Locus 10226

Sequence ID	3R_DroMel_CAF1
Location	27,413,740 – 27,413,851
Length	111
Max. P	0.812360

overview

Window 1

Location	27,413,740 – 27,413,851
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.28
Mean single sequence MFE	-33.17
Consensus MFE	-22.15
Energy contribution	-22.85
Covariance contribution	0.70
Combinations/Pair	1.28
Mean z-score	-2.09
Structure conservation index	0.67
SVM decision value	0.65
SVM RNA-class probability	0.812360
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27413740 111 + 27905053
AGAACCUUCGGCAACAGAUCUUGGAUCUGGAAGAUGCUGGUAUUUUGCCGGUGGUGCUGAACUUUGCGCUCAAGGAACUAAAUCUGUAAGCGUAGAGAUUUGGAUUUUACU
....(((((((((.((((((...))))))......((((((.....))))))..)))))))(((((((((...(((......)))...)))))))))....))........ ( -37.20)
>DroSec_CAF1 15866 111 + 1
AGAACCUUCGGCAACAGAUCCUGGACCUGGAAGAUGCUGGUAUCUUGCCGGUGGUACUGAACUUUGCGCUCAAGGAACUAAAUCUGUAAGCGUAGAGAUUUUGAUUUUCCA
((.(((.((((((.....(((.......)))(((((....))))))))))).))).))...(((((((((...(((......)))...))))))))).............. ( -33.10)
>DroSim_CAF1 15668 111 + 1
AGAACCUAAGGCAACAGAUCCUGGAUCUGGAAGAUGCUGGUAUCUUGCCGGUGGUGCUGAACUUUGCGCUCAAGGAACUAAAUUUGUAAGCGUAGAGAUUUUGAUUUUCCA
((.(((...(((..((((((...)))))).((((((....)))))))))...))).))...(((((((((((((........))))..))))))))).............. ( -33.10)
>DroEre_CAF1 16188 99 + 1
AGAACCUUCGACAACAGAUCCUGGAUCUGGAAGAUGCUGGCCUUUUGCCGGUGGUUUUGAACUUUGCGCUCAAGGAACUAAAUCUGUAAGCGUAGAGU-U-----------
((((((........((((((...))))))......((((((.....)))))))))))).(((((((((((...(((......)))...))))))))))-)----------- ( -35.10)
>DroYak_CAF1 16087 110 + 1
AGAACCUUCGACAACAGAUCCUGGAUCUGGAGGAUGCUGGUCUUUUGCCGGUGGUUCUGAACUUUGCGCUCAAGGAAUUGAACCUGUAAGCGUGCAGU-UCCGAUUUUAAA
((((((.(((.(((.(((((..(.(((.....))).).))))).))).))).))))))(((((.((((((..(((.......)))...)))))).)))-)).......... ( -36.40)
>DroAna_CAF1 16216 108 + 1
AAAACCUACGUCAGCAGAUCCUAAACCUGGAAGAUGCUGGCCUGCUUCCAGUAGUUUUGAACUUUGCGCUUAAGGAAUUAAAUCUUUAAAUAAAAAAGUU---AUUUUGUA
.........(((((((..(((.......)))...)))))))((((.....)))).....((((((....(((((((......))))))).....))))))---........ ( -24.10)
>consensus
AGAACCUUCGGCAACAGAUCCUGGAUCUGGAAGAUGCUGGUAUUUUGCCGGUGGUUCUGAACUUUGCGCUCAAGGAACUAAAUCUGUAAGCGUAGAGAUUU_GAUUUUACA
((.(((........((((((...))))))......((((((.....))))))))).))...(((((((((...(((......)))...))))))))).............. (-22.15 = -22.85 +   0.70)

alignment

secondary structure

dotplot

Window 2

Location	27,413,740 – 27,413,851
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.28
Mean single sequence MFE	-25.68
Consensus MFE	-18.54
Energy contribution	-17.80
Covariance contribution	-0.74
Combinations/Pair	1.41
Mean z-score	-1.22
Structure conservation index	0.72
SVM decision value	-0.00
SVM RNA-class probability	0.531291
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27413740 111 - 27905053
AGUAAAAUCCAAAUCUCUACGCUUACAGAUUUAGUUCCUUGAGCGCAAAGUUCAGCACCACCGGCAAAAUACCAGCAUCUUCCAGAUCCAAGAUCUGUUGCCGAAGGUUCU
...................((((((..((......))..))))))........((.(((..((((((.....(((.(((((........))))))))))))))..))).)) ( -24.20)
>DroSec_CAF1 15866 111 - 1
UGGAAAAUCAAAAUCUCUACGCUUACAGAUUUAGUUCCUUGAGCGCAAAGUUCAGUACCACCGGCAAGAUACCAGCAUCUUCCAGGUCCAGGAUCUGUUGCCGAAGGUUCU
.((((.....((((((.((....)).))))))..)))).(((((.....)))))(.(((..(((((((((......)))...((((((...))))))))))))..))).). ( -27.30)
>DroSim_CAF1 15668 111 - 1
UGGAAAAUCAAAAUCUCUACGCUUACAAAUUUAGUUCCUUGAGCGCAAAGUUCAGCACCACCGGCAAGAUACCAGCAUCUUCCAGAUCCAGGAUCUGUUGCCUUAGGUUCU
((((..................................((((((.....)))))).......((.(((((......)))))))...))))(((((((......))))))). ( -20.20)
>DroEre_CAF1 16188 99 - 1
-----------A-ACUCUACGCUUACAGAUUUAGUUCCUUGAGCGCAAAGUUCAAAACCACCGGCAAAAGGCCAGCAUCUUCCAGAUCCAGGAUCUGUUGUCGAAGGUUCU
-----------(-(((...((((((..((......))..))))))...))))...((((..((((((.(((((.(.(((.....))).).)).))).))))))..)))).. ( -24.70)
>DroYak_CAF1 16087 110 - 1
UUUAAAAUCGGA-ACUGCACGCUUACAGGUUCAAUUCCUUGAGCGCAAAGUUCAGAACCACCGGCAAAAGACCAGCAUCCUCCAGAUCCAGGAUCUGUUGUCGAAGGUUCU
..........((-(((...((((((.(((.......)))))))))...)))))((((((..((((((.....(((.(((((........))))))))))))))..)))))) ( -36.70)
>DroAna_CAF1 16216 108 - 1
UACAAAAU---AACUUUUUUAUUUAAAGAUUUAAUUCCUUAAGCGCAAAGUUCAAAACUACUGGAAGCAGGCCAGCAUCUUCCAGGUUUAGGAUCUGCUGACGUAGGUUUU
........---..((((.......)))).........(((((((....(((.....))).(((((((...(....)..))))))))))))))((((((....))))))... ( -21.00)
>consensus
UGGAAAAUC_AAAUCUCUACGCUUACAGAUUUAGUUCCUUGAGCGCAAAGUUCAGAACCACCGGCAAAAGACCAGCAUCUUCCAGAUCCAGGAUCUGUUGCCGAAGGUUCU
...................((((((..((......))..))))))........((.(((..((((((.....(((.(((((........))))))))))))))..))).)) (-18.54 = -17.80 +  -0.74)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:58 2006