Locus 2560

Sequence ID	3R_DroMel_CAF1
Location	6,935,333 – 6,935,509
Length	176
Max. P	0.999762

overview

Window 6

Location	6,935,333 – 6,935,447
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	96.49
Mean single sequence MFE	-40.21
Consensus MFE	-37.68
Energy contribution	-37.76
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-2.10
Structure conservation index	0.94
SVM decision value	3.18
SVM RNA-class probability	0.998680
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6935333 114 - 27905053
ACAGGCCACAUGCUUCUGCAGUAGUUGCAGCUGCCGUCAGGGAAACCACAAAAUGUUAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGGCCAUUAAGGUGAACGUU
...((((((.(((....)))(.((((((((((((.....((....))..........(((..............))))))))))))))).).).)))))............... ( -38.94)
>DroSec_CAF1 83978 114 - 1
ACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGCAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGGCCAUUAAGGUGAACGCU
..(((((...)))))..((.(.((((((((((((.((..((....)).......((((..........))))..)).)))))))))))).).(((.(((.....))).))))). ( -42.40)
>DroSim_CAF1 85271 114 - 1
ACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGCAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGCCCAUUAAGGUGAACGUU
..(((((...))))).....(.((((((((((((.((..((....)).......((((..........))))..)).)))))))))))).)(((((((......))).)))).. ( -38.20)
>DroEre_CAF1 85848 114 - 1
ACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGGCCAUUAAGGUGAACGUC
..(((((...))))).....(.((((((((((((.((..((....)).......((((..........))))..)).)))))))))))).)((((.(((.....))).)))).. ( -42.20)
>DroYak_CAF1 85981 114 - 1
ACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGUGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGGCCAUUAAGGUGAACGUC
..(((((...))))).....(.((((((((((((.((..(((....))).....((((..........))))..)).)))))))))))).)((((.(((.....))).)))).. ( -39.30)
>consensus
ACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCUGCAGCUGCGACUUCCGUUGGCCAUUAAGGUGAACGUU
..((((.....)))).....(.((((((((((((.((..((....)).......((((..........))))..)).)))))))))))).)((((.(((.....))).)))).. (-37.68 = -37.76 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	6,935,370 – 6,935,479
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	96.88
Mean single sequence MFE	-28.25
Consensus MFE	-26.05
Energy contribution	-26.49
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.92
SVM decision value	0.45
SVM RNA-class probability	0.742352
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6935370 109 - 27905053
UUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAUGCUUCUGCAGUAGUUGCAGCUGCCGUCAGGGAAACCACAAAAUGUUAGCCUUAAAAAUGAUCCGCU
..((....((((((((((((((.............(((.....))))))))))))))).))((((.(((..((....)).....))).))))..............)). ( -27.61)
>DroSec_CAF1 84015 109 - 1
UUGCCAAUUGAACCACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGCAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCU
..((..(((........((.(((((..........(((....(((..((((((...))))))..)))))).((....)).....))))).)).........)))..)). ( -26.73)
>DroSim_CAF1 85308 109 - 1
UUGCCAAUUGAACUACUGCACACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGCAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCU
..((....((((((((((((..(........)..(((((...))))).)))))))))).))((((.((...((....))......)).))))..............)). ( -26.00)
>DroEre_CAF1 85885 109 - 1
UUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCU
..((....((((((((((((((.............((((...)))))))))))))))).))((((.((...((....))......)).))))..............)). ( -31.31)
>DroYak_CAF1 86018 109 - 1
UUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGUGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCU
..((....((((((((((((((.............((((...)))))))))))))))).))((((.((...(((....)))....)).))))..............)). ( -29.61)
>consensus
UUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGGGGAAACCACAAAAUGUCAGCCUUAAAAAUGAUCCGCU
..((....((((((((((((((.............(((.....))))))))))))))).))((((.((...((....))......)).))))..............)). (-26.05 = -26.49 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	6,935,407 – 6,935,509
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	97.65
Mean single sequence MFE	-33.96
Consensus MFE	-31.48
Energy contribution	-31.92
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.23
Structure conservation index	0.93
SVM decision value	3.03
SVM RNA-class probability	0.998183
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6935407 102 + 27905053
CUGACGGCAGCUGCAACUACUGCAGAAGCAUGUGGCCUGUCUGAUUUAUGUCUGCAGUAGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGAAGCCAAAA
.....(((...((.(((((((((((..(((((...(......)...))))))))))))))))))((((.((((......)))).)))).......))).... ( -31.40)
>DroSec_CAF1 84052 102 + 1
CCGGCGGCAGCUGCAACUACUGCAGAAGCCUGUGGCCUGUCUGAUUUAUGUCUGCAGUGGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGCAGCCAAAA
..(((.((((.((.((((((((((((.(((...)))(.....).......))))))))))))))((((.((((......)))).))))..)))).))).... ( -35.40)
>DroSim_CAF1 85345 102 + 1
CCGGCGGCAGCUGCAACUACUGCAGAAGCCUGUGGCCUGUCUGAUUUAUGUGUGCAGUAGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGCAGCCAAAA
..(((.((((.((.((((((((((.(.(((...)))(.....).......).))))))))))))((((.((((......)))).))))..)))).))).... ( -31.60)
>DroEre_CAF1 85922 102 + 1
CCGGCGGCAGCUGCAACUACUGCAGAAGCCUGUGGCCUGUCUGAUUUAUGUCUGCAGUAGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGCAGCCAAAA
..(((.((((.((.((((((((((((.(((...)))(.....).......))))))))))))))((((.((((......)))).))))..)))).))).... ( -35.70)
>DroYak_CAF1 86055 102 + 1
CCGGCGGCAGCUGCAACUACUGCAGAAGCCUGUGGCCUGUCUGAUUUAUGUCUGCAGUAGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGCAGCCAAAA
..(((.((((.((.((((((((((((.(((...)))(.....).......))))))))))))))((((.((((......)))).))))..)))).))).... ( -35.70)
>consensus
CCGGCGGCAGCUGCAACUACUGCAGAAGCCUGUGGCCUGUCUGAUUUAUGUCUGCAGUAGUUCAAUUGGCAAUGACAAAGUUGGCAAUCAUUGCAGCCAAAA
..(((.((((.((.((((((((((((.((.....))(.....).......))))))))))))))((((.((((......)))).))))..)))).))).... (-31.48 = -31.92 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	6,935,407 – 6,935,509
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	97.65
Mean single sequence MFE	-32.87
Consensus MFE	-32.29
Energy contribution	-32.57
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.41
Structure conservation index	0.98
SVM decision value	4.02
SVM RNA-class probability	0.999762
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6935407 102 - 27905053
UUUUGGCUUCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAUGCUUCUGCAGUAGUUGCAGCUGCCGUCAG
....(((..(((((((..........)))))))....(((((((((((((((.............(((.....))))))))))))))).)))..)))..... ( -28.81)
>DroSec_CAF1 84052 102 - 1
UUUUGGCUGCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACCACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGG
...((((.((((((((..........))))))))((.((((((.((((((((.............((((...)))))))))))).))).))).))..)))). ( -31.71)
>DroSim_CAF1 85345 102 - 1
UUUUGGCUGCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACUACUGCACACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGG
...((((.((((((((..........))))))))((.(((((((((((((..(........)..(((((...))))).)))))))))).))).))..)))). ( -31.40)
>DroEre_CAF1 85922 102 - 1
UUUUGGCUGCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGG
...((((.((((((((..........))))))))((.(((((((((((((((.............((((...)))))))))))))))).))).))..)))). ( -36.21)
>DroYak_CAF1 86055 102 - 1
UUUUGGCUGCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGG
...((((.((((((((..........))))))))((.(((((((((((((((.............((((...)))))))))))))))).))).))..)))). ( -36.21)
>consensus
UUUUGGCUGCAAUGAUUGCCAACUUUGUCAUUGCCAAUUGAACUACUGCAGACAUAAAUCAGACAGGCCACAGGCUUCUGCAGUAGUUGCAGCUGCCGCCGG
...((((.((((((((..........))))))))((.(((((((((((((((.............(((.....))))))))))))))).))).))..)))). (-32.29 = -32.57 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:20 2006