Locus 1203

Sequence ID	3L_DroMel_CAF1
Location	3,424,408 – 3,424,598
Length	190
Max. P	0.896700

overview

Window 2

Location	3,424,408 – 3,424,499
Length	91
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	91.23
Mean single sequence MFE	-26.66
Consensus MFE	-22.14
Energy contribution	-23.10
Covariance contribution	0.96
Combinations/Pair	1.05
Mean z-score	-1.69
Structure conservation index	0.83
SVM decision value	0.99
SVM RNA-class probability	0.896700
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3424408 91 + 23771897
GACCGGAGGAUAAACAACGGCCGCGGACUUAAAAAGUAUAC------------AAGAGCAGCGAAGAUUGCCGGUUCGCUGCUUAAUUAGCCGCGGUGACCCU
..(((..(......)..)))(((((((((.....)))....------------..((((((((((.........))))))))))......))))))....... ( -30.20)
>DroSec_CAF1 39235 91 + 1
GACCGGAGGAUAAACAACGGCCGCGGACUUAAAAAGUAUAA------------AAGAGCAGCGAAGAUUGCCGGAUCGCUGCUUAAUUAGCCGCGGUGACCCU
..(((..(......)..)))(((((((((.....)))....------------..(((((((((...........)))))))))......))))))....... ( -29.20)
>DroSim_CAF1 28086 91 + 1
GACCGGAGGAUAAACAACGGCCGCGGACUUAAAAAGUAUAA------------AAGAGCAGCGAAGAUUGCCGGAUCGCUGCUUAAUUAGCCGCGGUGACCCU
..(((..(......)..)))(((((((((.....)))....------------..(((((((((...........)))))))))......))))))....... ( -29.20)
>DroEre_CAF1 39696 91 + 1
GACCGGAGGAUAAACAACGGCUGCAGACUUAAAAAGUAUAA------------AAGAGCAGCGAAGAUUGCCGGAUCGCUGCUUAAUUAGCCACGGUGACCCU
.((((..(......)...(((((...(((.....)))....------------..(((((((((...........)))))))))...))))).))))...... ( -25.00)
>DroYak_CAF1 38346 103 + 1
GACCGGAGGAUAAACAACGGCUGCAGACUUAAAAUGUAUAAAAAAAAAAAGAAAAGAGCAACGAAGAUUGCCGGUUCGCUGCUUAAUUAGCCACGGUGACCCU
.((((..(......)...((((((((((.......)).............(((..(.((((......)))))..))).))))......)))).))))...... ( -19.70)
>consensus
GACCGGAGGAUAAACAACGGCCGCGGACUUAAAAAGUAUAA____________AAGAGCAGCGAAGAUUGCCGGAUCGCUGCUUAAUUAGCCGCGGUGACCCU
..(((..(......)..)))(((((((((.....)))..................(((((((((...........)))))))))......))))))....... (-22.14 = -23.10 +   0.96)

alignment

secondary structure

dotplot

Window 3

Location	3,424,408 – 3,424,499
Length	91
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	91.23
Mean single sequence MFE	-24.68
Consensus MFE	-23.88
Energy contribution	-23.24
Covariance contribution	-0.64
Combinations/Pair	1.14
Mean z-score	-1.08
Structure conservation index	0.97
SVM decision value	0.05
SVM RNA-class probability	0.558718
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3424408 91 - 23771897
AGGGUCACCGCGGCUAAUUAAGCAGCGAACCGGCAAUCUUCGCUGCUCUU------------GUAUACUUUUUAAGUCCGCGGCCGUUGUUUAUCCUCCGGUC
(((((.((.((((((.....(((((((((.........)))))))))...------------((..(((.....)))..)))))))).))..)))))...... ( -28.10)
>DroSec_CAF1 39235 91 - 1
AGGGUCACCGCGGCUAAUUAAGCAGCGAUCCGGCAAUCUUCGCUGCUCUU------------UUAUACUUUUUAAGUCCGCGGCCGUUGUUUAUCCUCCGGUC
(((((.((.((((((.....((((((((...........))))))))...------------....(((.....)))....)))))).))..)))))...... ( -26.00)
>DroSim_CAF1 28086 91 - 1
AGGGUCACCGCGGCUAAUUAAGCAGCGAUCCGGCAAUCUUCGCUGCUCUU------------UUAUACUUUUUAAGUCCGCGGCCGUUGUUUAUCCUCCGGUC
(((((.((.((((((.....((((((((...........))))))))...------------....(((.....)))....)))))).))..)))))...... ( -26.00)
>DroEre_CAF1 39696 91 - 1
AGGGUCACCGUGGCUAAUUAAGCAGCGAUCCGGCAAUCUUCGCUGCUCUU------------UUAUACUUUUUAAGUCUGCAGCCGUUGUUUAUCCUCCGGUC
(((((.((..(((((.....((((((((...........))))))))...------------....(((.....)))....)))))..))..)))))...... ( -22.90)
>DroYak_CAF1 38346 103 - 1
AGGGUCACCGUGGCUAAUUAAGCAGCGAACCGGCAAUCUUCGUUGCUCUUUUCUUUUUUUUUUUAUACAUUUUAAGUCUGCAGCCGUUGUUUAUCCUCCGGUC
(((((.((..(((((.....(((((((((.........)))))))))............................(....))))))..))..)))))...... ( -20.40)
>consensus
AGGGUCACCGCGGCUAAUUAAGCAGCGAUCCGGCAAUCUUCGCUGCUCUU____________UUAUACUUUUUAAGUCCGCGGCCGUUGUUUAUCCUCCGGUC
(((((.((..(((((.....((((((((...........))))))))............................(....))))))..))..)))))...... (-23.88 = -23.24 +  -0.64)

alignment

secondary structure

dotplot

Window 4

Location	3,424,499 – 3,424,598
Length	99
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	91.45
Mean single sequence MFE	-23.40
Consensus MFE	-18.57
Energy contribution	-19.17
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.37
Structure conservation index	0.79
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3424499 99 + 23771897
CAAGGCUAAGUUUCCAAAAGGUGGAUGAUCAUCAACAACAAUUGGCCUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCGAUGGG-GAAGUUGUU------
(((....((((((((..........(((((((((.((.....))...)))))))))........))))))))....)))....((((...-...))))..------ ( -21.47)
>DroSec_CAF1 39326 99 + 1
CAAGGCUAAGUUUCCAAAAGGUGGAUGAUCAUGAACAACAAUUGGCCUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCUAUGGG-GAAGUUGAU------
......(((.(((((...((((.(((..............))).)))).....(((((..(((((....))))).)))))........))-))).)))..------ ( -19.14)
>DroSim_CAF1 28177 99 + 1
CAAGGCUAAGUUUCCAAAAGGUGGAUGAUCAUCAACAACAAUUGGCCUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCGAUGGG-GAAGUUGAU------
(((....((((((((..........(((((((((.((.....))...)))))))))........))))))))....)))...(((((...-...))))).------ ( -23.47)
>DroEre_CAF1 39787 97 + 1
CAAGGCUAAGUAUCCAA-AGGUGGAUGAUCAUCA---ACAAUUGGCCUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCGAUGGGGGAAGUUAUUU-----
....(((....(((((.-...)))))((((((((---..........))))))))))).........(((((((.((((....))))...)))))))....----- ( -21.30)
>DroYak_CAF1 38449 102 + 1
CAAGGCUAAGUAUCCAAAAGGUGGAUGAUCAUCA---ACAAUUGGACUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCAAUGGG-GAAGUUUUUCUUUUU
....(((....(((((.....)))))((((((((---..........)))))))))))((((((..((((((((.((((....))))..)-)))))))..)))))) ( -31.60)
>consensus
CAAGGCUAAGUUUCCAAAAGGUGGAUGAUCAUCAACAACAAUUGGCCUGAUGAUCGGUGAAAAGGGGAACUUUUAAUUGAAUUCGAUGGG_GAAGUUGUU______
(((....((((((((..........(((((((((....(....)...)))))))))........))))))))....)))........................... (-18.57 = -19.17 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:05 2006