Locus 2666

Sequence ID	2R_DroMel_CAF1
Location	9,405,357 – 9,405,517
Length	160
Max. P	0.872244

overview

Window 5

Location	9,405,357 – 9,405,477
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.75
Mean single sequence MFE	-39.85
Consensus MFE	-26.62
Energy contribution	-25.88
Covariance contribution	-0.75
Combinations/Pair	1.34
Mean z-score	-2.19
Structure conservation index	0.67
SVM decision value	0.88
SVM RNA-class probability	0.872244
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9405357 120 + 20766785
AUUUGUGCUGCCUCGGUAGCGGUUUCCUUGUAAUCCGGCUCAGGAGUAGGAUCUUUUUUAAUAGAUUCAGGAAAUUCUGUAUUUUGAGCUGGAUCGGGAGUUGGUUCCUUUUGAACAGGC
.((((((((((....)))))((..(((((.(.(((((((((((((...((((((........)))))).((.....))...))))))))))))).).)))..))..))......))))). ( -38.50)
>DroSec_CAF1 17221 120 + 1
AUUUGUGCUGGCUCGGUAGUGUUCUCCUUGUAAUCCGGCUCAGGAGUUGGAUCUUUUUUAACAGAUUCAACGAAUUCUGCAUUUUGGGCUGGCUCGGGAGUUAGUUCCUUUUGAGCAGGC
......(((.(((((((((.((((((((.((......))..))))(((((((((........))))))))))))).)))).....(((((((((....)))))))))....))))).))) ( -39.90)
>DroEre_CAF1 17204 120 + 1
AUCUGCGCUGGCUCUCUAGUGCUCUUCUUGGAAUCCGGCUCGGGAGUUAGAUCUUUUUUAACUGAUGCGGUGGAUUCUGCAUUUUGGGCUGGCUCGGGAGUUAGUUGCUCUUGAACGGGC
.((((.((..((((...(((((.......((((((((.(.((..(((((((.....)))))))..)).).)))))))))))))..))))..))((((((((.....)))))))).)))). ( -46.51)
>DroYak_CAF1 17205 120 + 1
AUCUGUGCUAGCUGUGUAGUGUUUUCCUUGUAUUCCGGCUUAGGAGUUAGAUCUUUCUUAACUGAUUCGGUGAAUUCUGCAUUUGGAGCUGGCUCGGGAGUUAGUUCCUUUUGAACGGGC
.((((.(((((((((((((.((((.((......(((......)))((((((....)).))))......)).)))).))))))....))))))).)))).((..((((.....))))..)) ( -34.50)
>consensus
AUCUGUGCUGGCUCGGUAGUGUUCUCCUUGUAAUCCGGCUCAGGAGUUAGAUCUUUUUUAACAGAUUCAGUGAAUUCUGCAUUUUGAGCUGGCUCGGGAGUUAGUUCCUUUUGAACAGGC
.....((((((....)))))).....(((((...(((((((((((((((((.....)))))).....(((......)))..))))))))))).(((((((.......)))))))))))). (-26.62 = -25.88 +  -0.75)

alignment

secondary structure

dotplot

Window 6

Location	9,405,397 – 9,405,517
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-39.05
Consensus MFE	-29.21
Energy contribution	-28.90
Covariance contribution	-0.31
Combinations/Pair	1.19
Mean z-score	-1.82
Structure conservation index	0.75
SVM decision value	0.46
SVM RNA-class probability	0.746921
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9405397 120 + 20766785
CAGGAGUAGGAUCUUUUUUAAUAGAUUCAGGAAAUUCUGUAUUUUGAGCUGGAUCGGGAGUUGGUUCCUUUUGAACAGGCUUAGGAGAUGUCUCCGUUUCAGCUGGCCUGGAACUUGUGU
((.((((((((.((..(((....((((((((((((.....)))))...)))))))..)))..)).))))......((((((...((((((....))))))....))))))..)))).)). ( -34.80)
>DroSec_CAF1 17261 120 + 1
CAGGAGUUGGAUCUUUUUUAACAGAUUCAACGAAUUCUGCAUUUUGGGCUGGCUCGGGAGUUAGUUCCUUUUGAGCAGGCUUGGGAGAUGUCUCCGUUUCAGCUGGCCUGGAACUUGUGU
((((.(((((((((........)))))))))..........(((..(((..(((.((((((..((((.....))))..)))).((((....))))...)))))..)))..)))))))... ( -43.50)
>DroEre_CAF1 17244 120 + 1
CGGGAGUUAGAUCUUUUUUAACUGAUGCGGUGGAUUCUGCAUUUUGGGCUGGCUCGGGAGUUAGUUGCUCUUGAACGGGCUUGGGAGUUGUCUCCGUUUCAGCUGGCUUGGAACUUGUGU
((.((((....(((...(((.((((.((((.((((...((.(((..((((.(.((((((((.....)))))))).).))))..))))).)))))))).)))).)))...))))))).)). ( -41.20)
>DroYak_CAF1 17245 120 + 1
UAGGAGUUAGAUCUUUCUUAACUGAUUCGGUGAAUUCUGCAUUUGGAGCUGGCUCGGGAGUUAGUUCCUUUUGAACGGGCUUGGGAGAUGCCUCCGUUUCAGCUGGCCUGGAACUUGUGU
..((((....((((..(....(((.(((((((.......)))).((((((((((....))))))))))....))))))....)..))))..))))(((((((.....)))))))...... ( -36.70)
>consensus
CAGGAGUUAGAUCUUUUUUAACAGAUUCAGUGAAUUCUGCAUUUUGAGCUGGCUCGGGAGUUAGUUCCUUUUGAACAGGCUUGGGAGAUGUCUCCGUUUCAGCUGGCCUGGAACUUGUGU
(((((.(((((((..........)))))))....)))))......(((((.(.(((((((.......))))))).).))))).((((....))))(((((((.....)))))))...... (-29.21 = -28.90 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:47 2006