((((...(((((....)))))..---.))))...))))....)))))) ( -42.30)
>DroSim_CAF1 1274 96 - 1
UUGGGUAGAGGUCGCUGGUUGCCGCC---GGGCAGUGGAAAGUUGGGCGGCAUGUGCUGCUGCAUUAGAGGAUGCUG---AGGCAAUUGCGGAAUAUUCCCG
..(((...(..((((....(((((((---.(((........))).)))))))..((((...(((((....)))))..---.))))...))))..)...))). ( -39.20)
>DroEre_CAF1 1377 96 - 1
UUGGGUAGAGGUCGCUGGUUGCCGCC---GGGCAGUGGAAAGUUUGGCGGCAUGUGUUGCUGCAUCAGCGGAUGCUG---GGGCAAUUGCGGAAUAUUCCCG
..(((...(..((((.((((((((((---((((........)))))))(((((.(((((......))))).))))).---.)))))))))))..)...))). ( -41.50)
>DroYak_CAF1 1303 96 - 1
UUGGGUAGAGGUCGCUGGUUGCCGCC---GGGCAGUGGAAAGUUUGGCAGCAUGUGCUGCUGUAUUAGCGGAUGCUG---GGGUAAUUGCGGAAUAUUCCCG
..(((...(..((((.((((((((((---((((........)))))))(((((.(((((......))))).))))).---.)))))))))))..)...))). ( -40.50)
>DroAna_CAF1 1177 102 - 1
UUGGGCAGUGGACGCUGAUUGCCGCCAUUGGGCAGCGGAUAGUUCAGCGGUAGGUAAUUGGGCAUCAGCGGGUGCUGCGCAGGCAGUGGUGGCAUAUUUCCG
.((.((((((..(((((((.((((((....))).((.((....)).))............))))))))))..)))))).))((.((((......)))).)). ( -40.20)
>consensus
UUGGGUAGAGGUCGCUGGUUGCCGCC___GGGCAGUGGAAAGUUGGGCGGCAUGUGCUGCUGCAUUAGAGGAUGCUG___AGGCAAUUGCGGAAUAUUCCCG
..(((......((((.((((((((((....)))............((((((....))))))(((((....)))))......)))))))))))......))). (-31.88 = -31.33 +  -0.55)

alignment

secondary structure

dotplot

Window 8

Location	12,870,880 – 12,870,976
Length	96
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-26.73
Consensus MFE	-17.49
Energy contribution	-18.05
Covariance contribution	0.56
Combinations/Pair	1.25
Mean z-score	-1.53
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.580869
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12870880 96 + 27905053
UCCACAAGCUCUGCCCACGGCCCUGAACAAUUUCGCGAUGCAUCCAAGCUUCAAUGCGAUGCGCGCCGCUGGAAU---CCAUCCAGGGGCUUUUAUGCA
.......((...((((.((((...(((....)))((...(((((...((......)))))))))))))(((((..---...)))))))))......)). ( -30.10)
>DroVir_CAF1 1949 93 + 1
CCCACU---UUUGCCCACGGCGCUCAACAAUUUUGCCAUGCAUCCGAGCUUUAAUGCAAUGCGCGCCGUUGGCAU---GCACCCGGCGGCCUUUAUGCA
.((...---..((((.(((((((.((.......(((...))).....((......))..)).))))))).)))).---((.....)))).......... ( -27.50)
>DroGri_CAF1 2636 96 + 1
UCCUCA---UUUGCCCACUGCACUCAACAACUUUGCCAUGCAUCCGAGCUUCAAUGCGAUGCGUGCCGUUGGCAUCCCGCACCCCGCAACCUUUAUGCA
......---..((((.((.((((.(((.....)))....(((((...((......))))))))))).)).))))...........(((.......))). ( -21.90)
>DroEre_CAF1 1473 96 + 1
UCCACACGCUUUGCCCACGGCCCUCAACAAUUUUGCGAUGCAUCCGAGCUUCAAUGCGAUGCGCGCCGCUGGGCU---GCAUCCAGCCGCGUUUAUGCA
.....((((...(((((((((.(.(((.....))).)..(((((...((......)))))))..)))).))))).---((.....)).))))....... ( -28.70)
>DroMoj_CAF1 1447 91 + 1
UCCACA---UCUGCCCACGGCGCUCAACAACUUUGCCAUGCAUCCCAGCUUCAAUGCGAUGCGCGCCGUUGGCUU---GCAUUCAGCGGCCUACAUG--
.((...---...(((.(((((((.(((.....)))....(((((.((.......)).)))))))))))).)))..---((.....))))........-- ( -28.60)
>DroPer_CAF1 1097 93 + 1
CCCACA---UCUGCCCACAGCCCUAAACAACUUUGCAAUGCAUCCAAGUUUCAAUGCAAUGCGAGCUGCUGGCUU---GCAUCCGGCGGCCUUUAUGCA
......---..........((...........(((((.(((((..........))))).)))))((((((((...---....))))))))......)). ( -23.60)
>consensus
UCCACA___UCUGCCCACGGCCCUCAACAACUUUGCCAUGCAUCCGAGCUUCAAUGCGAUGCGCGCCGCUGGCAU___GCAUCCAGCGGCCUUUAUGCA
............((.....)).............((..((((((...((......)))))))).((((((((..........))))))))......)). (-17.49 = -18.05 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	12,870,880 – 12,870,976
Length	96
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-33.82
Consensus MFE	-21.84
Energy contribution	-21.68
Covariance contribution	-0.16
Combinations/Pair	1.31
Mean z-score	-1.52
Structure conservation index	0.65
SVM decision value	0.05
SVM RNA-class probability	0.557118
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12870880 96 - 27905053
UGCAUAAAAGCCCCUGGAUGG---AUUCCAGCGGCGCGCAUCGCAUUGAAGCUUGGAUGCAUCGCGAAAUUGUUCAGGGCCGUGGGCAGAGCUUGUGGA
.((......))(((((((..(---.(((..((((...(((((.((........))))))).))))))).)..)))))))(((..(((...)))..))). ( -34.20)
>DroVir_CAF1 1949 93 - 1
UGCAUAAAGGCCGCCGGGUGC---AUGCCAACGGCGCGCAUUGCAUUAAAGCUCGGAUGCAUGGCAAAAUUGUUGAGCGCCGUGGGCAAA---AGUGGG
(((((...((...))..))))---)((((.((((((((((((((......))...)))))..((((....))))..))))))).))))..---...... ( -34.50)
>DroGri_CAF1 2636 96 - 1
UGCAUAAAGGUUGCGGGGUGCGGGAUGCCAACGGCACGCAUCGCAUUGAAGCUCGGAUGCAUGGCAAAGUUGUUGAGUGCAGUGGGCAAA---UGAGGA
.(((.......)))(.((((((...((((...)))))))))).)......(((((..(((((..(((.....))).))))).)))))...---...... ( -29.80)
>DroEre_CAF1 1473 96 - 1
UGCAUAAACGCGGCUGGAUGC---AGCCCAGCGGCGCGCAUCGCAUUGAAGCUCGGAUGCAUCGCAAAAUUGUUGAGGGCCGUGGGCAAAGCGUGUGGA
..(((..((((.((.....))---.(((((.((((.((((((((......))...))))).(((((....)).)))).)))))))))...))))))).. ( -35.70)
>DroMoj_CAF1 1447 91 - 1
--CAUGUAGGCCGCUGAAUGC---AAGCCAACGGCGCGCAUCGCAUUGAAGCUGGGAUGCAUGGCAAAGUUGUUGAGCGCCGUGGGCAGA---UGUGGA
--(((((..((((((......---.)))..((((((((((((.((.......)).)))))..((((....))))..))))))).)))..)---)))).. ( -36.10)
>DroPer_CAF1 1097 93 - 1
UGCAUAAAGGCCGCCGGAUGC---AAGCCAGCAGCUCGCAUUGCAUUGAAACUUGGAUGCAUUGCAAAGUUGUUUAGGGCUGUGGGCAGA---UGUGGG
(((((...((...))..))))---).(((.((((((((((.((((((.(....).)))))).)))(((....))).))))))).)))...---...... ( -32.60)
>consensus
UGCAUAAAGGCCGCUGGAUGC___AUGCCAACGGCGCGCAUCGCAUUGAAGCUCGGAUGCAUGGCAAAAUUGUUGAGGGCCGUGGGCAAA___UGUGGA
..((((......((.....)).....(((.((((((((((((((......))...)))))...(((....)))...))))))).)))......)))).. (-21.84 = -21.68 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:32 2006