Locus 1280

Sequence ID	2R_DroMel_CAF1
Location	5,018,167 – 5,018,283
Length	116
Max. P	0.999209

overview

Window 6

Location	5,018,167 – 5,018,270
Length	103
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	78.95
Mean single sequence MFE	-42.66
Consensus MFE	-30.06
Energy contribution	-31.18
Covariance contribution	1.12
Combinations/Pair	1.07
Mean z-score	-2.19
Structure conservation index	0.70
SVM decision value	1.59
SVM RNA-class probability	0.965726
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5018167 103 + 20766785
GGAGAAAGGCGAGAGGAG----------------AAAGGGAAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUAGCCUCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGA
((((((((.((.((((((----------------((.....(.((((((((.(((.(((..(((....)))..)))..))))))))))).)...))))).))))).))))))))..... ( -49.80)
>DroSec_CAF1 72391 101 + 1
GGAGCAAGGCGAGAGUAG----------------AAAGGGAAGUGCGCUGGUGAGAAGACACGCAUUUGCGCACUG--CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGA
((((.((((((((((.((----------------((.(((.(((((((..(((.(......).)))..))))))).--)))((.....))....)))))))))..)))))))))..... ( -42.80)
>DroSim_CAF1 75675 87 + 1
GGA--------------G----------------AAAGGGAAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGA
(((--------------(----------------((((((.(((((((..(((.(......).)))..))))))).--)))...((.(((.(((....))).))))))))))))..... ( -36.70)
>DroEre_CAF1 69389 110 + 1
GGAGAAAC------UGAGAAACG-GAGAAAGGGAGAAGGGAAGUCCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCUCCAGUGUGGUGAGUUCGCUCUCCGGCUUUCUCCGGGGA
........------.......((-((((((((((((.(.(((.((((((((......(((((((....)))...))--)).))))))....)).))).))))))..))))))))).... ( -43.40)
>DroYak_CAF1 77833 117 + 1
GGAGAAGGGAGAUAGGAGAAAGGAGGGAAAGGGAAGAGGCAAGUCCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCACCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGA
..............((((((((...(((.((((((....((....((((((((.(.(((..(((....)))..)))--)))))))))...))..)))))).)))..))))))))..... ( -40.60)
>consensus
GGAGAAAGG_GA_AGGAG________________AAAGGGAAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUG__CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGA
(((((((..............................(.......)(((((.((((.(((.(((.....(((((((......)))))))))).))).)))).))))))))))))..... (-30.06 = -31.18 +   1.12)

alignment

secondary structure

dotplot

Window 7

Location	5,018,167 – 5,018,270
Length	103
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	78.95
Mean single sequence MFE	-38.00
Consensus MFE	-24.18
Energy contribution	-25.86
Covariance contribution	1.68
Combinations/Pair	1.08
Mean z-score	-3.39
Structure conservation index	0.64
SVM decision value	3.43
SVM RNA-class probability	0.999209
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5018167 103 - 20766785
UCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGAGGCUAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUUCCCUUU----------------CUCCUCUCGCCUUUCUCC
.....((((((((.(((((.(((((((((......))))(((..(((((((...((.(((......))))))))))))..)))))----------------)))))).)).)))))))) ( -42.70)
>DroSec_CAF1 72391 101 - 1
UCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG--CAGUGCGCAAAUGCGUGUCUUCUCACCAGCGCACUUCCCUUU----------------CUACUCUCGCCUUGCUCC
.....((((.(((.((((((((((.....((.....))(((--.(((((((...((.(((......)))))))))))).))))))----------------)).))).)).))).)))) ( -38.70)
>DroSim_CAF1 75675 87 - 1
UCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUUCCCUUU----------------C--------------UCC
...((((......)))).((((((.....((.....))(((--.(((((((...((.(((......)))))))))))).))))))----------------)--------------)). ( -32.80)
>DroEre_CAF1 69389 110 - 1
UCCCCGGAGAAAGCCGGAGAGCGAACUCACCACACUGGAGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGGACUUCCCUUCUCCCUUUCUC-CGUUUCUCA------GUUUCUCC
....(((((((((..((((((.(((.((....(.(((((((--..(..(((....)))..)..)))..)))).))).))).).))))))))))))-)).......------........ ( -36.40)
>DroYak_CAF1 77833 117 - 1
UCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGUGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGGACUUGCCUCUUCCCUUUCCCUCCUUUCUCCUAUCUCCCUUCUCC
.....((((((((..((((((.(((.........(((((((--..(..(((....)))..)....))))))).((.....))..))).))))))...)))))))).............. ( -39.40)
>consensus
UCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG__CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUUCCCUUU________________CUCCU_UC_CCUUUCUCC
.....((((((((..((.(((....))).)).(.(((((((....(..(((....)))..)...))).)))).).....................................)))))))) (-24.18 = -25.86 +   1.68)

alignment

secondary structure

dotplot

Window 8

Location	5,018,191 – 5,018,283
Length	92
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	93.40
Mean single sequence MFE	-33.12
Consensus MFE	-29.10
Energy contribution	-29.34
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.15
Structure conservation index	0.88
SVM decision value	-0.04
SVM RNA-class probability	0.513113
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5018191 92 + 20766785
AAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUAGCCUCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGACGCCUCUCGUUUU----
.(.((((((((.(((.(((..(((....)))..)))..))))))))))).)(((.....(((((((......))))))).....))).....---- ( -35.00)
>DroSec_CAF1 72415 90 + 1
AAGUGCGCUGGUGAGAAGACACGCAUUUGCGCACUG--CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGACGCCUCUCGUUUU----
.((.(((((((.((((..((.(((.....(((((((--....)))))))))).))..)))).))))).......(....)))))........---- ( -32.40)
>DroSim_CAF1 75685 90 + 1
AAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGACGCCUCUCGUUUU----
.((.(((((((.((((..((.(((.....(((((((--....)))))))))).))..)))).))))).......(....)))))........---- ( -31.80)
>DroEre_CAF1 69422 94 + 1
AAGUCCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCUCCAGUGUGGUGAGUUCGCUCUCCGGCUUUCUCCGGGGACGCCUCUCGGUUUUUUA
..((((.((((.((((.(.(..((....))((((((--....))))))((.(((....))).))).))))).))))))))(((....)))...... ( -34.20)
>DroYak_CAF1 77873 90 + 1
AAGUCCGCUGGUGAGAUGGCACGCAUUUGCGCACUG--CCACCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGACGCCUCUCGUUUU----
..(((((((((.((((..((.(((.....(((((((--....)))))))))).))..)))).)))))...(....)))))............---- ( -32.20)
>consensus
AAGUGCGCUGGUGAGAUGGCACGCAUUUGCGCACUG__CCCCCAGUGUGGUGAGUUCUCUCUCCGGCUUUCUCCGGGGACGCCUCUCGUUUU____
......(((((.((((.(((.(((.....(((((((......)))))))))).))).)))).)))))......(((((.....)))))........ (-29.10 = -29.34 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	5,018,191 – 5,018,283
Length	92
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.40
Mean single sequence MFE	-32.46
Consensus MFE	-25.78
Energy contribution	-26.22
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.79
SVM decision value	0.84
SVM RNA-class probability	0.863263
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5018191 92 - 20766785
----AAAACGAGAGGCGUCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGAGGCUAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUU
----.....(((((((.((((.((......))((.(((....))).)).....)))).))).(..(((....)))..)..))))............ ( -31.10)
>DroSec_CAF1 72415 90 - 1
----AAAACGAGAGGCGUCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG--CAGUGCGCAAAUGCGUGUCUUCUCACCAGCGCACUU
----....(....)..((((((((.(.....)((.(((....))).))...)))))))--)(((((((...((.(((......)))))))))))). ( -33.30)
>DroSim_CAF1 75685 90 - 1
----AAAACGAGAGGCGUCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUU
----.....(((((((((((((((.(.....)((.(((....))).))...)))))))--)...((((....))))))).))))............ ( -35.00)
>DroEre_CAF1 69422 94 - 1
UAAAAAACCGAGAGGCGUCCCCGGAGAAAGCCGGAGAGCGAACUCACCACACUGGAGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGGACUU
.......(((.(((.((..(((((......)))).)..))..)))......(((((((--..(..(((....)))..)..)))..))))))).... ( -31.40)
>DroYak_CAF1 77873 90 - 1
----AAAACGAGAGGCGUCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGUGG--CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGGACUU
----....(....)..((((((((......)))).(((....)))......(((((((--..(..(((....)))..)....))))))).)))).. ( -31.50)
>consensus
____AAAACGAGAGGCGUCCCCGGAGAAAGCCGGAGAGAGAACUCACCACACUGGGGG__CAGUGCGCAAAUGCGUGCCAUCUCACCAGCGCACUU
.........(((((((.(((((((.(.....)((.(((....))).))...)))))))......((((....))))))).))))............ (-25.78 = -26.22 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:51 2006