Locus 1645

Sequence ID X_DroMel_CAF1
Location 4,663,565 – 4,663,759
Length 194
Max. P 0.999970
window2700 window2701 window2702 window2703 window2704

overview

Window 0

Location 4,663,565 – 4,663,684
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 75.31
Mean single sequence MFE -31.85
Consensus MFE -19.33
Energy contribution -20.45
Covariance contribution 1.12
Combinations/Pair 1.08
Mean z-score -3.25
Structure conservation index 0.61
SVM decision value 4.21
SVM RNA-class probability 0.999837
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663565 119 + 22224390
-UUGAGGGAAAUGGGAAAAGCAUAUUAUAAUGUACUUUAGGACGCUUUACAAAGAAAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCAAAUUUG
-(((..((((((((((((((..........(((((((((.....(((....)))...((((......))))...)))))))))))))))))))..(((.....)))))))..)))..... ( -25.90)
>DroSec_CAF1 24898 120 + 1
GUUCGCGUGAAUGGGAAAAGCUUUCUAUAAAGUACUUUAGGACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUG
((((((.((((.((((...............((((((((....(((......))).(((((....).))))...))))))))..(((((((....))))))))))).))))))))))... ( -36.30)
>DroEre_CAF1 25686 117 + 1
GAUCGCAUGGCUGGGAAAAGCUUUU-UUAAUGUACUUUAGAACUCUUUACGUUG--AAAGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAGCUGGGAGAAUCCUUUUCAGCGAAUUUG
..((((..((((((((((((.((((-((((((((....((....)).)))))))--))))).....(((((....)))))...))))))))))))(((.....))).....))))..... ( -36.90)
>DroYak_CAF1 22076 93 + 1
GAUCGCUUGAAUGGGAAAAGCUUUU------------------------CGUUU--AAA-UAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCGGGGAGAAUCCCUUUCAGCGAAUUUG
..(((((.(((.((((...(((((.------------------------.((((--(((-........))))))))))))....(((((((....))))))))))).))))))))..... ( -28.30)
>consensus
GAUCGCGUGAAUGGGAAAAGCUUUU_AUAAUGUACUUUAGGACGCUUUACGUAG__AAAGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUG
..((((.((((.((((..................................................(((((....)))))....(((((((....))))))))))).))))))))..... (-19.33 = -20.45 +   1.12)

alignment

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secondary structure

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Window 1

Location 4,663,565 – 4,663,684
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.31
Mean single sequence MFE -30.60
Consensus MFE -21.96
Energy contribution -22.40
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -3.45
Structure conservation index 0.72
SVM decision value 5.05
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663565 119 - 22224390
CAAAUUUGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUCCCUUUUUCUUUGUAAAGCGUCCUAAAGUACAUUAUAAUAUGCUUUUCCCAUUUCCCUCAA-
.........(((...((......))((((((((((((((((((((((..((((.((.......)).)))))))))).((.(....).)).......))))))))))))))))...))).- ( -23.60)
>DroSec_CAF1 24898 120 - 1
CAAAUUCGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGGUUCCCUUUUGCUGCAUGAAGCGUCCUAAAGUACUUUAUAGAAAGCUUUUCCCAUUCACGCGAAC
....(((((((((..((......))...((((((((((...((.....(((((((.((......((((......)))).....)).))))))).))...)))))))))))))).))))). ( -34.50)
>DroEre_CAF1 25686 117 - 1
CAAAUUCGCUGAAAAGGAUUCUCCCAGCUGGGAAAAGUGUACUUUAUUUAAAGUGAUUUCCUUU--CAACGUAAAGAGUUCUAAAGUACAUUAA-AAAAGCUUUUCCCAGCCAUGCGAUC
.....((((((....((......)).((((((((((((((((((((((((...(((.......)--))...))))......)))))))).....-....)))))))))))))).)))).. ( -33.70)
>DroYak_CAF1 22076 93 - 1
CAAAUUCGCUGAAAGGGAUUCUCCCCGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUUA-UUU--AAACG------------------------AAAAGCUUUUCCCAUUCAAGCGAUC
.....(((((....(((......)))((((((((((((....((((..((((....))))-..)--)))..------------------------....))))))))))))..))))).. ( -30.60)
>consensus
CAAAUUCGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGUACUUUAUUUAAAGUGAUUCCCUUU__CAACGUAAAGCGUCCUAAAGUACAUUAU_AAAAGCUUUUCCCAUUCACGCGAAC
.....((((......((......)).((((((((((((.((((((....)))))).....((((........)))).......................))))))))))))...)))).. (-21.96 = -22.40 +   0.44)

alignment

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secondary structure

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Window 2

Location 4,663,604 – 4,663,724
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.33
Mean single sequence MFE -25.75
Consensus MFE -18.33
Energy contribution -17.95
Covariance contribution -0.38
Combinations/Pair 1.08
Mean z-score -2.59
Structure conservation index 0.71
SVM decision value 1.12
SVM RNA-class probability 0.918598
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663604 120 + 22224390
GACGCUUUACAAAGAAAAAGGGAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCAAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAA
.((.((((.....(..(((((((...(((((....)))))....(((((((....))))))))))))))...)...((((((((......))).)))))............)))).)).. ( -24.60)
>DroSec_CAF1 24938 120 + 1
GACGCUUCAUGCAGCAAAAGGGAACCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAA
.((..(((.(((.((.(((((((...(((((....)))))....(((((((....))))))))))))))..)).......((((......))))))).)))..))............... ( -26.00)
>DroEre_CAF1 25725 118 + 1
AACUCUUUACGUUG--AAAGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAGCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACGUCAAAAGGGUAA
.(((((((.(((((--((((((....(((((....)))))....(((((((....)))))))))).))))))))..((((((((......))).)))))............))))))).. ( -33.60)
>DroYak_CAF1 22101 108 + 1
---------CGUUU--AAA-UAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCGGGGAGAAUCCCUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAA
---------.((((--(((-........))))))).........(((((((....))))))).((((((..((...((((((((......))).)))))....))......))))))... ( -18.80)
>consensus
GACGCUUUACGUAG__AAAGGAAAUCACUUUAAAUAAAGUACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAA
.......................(((.((((.......((((..(((((((....)))))))..............((((((((......))).)))))....))))....))))))).. (-18.33 = -17.95 +  -0.38)

alignment

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secondary structure

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Window 3

Location 4,663,644 – 4,663,759
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.20
Mean single sequence MFE -23.88
Consensus MFE -17.46
Energy contribution -17.77
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.73
SVM decision value 0.05
SVM RNA-class probability 0.558503
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663644 115 + 22224390
ACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCAAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAACA-----AAGAAUACCAUGGGAAUAUUCCUUGAG
.((((((.(((..(((..((.....))..)))....((((((((......))).)))))...............))).))))))..((-----(.(((((((...))..))))).))).. ( -24.20)
>DroSec_CAF1 24978 115 + 1
ACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGUGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAGUGAAAA-----AAGAAUACCAUGGGAAUAUUCCUUGAG
.((((((((((....))))))((((((((..((...(((((......)))))..))..((........))))))))))..))))....-----........((.((((....)))))).. ( -23.10)
>DroEre_CAF1 25763 113 + 1
ACACUUUUCCCAGCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACGUCAAAAGGGUAAAA-------GGGAAAAAACACCAUGGGAAUAUUCCUUGAG
....(((((((.((((..((.....))..))))...((((((((......))).))))).......................-------))))))).....((.((((....)))))).. ( -25.10)
>DroYak_CAF1 22129 120 + 1
ACACUUUUCCCAUCGGGGAGAAUCCCUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAAAAAAAAUGGGGAAAAACACCAUGGGAAUAUUGCUUGAG
......(((((((.((......(((((.........((((((((......))).))))).....(((.((....)))))..........)))))......)))))))))........... ( -23.10)
>consensus
ACACUUUUCCCAUCUGGGAGAAUCCUUUUCAGCGAAUUUGCGUUAAAAUAAACAGCAAGAAAAGUACAUCAAAAGGGUAAAAUGAAAA_____AAAAACACCAUGGGAAUAUUCCUUGAG
.....((((((....))))))((((((((..((...((((((((......))).)))))....)).....)))))))).......................((.((((....)))))).. (-17.46 = -17.77 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,663,644 – 4,663,759
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.20
Mean single sequence MFE -24.65
Consensus MFE -17.02
Energy contribution -16.64
Covariance contribution -0.38
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.69
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4663644 115 - 22224390
CUCAAGGAAUAUUCCCAUGGUAUUCUU-----UGUUCACUUUACCCUUUUGAUGUACUUUUCUUGCUGUUUAUUUUAACGCAAAUUUGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGU
..(((((((((((.....)))))))))-----))..((((((..((((((.(.(((......((((.(((......)))))))...)))).))))))....((((....)))))))))). ( -28.70)
>DroSec_CAF1 24978 115 - 1
CUCAAGGAAUAUUCCCAUGGUAUUCUU-----UUUUCACUUUACCCUUUUGAUGUACUUUUCUUGCUGUUUAUUUUAACACAAAUUCGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGU
...((((((((((.....)))))))))-----)...((((((.(((.((((..(..((((((..((((((......)))).......)).))))))....)...)))).))).)))))). ( -24.91)
>DroEre_CAF1 25763 113 - 1
CUCAAGGAAUAUUCCCAUGGUGUUUUUUCCC-------UUUUACCCUUUUGACGUACUUUUCUUGCUGUUUAUUUUAACGCAAAUUCGCUGAAAAGGAUUCUCCCAGCUGGGAAAAGUGU
.(((((((....)))...((((.........-------...))))...))))..((((((((((((((....(((((.((......)).))))).((.....)))))).)))))))))). ( -21.20)
>DroYak_CAF1 22129 120 - 1
CUCAAGCAAUAUUCCCAUGGUGUUUUUCCCCAUUUUUUUUUUACCCUUUUGAUGUACUUUUCUUGCUGUUUAUUUUAACGCAAAUUCGCUGAAAGGGAUUCUCCCCGAUGGGAAAAGUGU
.....(((...(((((((((.(.....).))............(((((((..((........((((.(((......)))))))...))..)))))))..........)))))))...))) ( -23.80)
>consensus
CUCAAGGAAUAUUCCCAUGGUAUUCUU_____UUUUCACUUUACCCUUUUGAUGUACUUUUCUUGCUGUUUAUUUUAACGCAAAUUCGCUGAAAAGGAUUCUCCCAGAUGGGAAAAGUGU
...........(((((((((((...................)))).....((....((((((..((((((......)))).......)).))))))...))......)))))))...... (-17.02 = -16.64 +  -0.38)

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 10:15:38 2006