Locus 6507

Sequence ID	3R_DroMel_CAF1
Location	17,160,956 – 17,161,059
Length	103
Max. P	0.997100

overview

Window 4

Location	17,160,956 – 17,161,059
Length	103
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	69.64
Mean single sequence MFE	-29.10
Consensus MFE	-13.80
Energy contribution	-15.47
Covariance contribution	1.67
Combinations/Pair	1.38
Mean z-score	-2.70
Structure conservation index	0.47
SVM decision value	2.80
SVM RNA-class probability	0.997100
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17160956 103 + 27905053
CCGAAAGUGUGUCCCAAAGUCGAAACAAGAACCUCCCUUUUAAGGAUCAUAAAGGAGUUACUUGUAACUUAAUGUGUUUCGACUUUGCUUACGCUUUUG----------UUGG
.((((((((((...(((((((((((((.((.(((........))).))......((((((....))))))....)))))))))))))..))))))))))----------.... ( -37.20)
>DroSec_CAF1 70167 106 + 1
CCGAAAGUGUGUCCCAAAGUCGAAACUAGAACAUCCCUUUCUAGGAUCUUAACGGAGUUACUUUUAGCUUGAUGUGUUUCGACUUUGCCCACGUUUUUUUUU-------UUUG
..(((((((((...((((((((((((....((((((((....))).........((((((....)))))))))))))))))))))))..)))))))))....-------.... ( -30.00)
>DroSim_CAF1 61470 108 + 1
CCGGAAGUGUGUCCCAAAGUCGAAACUAGAACAUACCGUUCAAGGAUCUUAACGGAGUUACUUUUAGCUUGA-----UUCGACUUUGCCCACUUUUUUUUUUUUGUUUUUUGG
..(((((((.(...((((((((((.((.((((.....)))).))..........((((((....))))))..-----)))))))))).))))))))................. ( -25.30)
>DroEre_CAF1 61364 102 + 1
CCGGAAGUGAGUCCCAAAGUCGAAACUAUAACAUCCCUUUCU-GUAGUUUAAAGGAGUUACUUCUAGCUUGAUGUGUUUCGACUUCGCUCACGCUUUUC----------UUGG
((((((((((((....((((((((((....((((((((((..-.......)))))(((((....))))).))))))))))))))).))))))....)))----------.))) ( -28.40)
>DroYak_CAF1 88932 102 + 1
CCGGAAGUGAGUCCCAAAGUCGAAACUAGAACAGCCCUUUCU-GUAUUUUAAAGAAGUUACAUCUAUCUUGAUUUGUUUCGACUUCGCUCACUCCUUUG----------UUGG
..(((.((((((....((((((((((....((((......))-))......((((((......)).)))).....)))))))))).)))))))))....----------.... ( -28.30)
>DroAna_CAF1 63370 87 + 1
CCAAAGGUGUGGCUCAAAGUCGAAGCUUGGGGAUUUCCUUUA-GCAGAU---------------UAUCCUUGUGAAGUUCGACUUUGUCCGUUCUUCAG----------UGAG
.((.(((..(((..(((((((((((((..(((....)))..)-))...(---------------(((....))))..)))))))))).)))..)))...----------)).. ( -25.40)
>consensus
CCGAAAGUGUGUCCCAAAGUCGAAACUAGAACAUCCCUUUCA_GGAUCUUAAAGGAGUUACUUCUAGCUUGAUGUGUUUCGACUUUGCCCACGCUUUUG__________UUGG
..(((((.(((...((((((((((((..(((.......))).............((((((....)))))).....))))))))))))..))).)))))............... (-13.80 = -15.47 +   1.67)

alignment

secondary structure

dotplot

Window 5

Location	17,160,956 – 17,161,059
Length	103
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	69.64
Mean single sequence MFE	-26.82
Consensus MFE	-13.08
Energy contribution	-12.89
Covariance contribution	-0.19
Combinations/Pair	1.27
Mean z-score	-2.55
Structure conservation index	0.49
SVM decision value	2.59
SVM RNA-class probability	0.995594
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17160956 103 - 27905053
CCAA----------CAAAAGCGUAAGCAAAGUCGAAACACAUUAAGUUACAAGUAACUCCUUUAUGAUCCUUAAAAGGGAGGUUCUUGUUUCGACUUUGGGACACACUUUCGG
((..----------.....((....))((((((((((((.....(((((....))))).......((.((((......)))).)).))))))))))))))............. ( -27.90)
>DroSec_CAF1 70167 106 - 1
CAAA-------AAAAAAAAACGUGGGCAAAGUCGAAACACAUCAAGCUAAAAGUAACUCCGUUAAGAUCCUAGAAAGGGAUGUUCUAGUUUCGACUUUGGGACACACUUUCGG
....-------..........(((..(((((((((((((((((..........((((...))))....(((....))))))))....))))))))))))...)))........ ( -26.20)
>DroSim_CAF1 61470 108 - 1
CCAAAAAACAAAAAAAAAAAAGUGGGCAAAGUCGAA-----UCAAGCUAAAAGUAACUCCGUUAAGAUCCUUGAACGGUAUGUUCUAGUUUCGACUUUGGGACACACUUCCGG
...................((((((.((((((((((-----....(((...((.(((.((((((((...)))).))))...))))))))))))))))))...).))))).... ( -23.40)
>DroEre_CAF1 61364 102 - 1
CCAA----------GAAAAGCGUGAGCGAAGUCGAAACACAUCAAGCUAGAAGUAACUCCUUUAAACUAC-AGAAAGGGAUGUUAUAGUUUCGACUUUGGGACUCACUUCCGG
....----------.......(((((((((((((((((...((......)).(((((((((((.......-...)))))).))))).))))))))))))...)))))...... ( -30.50)
>DroYak_CAF1 88932 102 - 1
CCAA----------CAAAGGAGUGAGCGAAGUCGAAACAAAUCAAGAUAGAUGUAACUUCUUUAAAAUAC-AGAAAGGGCUGUUCUAGUUUCGACUUUGGGACUCACUUCCGG
....----------....((((((((((((((((((((.....((((.((......))))))......((-((......))))....))))))))))))...))))))))... ( -30.20)
>DroAna_CAF1 63370 87 - 1
CUCA----------CUGAAGAACGGACAAAGUCGAACUUCACAAGGAUA---------------AUCUGC-UAAAGGAAAUCCCCAAGCUUCGACUUUGAGCCACACCUUUGG
....----------(..(((...((.(((((((((((((.....((((.---------------.(((..-...)))..))))..))).))))))))))..))....)))..) ( -22.70)
>consensus
CCAA__________CAAAAGAGUGAGCAAAGUCGAAACACAUCAAGCUAAAAGUAACUCCUUUAAGAUCC_AGAAAGGGAUGUUCUAGUUUCGACUUUGGGACACACUUCCGG
..........................((((((((((((.................................................))))))))))))(((......))).. (-13.08 = -12.89 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:02 2006