Locus 1044

Sequence ID	2L_DroMel_CAF1
Location	2,927,015 – 2,927,210
Length	195
Max. P	0.959617

overview

Window 8

Location	2,927,015 – 2,927,130
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.21
Mean single sequence MFE	-21.38
Consensus MFE	-17.32
Energy contribution	-17.56
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.66
Structure conservation index	0.81
SVM decision value	0.35
SVM RNA-class probability	0.700154
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927015 115 - 22407834
---ACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCCACUCCCUCCGCUCACCC--UCUCCCUUCUUCUCCACAGAAUAAAUGGCUAACUUUGUUGAU
---..((((.....))))......(((((((((......(((((((.........)))).................--.........((((....))))......)))...))))))))) ( -19.50)
>DroSec_CAF1 45269 112 - 1
---ACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCCAUCCCCUUCGCUCACCCCCUCUCCC---GACGCCACAGAAUAAAUGGCUAACUUUGUUG--
---..((((.....)))).................((((((.((((.........)))).........................---...((((.........)))).....))))))-- ( -19.90)
>DroSim_CAF1 46391 99 - 1
---ACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCC-------------ACCCCCUCUCCC---GUCGCCACAGAAUAAAUGGCUAACUUUGUUG--
---..((((.....)))).................((((((.((((.........))))-------------............---...((((.........)))).....))))))-- ( -19.90)
>DroEre_CAF1 46331 108 - 1
---ACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCCC-C---CCCGCUCGCCC--UCUCCCGG-CU--CCGCAGAAUAAAUGGCUAACUUUGUUGAU
---..((((.....))))......(((((((((......(((((((.........)))).-.---...((..(((.--......))-).--..))..........)))...))))))))) ( -23.30)
>DroYak_CAF1 46258 114 - 1
ACGACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCCCUC---CCCUCUCACCC--UCUCCCGU-AUCGCCACGGAAUAAAUGGCUAACUUUGUUGAU
.((((((((.....)))).......(((((.........((.((((.........)))))).---...........--....((((-......))))........)))))....)))).. ( -24.30)
>consensus
___ACGCCCAUUCAGGGCCAUCCCAUUAGCAAAUACAACAGCGGCUAUAAUUAUAAGCCA_C___CCCGCUCACCC__UCUCCC___GUCGCCACAGAAUAAAUGGCUAACUUUGUUGAU
.....((((.....)))).................((((((.((((.........))))...............................((((.........)))).....)))))).. (-17.32 = -17.56 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	2,927,055 – 2,927,170
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.82
Mean single sequence MFE	-40.86
Consensus MFE	-33.64
Energy contribution	-34.08
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.97
Structure conservation index	0.82
SVM decision value	1.50
SVM RNA-class probability	0.959617
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927055 115 + 22407834
GA--GGGUGAGCGGAGGGAGUGGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
..--(((..((.(.....(((((((.........)))))))(((.((.((((((........((((((((((.....---)))))))))).)))))).)).))).)))..)))....... ( -40.70)
>DroSec_CAF1 45304 117 + 1
GAGGGGGUGAGCGAAGGGGAUGGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
((.(((((((((.(......).)))..........(((((.(((.((((....)))).))).((((((((((.....---)))))))))))))))........)))))).))........ ( -39.90)
>DroSim_CAF1 46426 104 + 1
GAGGGGGU-------------GGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
((.(((((-------------(.(((.(((((...(((((.(((.((((....)))).))).((((((((((.....---))))))))))))))))))))))))))))).))........ ( -40.10)
>DroEre_CAF1 46368 111 + 1
GA--GGGCGAGCGGG---G-GGGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
.(--(.((..(((((---(-..((((.(((((...(((((.(((.((((....)))).))).((((((((((.....---)))))))))))))))))))))))).))))))....)).)) ( -42.40)
>DroYak_CAF1 46297 115 + 1
GA--GGGUGAGAGGG---GAGGGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGUCGUCGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
..--.((((...(((---((((((((.(((((...(((((.(((.((((....)))).))).(((((((((((......))))))))))))))))))))))))).)))).)))...)))) ( -41.20)
>consensus
GA__GGGUGAGCGGA___G_GGGCUUAUAAUUAUAGCCGCUGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU___CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCU
....(((((((..........((((.........))))(((....((.((((((........((((((((((........)))))))))).)))))).)).)))..)))))))....... (-33.64 = -34.08 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	2,927,093 – 2,927,210
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.80
Mean single sequence MFE	-42.02
Consensus MFE	-38.62
Energy contribution	-38.66
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.92
SVM decision value	1.36
SVM RNA-class probability	0.945806
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927093 117 + 22407834
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUCCGGGCGGCGUGCAAUCAGUUGAAUUGCAAUUGG
.((((((.((((((......)))).((((.((.((((---(((((((((((..(((......((.....)).....)))..)).))))))))))))).)).))))...)).))))))... ( -44.30)
>DroSec_CAF1 45344 117 + 1
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUUCGGGCGGCGUGCAAUCAGUUGAAUUGCAAUUGG
.((((((.((((((......)))).((((.((.((((---((((((..(((..(((......((.....)).....)))..)).)..)))))))))).)).))))...)).))))))... ( -42.50)
>DroSim_CAF1 46453 117 + 1
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUUCGGGCGGCGUGCAAUCAGUUGAAUUGCAAUUGG
.((((((.((((((......)))).((((.((.((((---((((((..(((..(((......((.....)).....)))..)).)..)))))))))).)).))))...)).))))))... ( -42.50)
>DroEre_CAF1 46402 117 + 1
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU---CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUUCGGCCGGAGUGCAAUCAGUUGAAUUGCAAUUGG
.(((((((((............((((((((((.....---)))))))))).((((......(((((.((....))))))).((....)))))))))))))))((((((.....)))))). ( -39.30)
>DroYak_CAF1 46332 120 + 1
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGUCGUCGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUUCGGGCGGAGUGCAAUCAGUUGAAUUGCAAUUGG
.((((((((((((...(..((.(((((((((((......)))))))))))(..(((......((.....)).....)))..).))..).))).)))))))))((((((.....)))))). ( -41.50)
>consensus
UGUUGUAUUUGCUAAUGGGAUGGCCCUGAAUGGGCGU___CGUUCGGGGCGUGGCAAUUAAAGCACCUUGUCCAAGUGCUGCGAUUUCGGGCGGCGUGCAAUCAGUUGAAUUGCAAUUGG
.((((((((((((...(((((.((((((((((........))))))))))(..(((......((.....)).....)))..).))))).))))).)))))))((((((.....)))))). (-38.62 = -38.66 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:55 2006