Locus 611

Sequence ID X_DroMel_CAF1
Location 1,687,295 – 1,687,560
Length 265
Max. P 0.996487
window987 window988 window989 window990 window991

overview

Window 7

Location 1,687,295 – 1,687,412
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.34
Mean single sequence MFE -42.62
Consensus MFE -32.34
Energy contribution -33.02
Covariance contribution 0.68
Combinations/Pair 1.13
Mean z-score -2.84
Structure conservation index 0.76
SVM decision value 1.87
SVM RNA-class probability 0.980905
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1687295 117 + 22224390
GAGCGUGAAAGUGAGUAGAGA--GAAUUUCGCUGUCUUAUUGAGCGAAUUUCGAAUGUCUCCCCAAAAGACCCGUUUCUUUCGGUGUAAGACUUUUGGCGCUCUCUUCUCGCCGCUCUC-
(((((.....(((((.(((((--(...((((((.........))))))..(((((.((((..((.(((((......))))).))....)))).)))))..)))))).))))))))))..- ( -38.90)
>DroSec_CAF1 27492 117 + 1
GAGCGUGAAAGUGAGUAGAGA--GAAUUUCGCUGUCGUAUUGAGCGAAUUUCGAAUGUCUCGUCAAAAGACCCGUUUCUUUCGGUGUAAGACUUUUGGCGCUCUCUUCUCGCCGCUCUC-
(((((.....(((((.(((((--(((.((((((.........)))))).)))........((((((((((((((.......))).))....))))))))).))))).))))))))))..- ( -41.80)
>DroSim_CAF1 21567 117 + 1
GAGCGUGAAGGUGAGUAGAGA--GAAUUUCGCUGUCGUAUUGAGCGAAUUUCGAAUGUCUCGUCAAAAGACCCGUUUCUUUCGGUGUAAGACUUUUGGCGCUCUCUUCUCGCCGCUCUC-
((((.....((((((.(((((--(((.((((((.........)))))).)))........((((((((((((((.......))).))....))))))))).))))).))))))))))..- ( -42.70)
>DroEre_CAF1 23210 119 + 1
GAGAGUGAGAUUGAGUGGAGAGCGAUUUUCGCAGUCGUGUUGAGCGAAUUCCGAAUGGCAUGCCAAAAGACCCGUUUCUUUCGGUGUAAGAGUUUUGGCGCUCUCUUCUCUCCACUCUC-
(((((((.((..(((.((((((((...((((...((((.....))))....))))...)..(((((((.(((((.......))).)).....)))))))))))))).))))))))))))- ( -46.10)
>DroYak_CAF1 21147 118 + 1
GAGAGUGAGAGUGAGUAGAGA--GAAUUUCGCAAUCGUGUUGAGCGAAAUCCGAAUCGCAUGCCAAAAGACCCGUUUCUUGAGGUGUAAGACUUUUGGCGCUCUCUUCUCGUCGCUCUCA
((((((((...((((.(((((--(.(((((((...........)))))))...........(((((((((((((.....)).)))......)))))))).)))))).)))))))))))). ( -43.60)
>consensus
GAGCGUGAAAGUGAGUAGAGA__GAAUUUCGCUGUCGUAUUGAGCGAAUUUCGAAUGUCUCGCCAAAAGACCCGUUUCUUUCGGUGUAAGACUUUUGGCGCUCUCUUCUCGCCGCUCUC_
(((.(((...(((((.(((((..(((.(((((...........))))).)))........((((((((((((((.......))).))....))))))))).))))).)))))))).))). (-32.34 = -33.02 +   0.68) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,687,295 – 1,687,412
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.34
Mean single sequence MFE -38.12
Consensus MFE -27.40
Energy contribution -28.52
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -3.00
Structure conservation index 0.72
SVM decision value 1.38
SVM RNA-class probability 0.948431
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1687295 117 - 22224390
-GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGGGGAGACAUUCGAAAUUCGCUCAAUAAGACAGCGAAAUUC--UCUCUACUCACUUUCACGCUC
-..((((((.(((.(((((.........(((((...((((((((......)))))))).)))))....(((.((((((.........)))))).)))--))))).))).).....))))) ( -39.00)
>DroSec_CAF1 27492 117 - 1
-GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGACGAGACAUUCGAAAUUCGCUCAAUACGACAGCGAAAUUC--UCUCUACUCACUUUCACGCUC
-..((((((.(((.(((((.........(((((...(((.......)))(((....))))))))....(((.((((((.........)))))).)))--))))).))).).....))))) ( -34.30)
>DroSim_CAF1 21567 117 - 1
-GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGACGAGACAUUCGAAAUUCGCUCAAUACGACAGCGAAAUUC--UCUCUACUCACCUUCACGCUC
-..((((((.(((.(((((.........(((((...(((.......)))(((....))))))))....(((.((((((.........)))))).)))--))))).))).)).....)))) ( -35.20)
>DroEre_CAF1 23210 119 - 1
-GAGAGUGGAGAGAAGAGAGCGCCAAAACUCUUACACCGAAAGAAACGGGUCUUUUGGCAUGCCAUUCGGAAUUCGCUCAACACGACUGCGAAAAUCGCUCUCCACUCAAUCUCACUCUC
-((((((((((((..(((((((((((((..(((....(....)....)))..)))))))...((....))..(((((...........)))))....))))))..)))..)).))))))) ( -42.00)
>DroYak_CAF1 21147 118 - 1
UGAGAGCGACGAGAAGAGAGCGCCAAAAGUCUUACACCUCAAGAAACGGGUCUUUUGGCAUGCGAUUCGGAUUUCGCUCAACACGAUUGCGAAAUUC--UCUCUACUCACUCUCACUCUC
((((((....(((.(((((((((((((((......((((........))))))))))))..)).....(((((((((...........)))))))))--))))).))).))))))..... ( -40.10)
>consensus
_GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGGCGAGACAUUCGAAAUUCGCUCAAUACGACAGCGAAAUUC__UCUCUACUCACUUUCACGCUC
.(((((....(((.(((((..((((((((.(((....(....)....))).)))))))).........(((.(((((...........))))).)))..))))).))).)))))...... (-27.40 = -28.52 +   1.12) 

alignment

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secondary structure

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Window 9

Location 1,687,333 – 1,687,447
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.57
Mean single sequence MFE -34.12
Consensus MFE -27.04
Energy contribution -28.20
Covariance contribution 1.16
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.79
SVM decision value 1.03
SVM RNA-class probability 0.903383
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1687333 114 - 22224390
AAUUCAAACGAACGACGUCGACGUCGCUGCGAAAA------GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGGGGAGACAUUCGAAAUUCGCUCA
........((..(((((....)))))...))....------..((((((((.........))))....(((((...((((((((......)))))))).)))))...........)))). ( -37.60)
>DroSec_CAF1 27530 114 - 1
AAUUUAAACGAACGACGUCGACGUCGCAGCGAAAA------GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGACGAGACAUUCGAAAUUCGCUCA
........((..(((((....)))))...))....------..((((((((.........))))....(((((...(((.......)))(((....))))))))...........)))). ( -32.90)
>DroSim_CAF1 21605 114 - 1
AAUUUAAACGAACGACGUCGACGUCGCAGCGAAAA------GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGACGAGACAUUCGAAAUUCGCUCA
........((..(((((....)))))...))....------..((((((((.........))))....(((((...(((.......)))(((....))))))))...........)))). ( -32.90)
>DroEre_CAF1 23250 114 - 1
AAUUCGAGUGAACGACGUCGACGCCGCAGCGAAAA------GAGAGUGGAGAGAAGAGAGCGCCAAAACUCUUACACCGAAAGAAACGGGUCUUUUGGCAUGCCAUUCGGAAUUCGCUCA
.....(((((((...(.....(((....)))....------..((((((......(((((........)))))...((((((((......))))))))....)))))))...))))))). ( -32.70)
>DroYak_CAF1 21185 120 - 1
AAUUCGAGUGAACGACGUCGACGUCGGCGCCAAAAAAAAAUGAGAGCGACGAGAAGAGAGCGCCAAAAGUCUUACACCUCAAGAAACGGGUCUUUUGGCAUGCGAUUCGGAUUUCGCUCA
.....(.(((..(((((....))))).))))............((((((...(((..(...((((((((......((((........))))))))))))...)..))).....)))))). ( -34.50)
>consensus
AAUUCAAACGAACGACGUCGACGUCGCAGCGAAAA______GAGAGCGGCGAGAAGAGAGCGCCAAAAGUCUUACACCGAAAGAAACGGGUCUUUUGGCGAGACAUUCGAAAUUCGCUCA
........((..(((((....)))))...))............((((((...(((.....(((((((((.(((....(....)....))).))))))))).....))).....)))))). (-27.04 = -28.20 +   1.16) 

alignment

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secondary structure

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Window 0

Location 1,687,412 – 1,687,525
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.28
Mean single sequence MFE -40.85
Consensus MFE -35.52
Energy contribution -34.88
Covariance contribution -0.64
Combinations/Pair 1.15
Mean z-score -2.33
Structure conservation index 0.87
SVM decision value 2.70
SVM RNA-class probability 0.996487
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1687412 113 - 22224390
U--UUUUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGGAAUUCAAACGAACGACGUCGACGUCGCUGCGAAAA-----
.--.((((....))))((((((((.(....).))))))))(((((((((.(((..(((((..((....(((((........)))))..))..)))))))).))))))))).....----- ( -42.70)
>DroSec_CAF1 27609 114 - 1
UU-UUUUGUCCGCGGAGCGCGCAGCGAUUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUCAAACGGAAUUUAAACGAACGACGUCGACGUCGCAGCGAAAA-----
.(-((((((.(((...((((((((.(....).)))))))))))((((((.(((..(((((..(((.......)))..((.........))..)))))))).)))))).)))))))----- ( -40.20)
>DroSim_CAF1 21684 113 - 1
U--UUUUGUCGGCGGAGCGCGCAGCGAUUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGGAAUUUAAACGAACGACGUCGACGUCGCAGCGAAAA-----
.--((((((...((..((((((((.(....).)))))))).))((((((.(((..(((((.((....))........((.........))..)))))))).)))))).)))))).----- ( -38.10)
>DroEre_CAF1 23329 114 - 1
UAU-UUUGUCGGCGGAGCGCGCAGCGAAUAACCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGAAAUUCGAGUGAACGACGUCGACGCCGCAGCGAAAA-----
..(-(((((.......((((((((........))))))))((((((.(((((..(((((((((..................)))))).)))....))))).)))))).)))))).----- ( -40.67)
>DroYak_CAF1 21265 119 - 1
-AUUUGUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGUGAAUCGUCGAAUGAAAAUGAAUGAAACGAAAUUCGAGUGAACGACGUCGACGUCGGCGCCAAAAAAAAA
-......((((.((..((((((((.(....).)))))))).)).))))((((..(((((((((..................)))))).))).(((((....))))).))))......... ( -42.57)
>consensus
U__UUUUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGGAAUUCAAACGAACGACGUCGACGUCGCAGCGAAAA_____
...........((...((((((((.(....).))))))))((((((.(((((..((((((..((((..((.......))...))))..)).))))))))).)))))).)).......... (-35.52 = -34.88 +  -0.64) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,687,447 – 1,687,560
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.16
Mean single sequence MFE -37.70
Consensus MFE -32.84
Energy contribution -33.28
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.87
SVM decision value 1.36
SVM RNA-class probability 0.946077
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1687447 113 - 22224390
CGUCGUGGGAAA-ACA----GUUUGAUUUAAUUUUUGGUUU--UUUUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGG
....((......-)).----((((.(((((..((((.((((--....((((.((..((((((((.(....).)))))))).)).))))((((...)))))))).))))))))).)))).. ( -35.40)
>DroSec_CAF1 27644 114 - 1
CGUCGUGGGAAA-ACA----GUUUAAUUUAUUUUUCAGUUUU-UUUUGUCCGCGGAGCGCGCAGCGAUUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUCAAACGG
....((......-)).----((((.(((((((((.((.....-......((((...((((((((.(....).))))))))))))((((((....))))))..))))))))))).)))).. ( -33.90)
>DroSim_CAF1 21719 113 - 1
CGUCGUGGGAAA-ACA----GUUUAAUUUAUUUUUCGGUUU--UUUUGUCGGCGGAGCGCGCAGCGAUUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGG
....((......-)).----((((.((((((((((((((((--..((((((.((..((((((((.(....).)))))))).)).)))))).))))))......)))))))))).)))).. ( -36.60)
>DroEre_CAF1 23364 119 - 1
CGUCGUGGGAAAAACACUUUGUUUGAUUUAUUUUUCGGUUUAU-UUUGUCGGCGGAGCGCGCAGCGAAUAACCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGA
....(((.......))).((((((.((((((((((((((((..-.((((((.((..((((((((........)))))))).)).)))))).))))))......)))))))))).)))))) ( -40.30)
>DroYak_CAF1 21305 114 - 1
CGUCGUGGGAAAAACACUUUGUUUGAUUUAUUUUU------AUUUGUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGUGAAUCGUCGAAUGAAAAUGAAUGAAACGA
....(((.......))).((((((.((((((((((------((((((((((.((..((((((((.(....).)))))))).)).))))).........))))))))))))))).)))))) ( -42.30)
>consensus
CGUCGUGGGAAA_ACA____GUUUGAUUUAUUUUUCGGUUU__UUUUGUCGGCGGAGCGCGCAGCGAAUGCUCUGCGUGUGCGGCGACGGCGAAUCGUCGAAUGAAAAUGAAUGAAACGG
....................((((.((((((((((............((((.((..((((((((.(....).)))))))).)).))))((((...))))....)))))))))).)))).. (-32.84 = -33.28 +   0.44) 

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 09:49:25 2006