Locus 1895

Sequence ID 3R_DroMel_CAF1
Location 5,421,155 – 5,421,293
Length 138
Max. P 0.908515
window3107 window3108 window3109

overview

Window 7

Location 5,421,155 – 5,421,254
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 95.62
Mean single sequence MFE -31.85
Consensus MFE -28.27
Energy contribution -27.65
Covariance contribution -0.62
Combinations/Pair 1.09
Mean z-score -1.52
Structure conservation index 0.89
SVM decision value -0.02
SVM RNA-class probability 0.522984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421155 99 + 27905053
UGGCCAAAGUUAUUGGAGUGGAAAGCCCCGAUUCGAAGGUGAAGUCGCUGGCUUUCCCCUCUCGAAAAAUCAGGCUAGAAAUUCCUGACCAGGUAGGUG
..(((.......((((((.((((((((.((((((....)...)))))..)))))))).))).)))....(((((..(....).)))))...)))..... ( -31.80)
>DroSec_CAF1 7897 99 + 1
UGGUCAAAGUUAUUGGAGUGGAAAGCCCCGAUUCGAAGGUGAAGUCGCUGGCUUUCCCCUCUCGAAAAAUCAGGCUAAAAAUUCCUGACCAGGUAGGUG
(((((.......((((((.((((((((.((((((....)...)))))..)))))))).))).)))......(((.........))))))))........ ( -29.90)
>DroEre_CAF1 8367 99 + 1
UGGCCAAAGUUAUUGGAGUGGAAAGCCUCGAUUUGAAGGUGAAGUCUCUGGCUUUCCCCUCUCGAAAAAUCAGGCUAGAAACUCCUGCCCAGGUAGGUG
(((((....((.((((((.((((((((..(((((.......)))))...)))))))).))).))).))....)))))....(.(((((....))))).) ( -35.40)
>DroYak_CAF1 8608 99 + 1
UGGCCAAAGUUAUUGGAGUGGAAAGCCCCGAUUCGAAGGUGAAGUCUCUGGCUUUCCCCUCUCGACAAAUCAGGCUAGAAACUCCUGACCAGGUAGGUG
(((((....((.((((((.((((((((..(((((....)...))))...)))))))).))).))).))....)))))....(((((....))).))... ( -30.30)
>consensus
UGGCCAAAGUUAUUGGAGUGGAAAGCCCCGAUUCGAAGGUGAAGUCGCUGGCUUUCCCCUCUCGAAAAAUCAGGCUAGAAACUCCUGACCAGGUAGGUG
(((((....((.((((((.((((((((..((((((....)).))))...)))))))).))).))).))....)))))....(((((....))).))... (-28.27 = -27.65 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,421,155 – 5,421,254
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 95.62
Mean single sequence MFE -30.90
Consensus MFE -27.86
Energy contribution -28.05
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -2.11
Structure conservation index 0.90
SVM decision value 1.06
SVM RNA-class probability 0.908515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421155 99 - 27905053
CACCUACCUGGUCAGGAAUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGCGACUUCACCUUCGAAUCGGGGCUUUCCACUCCAAUAACUUUGGCCA
.........(((((((((..((......))..))))(.(((.((((((((..(((.(((......)))))).)))))))).))))........))))). ( -33.60)
>DroSec_CAF1 7897 99 - 1
CACCUACCUGGUCAGGAAUUUUUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGCGACUUCACCUUCGAAUCGGGGCUUUCCACUCCAAUAACUUUGACCA
.........(((((((((..((......))..))))(.(((.((((((((..(((.(((......)))))).)))))))).))))........))))). ( -31.90)
>DroEre_CAF1 8367 99 - 1
CACCUACCUGGGCAGGAGUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGAGACUUCACCUUCAAAUCGAGGCUUUCCACUCCAAUAACUUUGGCCA
..........(((.(((((....((((((((((.....(((((..(((.......)))..)))))))))).)))))....)))))((.....)).))). ( -28.20)
>DroYak_CAF1 8608 99 - 1
CACCUACCUGGUCAGGAGUUUCUAGCCUGAUUUGUCGAGAGGGGAAAGCCAGAGACUUCACCUUCGAAUCGGGGCUUUCCACUCCAAUAACUUUGGCCA
......(((....)))........(((.((.((((.(.(((.((((((((...((.(((......)))))..)))))))).)))).)))).)).))).. ( -29.90)
>consensus
CACCUACCUGGUCAGGAAUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGAGACUUCACCUUCGAAUCGGGGCUUUCCACUCCAAUAACUUUGGCCA
.........(((((((((..((......))..))))(.(((.((((((((...((.(((......)))))..)))))))).))))........))))). (-27.86 = -28.05 +   0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,421,174 – 5,421,293
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.97
Mean single sequence MFE -34.02
Consensus MFE -27.33
Energy contribution -27.82
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.80
SVM decision value 0.02
SVM RNA-class probability 0.542191
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421174 119 - 27905053
CUCGAAAGCAAGGCAAA-ACGCCCCUUAUCUGAUAAAAAUCACCUACCUGGUCAGGAAUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGCGACUUCACCUUCGAAUCGGGGCUUUCC
((((((((..((((...-............((((....))))....(((....)))........))))...))))))))...((((((((..(((.(((......)))))).)))))))) ( -36.50)
>DroSec_CAF1 7916 118 - 1
CUCGAAAGCAAGGCAAA-ACGCCCCUUAUCUGAUAA-AAUCACCUACCUGGUCAGGAAUUUUUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGCGACUUCACCUUCGAAUCGGGGCUUUCC
((((((((..(((((((-(..((........(((..-.)))(((.....)))..))...)))).))))...))))))))...((((((((..(((.(((......)))))).)))))))) ( -35.60)
>DroEre_CAF1 8386 113 - 1
----AAAGUAAGGCUAA--CGCCCCUUAUCUGAUAA-AAUCACCUACCUGGGCAGGAGUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGAGACUUCACCUUCAAAUCGAGGCUUUCC
----.....((((((..--.((((..((..((((..-.))))..))...)))).(((((((((.((....(((..(....)..))).)).))))))))).............)))))).. ( -30.30)
>DroYak_CAF1 8627 115 - 1
----GAAGCAAGGCAAACACGCCCCUUAUCUGAUAA-AAUCACCUACCUGGUCAGGAGUUUCUAGCCUGAUUUGUCGAGAGGGGAAAGCCAGAGACUUCACCUUCGAAUCGGGGCUUUCC
----.......(((......)))((((.((.(((((-(....((.....))(((((.........)))))))))))))))))((((((((...((.(((......)))))..)))))))) ( -33.70)
>consensus
____AAAGCAAGGCAAA_ACGCCCCUUAUCUGAUAA_AAUCACCUACCUGGUCAGGAAUUUCUAGCCUGAUUUUUCGAGAGGGGAAAGCCAGAGACUUCACCUUCGAAUCGGGGCUUUCC
...........(((......)))((((.((((((....)))).......(((((((.........)))))))....))))))((((((((...((.(((......)))))..)))))))) (-27.33 = -27.82 +   0.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:07 2006