Locus 8481

Sequence ID	3L_DroMel_CAF1
Location	22,279,517 – 22,279,670
Length	153
Max. P	0.996543

overview

Window 0

Location	22,279,517 – 22,279,633
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.20
Mean single sequence MFE	-37.80
Consensus MFE	-31.58
Energy contribution	-33.20
Covariance contribution	1.62
Combinations/Pair	1.06
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	0.62
SVM RNA-class probability	0.800699
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22279517 116 - 23771897
AGAUGCAGAAGGAUGGAUUUGCCCGUCAGUCCCAAGGGCUGUGCGGAAGAACAACA----UCGCAGAAAACAGGCUCGAAUCAAUGUUUAAUCCUCGCCAGCAGCCGGAAACCUGGCCGC
..........((..(((((...((((((((((...)))))).))))..(((((...----(((.((........))))).....))))))))))...)).((.(((((....))))).)) ( -33.50)
>DroSec_CAF1 37897 116 - 1
AGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA----UCGCAGAAAACAGGCUUGAAUCAAAGUUUGAUCCUCGCCAGCAGCCGGAAACCUGGCCGC
....((.((.((((...(((((.....(((((...)))))((((....))))....----..)))))...(((((((......)))))))))))))))..((.(((((....))))).)) ( -42.30)
>DroSim_CAF1 29493 116 - 1
AGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA----UCGCAGAAAACAGGCUCGAAUCAAAGUUUGAUCCUCGCCAGCAGCCGGAAACCUGGCCGC
.((((......(((((......)))))(((((...)))))((((....))))..))----))..........(((..(.((((.....)))).)..))).((.(((((....))))).)) ( -41.30)
>DroEre_CAF1 36584 116 - 1
AGAUGCAGAAGGAUGGAGUUACCCGUCAGCCCCAAGGGCUCUGCGGAAGCACAACA----UGGCAGAAAACAGGCUCGAAUCAAAGUUUGAUCCUCGCCAGCAGCGAGAAACCUGGCCGC
....(((((..(((((......))))).((((...)))))))))((..((......----..))......((((.((((((....))))))..(((((.....)))))...)))).)).. ( -37.50)
>DroYak_CAF1 2665 106 - 1
AGAUGCAGCAGGAUGGAUUUACCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACAUACAUAGCAGAAAACAGGCUCGAAUCAAAGUUUGAUCCUCGCCAGCAGCA--------------
.(.(((.((..(((((......)))))(((((...)))))((((....))))..........))........(((..(.((((.....)))).)..))).))).).-------------- ( -34.40)
>consensus
AGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA____UCGCAGAAAACAGGCUCGAAUCAAAGUUUGAUCCUCGCCAGCAGCCGGAAACCUGGCCGC
...(((.....(((((......)))))(((((...)))))((((....))))..........))).......(((..(.((((.....)))).)..))).((.(((((....))))).)) (-31.58 = -33.20 +   1.62)

alignment

secondary structure

dotplot

Window 1

Location	22,279,557 – 22,279,670
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.66
Mean single sequence MFE	-42.32
Consensus MFE	-30.76
Energy contribution	-32.72
Covariance contribution	1.96
Combinations/Pair	1.03
Mean z-score	-1.83
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.586197
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22279557 113 + 23771897
UUCGAGCCUGUUUUCUGCGA----UGUUGUUCUUCCGCACAGCCCUUGGGACUGACGGGCAAAUCCAUCCUUCUGCAUCUGCAGCGUGC---UGUAGCGUACACUGCGGCUGUGUUAAUC
.....((((((....((((.----...........))))(((((....)).)))))))))..............(((.((((((.((((---......)))).)))))).)))....... ( -35.60)
>DroSec_CAF1 37937 116 + 1
UUCAAGCCUGUUUUCUGCGA----UGUUGUGCUUCCGCACAGCCCUUGGGGCUGACGGGCAAAUCCAUCCUUCUGCAUCUGCAGCGUGCUGCUGUAGCGUACGCUGCGGCUGGGUUAAUC
.....(((((((..((.(((----.(((((((....)))))))..))).))..))))))).((((((.((..........(((((((((.((....))))))))))))).)))))).... ( -50.20)
>DroSim_CAF1 29533 116 + 1
UUCGAGCCUGUUUUCUGCGA----UGUUGUGCUUCCGCACAGCCCUUGGGGCUGACGGGCAAAUCCAUCCUUCUGCAUCUGCAGCGUGCUGCUGUAGCGUACACUGCGGCUGGGUUAAUC
.....(((((((..((.(((----.(((((((....)))))))..))).))..))))))).((((((.....((((....))))......(((((((......))))))))))))).... ( -45.00)
>DroEre_CAF1 36624 113 + 1
UUCGAGCCUGUUUUCUGCCA----UGUUGUGCUUCCGCAGAGCCCUUGGGGCUGACGGGUAACUCCAUCCUUCUGCAUCUGCAGCGUGC---UGUAGCAUACUCUGCGGCGGGGUUAAUC
.....(((((((..((.(((----.(((.(((....))).)))...)))))..)))))))((((((......((((....))))...((---(((((......))))))))))))).... ( -40.90)
>DroYak_CAF1 2691 117 + 1
UUCGAGCCUGUUUUCUGCUAUGUAUGUUGUGCUUCCGCACAGCCCUUGGGGCUGACGGGUAAAUCCAUCCUGCUGCAUCUGCAGCCAGC---UGUACCAUACUCUGCGGCGGUGUUAAUC
.....(((((((....(((......(((((((....)))))))......))).))))))).....((((..(((((....)))))..((---((((........))))))))))...... ( -39.90)
>consensus
UUCGAGCCUGUUUUCUGCGA____UGUUGUGCUUCCGCACAGCCCUUGGGGCUGACGGGCAAAUCCAUCCUUCUGCAUCUGCAGCGUGC___UGUAGCGUACACUGCGGCUGGGUUAAUC
.....(((((((..((.(((.....(((((((....)))))))..))).))..))))))).((((((.((..((((....)))).........((((......)))))).)))))).... (-30.76 = -32.72 +   1.96)

alignment

secondary structure

dotplot

Window 2

Location	22,279,557 – 22,279,670
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.66
Mean single sequence MFE	-40.72
Consensus MFE	-35.50
Energy contribution	-36.66
Covariance contribution	1.16
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.87
SVM decision value	2.71
SVM RNA-class probability	0.996543
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22279557 113 - 23771897
GAUUAACACAGCCGCAGUGUACGCUACA---GCACGCUGCAGAUGCAGAAGGAUGGAUUUGCCCGUCAGUCCCAAGGGCUGUGCGGAAGAACAACA----UCGCAGAAAACAGGCUCGAA
.........(((((((((((..((....---)))))))))...(((.....((((..(((..((((((((((...)))))).))))..)))...))----))))).......)))).... ( -36.80)
>DroSec_CAF1 37937 116 - 1
GAUUAACCCAGCCGCAGCGUACGCUACAGCAGCACGCUGCAGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA----UCGCAGAAAACAGGCUUGAA
.......(.(((((((((((.(((....)).).))))))).((((......(((((......)))))(((((...)))))((((....))))..))----))..........)))).).. ( -46.60)
>DroSim_CAF1 29533 116 - 1
GAUUAACCCAGCCGCAGUGUACGCUACAGCAGCACGCUGCAGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA----UCGCAGAAAACAGGCUCGAA
.......(.(((((((((((.(((....)).).))))))).((((......(((((......)))))(((((...)))))((((....))))..))----))..........)))).).. ( -44.70)
>DroEre_CAF1 36624 113 - 1
GAUUAACCCCGCCGCAGAGUAUGCUACA---GCACGCUGCAGAUGCAGAAGGAUGGAGUUACCCGUCAGCCCCAAGGGCUCUGCGGAAGCACAACA----UGGCAGAAAACAGGCUCGAA
..........(((((((....(((....---)))..))))...((((((..(((((......))))).((((...)))))))((....))......----..))).......)))..... ( -34.80)
>DroYak_CAF1 2691 117 - 1
GAUUAACACCGCCGCAGAGUAUGGUACA---GCUGGCUGCAGAUGCAGCAGGAUGGAUUUACCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACAUACAUAGCAGAAAACAGGCUCGAA
..........(((((...(((((.....---.(((.((((....)))))))(((((......)))))(((((...)))))((((....))))..)))))...)).(....).)))..... ( -40.70)
>consensus
GAUUAACCCAGCCGCAGAGUACGCUACA___GCACGCUGCAGAUGCAGAAGGAUGGAUUUGCCCGUCAGCCCCAAGGGCUGUGCGGAAGCACAACA____UCGCAGAAAACAGGCUCGAA
..........((((((((((..((.......)))))))))...(((.....(((((......)))))(((((...)))))((((....))))..........))).......)))..... (-35.50 = -36.66 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:42 2006