Locus 5211

Sequence ID	X_DroMel_CAF1
Location	13,619,768 – 13,619,953
Length	185
Max. P	0.999936

overview

Window 8

Location	13,619,768 – 13,619,888
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-40.36
Consensus MFE	-38.08
Energy contribution	-38.32
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.84
Structure conservation index	0.94
SVM decision value	4.37
SVM RNA-class probability	0.999883
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13619768 120 + 22224390
AAACAACAAACAUCAAAAGUUGCCAACUUUUUUCUCUUGCGACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGC
..................((((......((((((...(((.......)))...))))))(((((((((((......)))).))).)))).(((((((...)))))))..))))....... ( -39.80)
>DroSec_CAF1 5639 120 + 1
AAGCAACAAACAUCAAAAGUUGCCAACUUUUUUCUGUCGCGACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGC
..(((((...........))))).....(((((((((.((....)).)))...))))))(((((((((((......)))).))).)))).(((((((...)))))))............. ( -41.10)
>DroSim_CAF1 5635 120 + 1
AAACAACAAACAUCAAAAGUUGCCAACUUUUUUCUCUUGCGACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGC
..................((((......((((((...(((.......)))...))))))(((((((((((......)))).))).)))).(((((((...)))))))..))))....... ( -39.80)
>DroEre_CAF1 5640 120 + 1
AAACAACAAACAUCAAAAGUUGCCAACUUUUUUCUCUUGCGACCGCAGCAGCCGAAGAAGCAGCGGCGUCAGCAGCGACGGCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGC
..................((((......((((((..((((.......))))..))))))(((((((((((......))).)))).)))).(((((((...)))))))..))))....... ( -40.60)
>DroYak_CAF1 5347 120 + 1
AAACAACAAACAUCAAAAGUUGCCAACUUUUUUCUCUUGCGACCGCAGCAGCCAAAGGAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGACGCGCUGGCAACAACAAAUUGC
..................((((....(((((..((.((((....)))).))..))))).(((((((((((......)))).))).)))).(((((((...)))))))..))))....... ( -40.50)
>consensus
AAACAACAAACAUCAAAAGUUGCCAACUUUUUUCUCUUGCGACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGC
..................((((......((((((...(((.......)))...))))))(((((((((((......)))).))).)))).(((((((...)))))))..))))....... (-38.08 = -38.32 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	13,619,768 – 13,619,888
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-50.70
Consensus MFE	-48.60
Energy contribution	-48.88
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-2.94
Structure conservation index	0.96
SVM decision value	4.67
SVM RNA-class probability	0.999936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13619768 120 - 22224390
GCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUCGCAAGAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGUUU
(((((.((((((((((((((((((((((((....))).))))))))..((..((((((.((.((....)).)).)))).))..))........)))))))))....))))...))))).. ( -51.20)
>DroSec_CAF1 5639 120 - 1
GCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUCGCGACAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGCUU
.((((((.((((((((((((((((((((((....))).)))))))).))))..(((((.((.((....)).)).))))).)))))))....))))))(((((...........))))).. ( -56.20)
>DroSim_CAF1 5635 120 - 1
GCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUCGCAAGAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGUUU
(((((.((((((((((((((((((((((((....))).))))))))..((..((((((.((.((....)).)).)))).))..))........)))))))))....))))...))))).. ( -51.20)
>DroEre_CAF1 5640 120 - 1
GCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGCCGUCGCUGCUGACGCCGCUGCUUCUUCGGCUGCUGCGGUCGCAAGAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGUUU
(((((.((((((((((((((((((((((((....))))).))))))..((..((((((.((..(....)..)).)))).))..))........)))))))))....))))...))))).. ( -49.60)
>DroYak_CAF1 5347 120 - 1
GCAAUUUGUUGUUGCCAGCGCGUCGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUCCUUUGGCUGCUGCGGUCGCAAGAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGUUU
(((((.(((((((((((((((((((..((..(((((..(((((((....)))))))))))).))..)))).)).....((....)).......)))))))))....))))...))))).. ( -45.30)
>consensus
GCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUCGCAAGAGAAAAAAGUUGGCAACUUUUGAUGUUUGUUGUUU
(((((.((((((((((((((((((((((((....))))).))))))(((....(((((.((.((....)).)).))))).)))..........)))))))))....))))...))))).. (-48.60 = -48.88 +   0.28)

alignment

secondary structure

dotplot

Window 0

Location	13,619,808 – 13,619,924
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.21
Mean single sequence MFE	-44.18
Consensus MFE	-42.60
Energy contribution	-42.80
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.96
SVM decision value	3.97
SVM RNA-class probability	0.999736
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13619808 116 + 22224390
GACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCACACUUUUCCAUUGUCUGAA-
.(((((((...........(((((((((((......)))).))).)))).(((((((...))))))).........)))))))..---(((.....)))....................- ( -43.60)
>DroSec_CAF1 5679 117 + 1
GACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUGGCACACUUUUCCAUUGUCUGAGG
..((.(((((...(((((.(((((((((((......)))).))).)))).(((((((...))))))).....((((.(((.....---)))..))))......)))))...)).))).)) ( -43.90)
>DroSim_CAF1 5675 117 + 1
GACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCACACUUUUCCAUUGUCUGGGG
.(((((((...........(((((((((((......)))).))).)))).(((((((...))))))).........)))))))..---(((.....))).......((((.....)))). ( -45.70)
>DroEre_CAF1 5680 116 + 1
GACCGCAGCAGCCGAAGAAGCAGCGGCGUCAGCAGCGACGGCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCAUAUUUUUCCAUUGUCUAAA-
.(((((((...........(((((((((((......))).)))).)))).(((((((...))))))).........)))))))..---(((.....)))....................- ( -43.60)
>DroYak_CAF1 5387 119 + 1
GACCGCAGCAGCCAAAGGAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGACGCGCUGGCAACAACAAAUUGCGGUAAGAAGCAUUCGUUGCACUUUUUUCCAUUGUCUGAA-
........(((.(((.((((((((((((((......)))).))).)))).(((((((...)))))))..((((....(((........)))...))))........))).))).)))..- ( -44.10)
>consensus
GACCGCAGCAUCCGAAGAAGCAGCGGCGUCAGCAGCGACGCCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA___GCAUUUUUUGCACACUUUUCCAUUGUCUGAA_
.(((((((...........(((((((((((......)))).))).)))).(((((((...))))))).........))))))).....(((.....)))..................... (-42.60 = -42.80 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	13,619,808 – 13,619,924
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.21
Mean single sequence MFE	-46.74
Consensus MFE	-40.91
Energy contribution	-41.51
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.88
SVM decision value	2.26
SVM RNA-class probability	0.991254
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13619808 116 - 22224390
-UUCAGACAAUGGAAAAGUGUGCAAAAAAUGC---UUACCGCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUC
-....(((((..((...(((.(((.....)))---....)))..))..)))))..(((((((((((((((....))).)))))))).))))..(((((.((.((....)).)).))))). ( -47.90)
>DroSec_CAF1 5679 117 - 1
CCUCAGACAAUGGAAAAGUGUGCCAAAAAUGC---UUACCGCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUC
...........((..((((((.......))))---)).))(((((.....)))))(((((((((((((((....))).)))))))).))))..(((((.((.((....)).)).))))). ( -46.60)
>DroSim_CAF1 5675 117 - 1
CCCCAGACAAUGGAAAAGUGUGCAAAAAAUGC---UUACCGCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUC
..(((.....)))....(((.(((.....)))---.))).(((((.....)))))(((((((((((((((....))).)))))))).))))..(((((.((.((....)).)).))))). ( -48.30)
>DroEre_CAF1 5680 116 - 1
-UUUAGACAAUGGAAAAAUAUGCAAAAAAUGC---UUACCGCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGCCGUCGCUGCUGACGCCGCUGCUUCUUCGGCUGCUGCGGUC
-....(((((..((.......(((.....)))---.........))..)))))..(((((((((((((((....))))).)))))).))))..(((((.((..(....)..)).))))). ( -43.99)
>DroYak_CAF1 5387 119 - 1
-UUCAGACAAUGGAAAAAAGUGCAACGAAUGCUUCUUACCGCAAUUUGUUGUUGCCAGCGCGUCGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUCCUUUGGCUGCUGCGGUC
-..(((.(((.(((.......(((((((((((........)).))))))))).(((((((...))))))).(((((..(((((((....))))))))))))))).))).)))........ ( -46.90)
>consensus
_UUCAGACAAUGGAAAAGUGUGCAAAAAAUGC___UUACCGCAAUUUGUUGUUGCCAGCGCGACGCUGGCUGCAGUCGGGCGUCGCUGCUGACGCCGCUGCUUCUUCGGAUGCUGCGGUC
.....(((((..((......(((.................))).))..)))))..(((((((((((((((....))))).)))))).))))..(((((.((.((....)).)).))))). (-40.91 = -41.51 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	13,619,848 – 13,619,953
Length	105
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	80.81
Mean single sequence MFE	-25.17
Consensus MFE	-19.30
Energy contribution	-19.50
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.77
SVM decision value	0.46
SVM RNA-class probability	0.746211
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13619848 105 + 22224390
CCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCACACUUUUCCAUUGUCUGAA--AAAAU-UAAA----AAAAGGGAAGCCCUAUACAA
(((.(((((((((((((...)))))))..........))))))..---(((.....)))....(((((........)))--))...-....----....)))............. ( -25.60)
>DroSec_CAF1 5719 104 + 1
CCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUGGCACACUUUUCCAUUGUCUGAGGGAA--------AUUAAAAAAGGAAACCCUAUACAA
(((....((((((((((...))))))).....((((.(((.....---)))..))))..............)))....)))..--------........(((....)))...... ( -26.10)
>DroSim_CAF1 5715 111 + 1
CCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCACACUUUUCCAUUGUCUGGGGGAAAAU-UAAAAUUAAAAAAGGAAACCCUAUACAA
....(((((((((((((...)))))))..........))))))..---(((.....)))...........((((.(((((......-..................))))).)))) ( -28.26)
>DroEre_CAF1 5720 99 + 1
GCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA---GCAUUUUUUGCAUAUUUUUCCAUUGUCUAAA--AAAAC-UAAAAAU---AAUAUAUAA-------AA
((..(((((((((((((...)))))))..........))))))..---)).(((((((.(((.........))).))))--)))..-.......---.........-------.. ( -22.50)
>DroYak_CAF1 5427 110 + 1
CCCGACUGCAGCCAGCGACGCGCUGGCAACAACAAAUUGCGGUAAGAAGCAUUCGUUGCACUUUUUUCCAUUGUCUGAA--AAAGUUUUAAAAU---AAGAAAUACCCUAUACAG
.....(((..(((((((...))))))).............((((....(((.....)))((((((((.........)))--)))))........---......)))).....))) ( -23.40)
>consensus
CCCGACUGCAGCCAGCGUCGCGCUGGCAACAACAAAUUGCGGUAA___GCAUUUUUUGCACACUUUUCCAUUGUCUGAA__AAAAU_UAAAAAU_AAAAAGGAAACCCUAUACAA
....(((((((((((((...)))))))..........)))))).....(((.....)))........................................................ (-19.30 = -19.50 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:27 2006