Locus 5766

Sequence ID	3L_DroMel_CAF1
Location	15,636,188 – 15,636,338
Length	150
Max. P	0.982000

overview

Window 8

Location	15,636,188 – 15,636,298
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.03
Mean single sequence MFE	-33.00
Consensus MFE	-31.20
Energy contribution	-31.26
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.95
SVM decision value	1.90
SVM RNA-class probability	0.982000
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15636188 110 + 23771897
AGGUUGCCAGGGCAAAAAUAAAAAUGGUAAA----------GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAA
...((((((...............)))))).----------....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))......... ( -32.06)
>DroSec_CAF1 58295 110 + 1
AGGUUGCCAGGGCAAAAAUAAAAAUGGUAAA----------GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAA
...((((((...............)))))).----------....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))......... ( -32.06)
>DroSim_CAF1 59263 110 + 1
AGGUUGCCAGGGCAAAAAUAAAAAUGGUAAA----------GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAGAAGUCAGGAUCGUCUGCUGAUCUGACGUUAA
...((((((...............)))))).----------....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))......... ( -32.06)
>DroYak_CAF1 63205 120 + 1
AGGUUGCCAGGGCCAAAGUAGAAAUGGAAAAAGGAGGAAUGGAACGAUCGCAGAGGGCUGAUCCCUCGGAACAGGGAUUGGGACUGGAGAAGUCAGGAUCGUCUGCUGAUCUGACGUUAA
..(((.(((...((.....................))..))))))(((((((((.(((..((((((......))))))..)((((.....))))....)).))))).))))......... ( -35.80)
>consensus
AGGUUGCCAGGGCAAAAAUAAAAAUGGUAAA__________GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAA
...((((((...............))))))...............(((((((((.(((..((((((......))))))..)((((.....))))....)).))))).))))......... (-31.20 = -31.26 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	15,636,188 – 15,636,298
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.03
Mean single sequence MFE	-25.02
Consensus MFE	-22.68
Energy contribution	-22.93
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.91
SVM decision value	1.45
SVM RNA-class probability	0.954840
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15636188 110 - 23771897
UUAACGUCAGAUCAGCAGACGAUCCUGACUUUUCGAAUCCCAAUCCCUGUUCCAAGGGAUCAGCCCUCUGCGAUCGUUC----------UUUACCAUUUUUAUUUUUGCCCUGGCAACCU
.........((((.((((((((..........))).......((((((......))))))......)))))))))....----------................((((....))))... ( -24.90)
>DroSec_CAF1 58295 110 - 1
UUAACGUCAGAUCAGCAGACGAUCCUGACUUUUCGAAUCCCAAUCCCUGUUCCAAGGGAUCAGCCCUCUGCGAUCGUUC----------UUUACCAUUUUUAUUUUUGCCCUGGCAACCU
.........((((.((((((((..........))).......((((((......))))))......)))))))))....----------................((((....))))... ( -24.90)
>DroSim_CAF1 59263 110 - 1
UUAACGUCAGAUCAGCAGACGAUCCUGACUUCUCGAAUCCCAAUCCCUGUUCCAAGGGAUCAGCCCUCUGCGAUCGUUC----------UUUACCAUUUUUAUUUUUGCCCUGGCAACCU
.........((((.(((((.(...((((......(.....)..(((((......))))))))).).)))))))))....----------................((((....))))... ( -24.20)
>DroYak_CAF1 63205 120 - 1
UUAACGUCAGAUCAGCAGACGAUCCUGACUUCUCCAGUCCCAAUCCCUGUUCCGAGGGAUCAGCCCUCUGCGAUCGUUCCAUUCCUCCUUUUUCCAUUUCUACUUUGGCCCUGGCAACCU
.....(((((.......(((((((..((((.....))))..............(((((.....)))))...)))))))...............(((.........)))..)))))..... ( -26.10)
>consensus
UUAACGUCAGAUCAGCAGACGAUCCUGACUUCUCGAAUCCCAAUCCCUGUUCCAAGGGAUCAGCCCUCUGCGAUCGUUC__________UUUACCAUUUUUAUUUUUGCCCUGGCAACCU
.........((((.(((((.(...((((...............(((((......))))))))).).)))))))))..............................((((....))))... (-22.68 = -22.93 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	15,636,219 – 15,636,338
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.77
Mean single sequence MFE	-40.47
Consensus MFE	-40.06
Energy contribution	-39.88
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.55
Structure conservation index	0.99
SVM decision value	1.62
SVM RNA-class probability	0.967856
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15636219 119 + 23771897
-GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAAUCGACUAAAUUGUAGCAGCUGAACUGUCAGUUUAGUUAAG
-....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))...........((((((((((..((((.....))))))))))))))... ( -39.80)
>DroSec_CAF1 58326 119 + 1
-GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAAUCGACUAAAUUGUAGCAGCUGAACUGUCAGUUUAGUUAAG
-....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))...........((((((((((..((((.....))))))))))))))... ( -39.80)
>DroSim_CAF1 59294 119 + 1
-GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAGAAGUCAGGAUCGUCUGCUGAUCUGACGUUAAUCGACUAAAUUGUAGCAGCUGAACUGUCAGUUUAGUUAAG
-....(((((((((...(..((((((......))))))..)(((((.........))))).))))).))))...........((((((((((..((((.....))))))))))))))... ( -39.80)
>DroYak_CAF1 63245 120 + 1
GGAACGAUCGCAGAGGGCUGAUCCCUCGGAACAGGGAUUGGGACUGGAGAAGUCAGGAUCGUCUGCUGAUCUGACGUUAAUCGACUAAAUUGUAGCAGCUGAACUGUCAGUUUAGUUAAG
.....(((((((((.(((..((((((......))))))..)((((.....))))....)).))))).))))...........((((((((((..((((.....))))))))))))))... ( -42.50)
>consensus
_GAACGAUCGCAGAGGGCUGAUCCCUUGGAACAGGGAUUGGGAUUCGAAAAGUCAGGAUCGUCUGCUGAUCUGACGUUAAUCGACUAAAUUGUAGCAGCUGAACUGUCAGUUUAGUUAAG
.....(((((((((.(((..((((((......))))))..)((((.....))))....)).))))).))))...........((((((((((..((((.....))))))))))))))... (-40.06 = -39.88 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:22 2006