Locus 733

Sequence ID X_DroMel_CAF1
Location 1,994,528 – 1,994,767
Length 239
Max. P 0.976318
window1182 window1183 window1184 window1185

overview

Window 2

Location 1,994,528 – 1,994,647
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.16
Mean single sequence MFE -28.70
Consensus MFE -23.14
Energy contribution -23.70
Covariance contribution 0.56
Combinations/Pair 1.19
Mean z-score -2.54
Structure conservation index 0.81
SVM decision value 1.62
SVM RNA-class probability 0.967793
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1994528 119 + 22224390
UAUUUCCCUCUUUCGCCUUUUCCUCACAAGUUCAACACAACAAGAAGUCGAGCAUGCGCUUUUCUUCUUGCCAUUUA-UAAUUGCCUUCAACUUAUUGCUCCUUGUGUUUGGGGCGAAUG
...........((((((((.....((((((..........(((((((..((((....))))..))))))).......-.....((............))..))))))...)))))))).. ( -30.10)
>DroSec_CAF1 26571 120 + 1
UAUUUCCCUCUUUUGCCUUUUCCUCACAUGUUGAACUGUACAAGAAUUCGAGCAUGCGCUCUUCUUCUUGCCAUUCAUUAAUUGCCUCCAACUUAUUGCUUGUUGUUUUUGGGGCGAACG
...............................((((.((..((((((...((((....))))...)))))).))))))....(((((((((((.........)))).....)))))))... ( -22.50)
>DroEre_CAF1 16312 118 + 1
UGUUUCCCUCUUUCGCCUCUUCCUCGCACGCUCAACUGUACAAGAAGCCGAGCAUGCGCUCUUCUUCUUGCCAUUCAUUAAUUGCCUCCAACUUAUUGCGCGUUGUUUUUGGGGCGCA--
.............((((((.....((.((((.(((.....(((((((..((((....))))..)))))))...........(((....)))....))).)))))).....))))))..-- ( -30.10)
>DroYak_CAF1 27200 118 + 1
UAUUUCCCUCUUUCGCCUCUUCCUCGUACGCUCAACUGUACAAGAAGUCGAGCAUGCGCUCUUCUUCUUGCCAUUCAUUAAUUGCCUCCAACUUAUUGCGCGUUGAUUUUGGGGCGCA--
.............((((((....(((.((((.(((.....(((((((..((((....))))..)))))))...........(((....)))....))).)))))))....))))))..-- ( -32.10)
>consensus
UAUUUCCCUCUUUCGCCUCUUCCUCACACGCUCAACUGUACAAGAAGUCGAGCAUGCGCUCUUCUUCUUGCCAUUCAUUAAUUGCCUCCAACUUAUUGCGCGUUGUUUUUGGGGCGAA__
...........((((((((.....((.((((.(((.....(((((((..((((....))))..)))))))...........(((....)))....))).)))))).....)))))))).. (-23.14 = -23.70 +   0.56)

alignment

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secondary structure

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Window 3

Location 1,994,528 – 1,994,647
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -33.73
Consensus MFE -23.52
Energy contribution -25.02
Covariance contribution 1.50
Combinations/Pair 1.03
Mean z-score -2.81
Structure conservation index 0.70
SVM decision value 1.00
SVM RNA-class probability 0.897286
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1994528 119 - 22224390
CAUUCGCCCCAAACACAAGGAGCAAUAAGUUGAAGGCAAUUA-UAAAUGGCAAGAAGAAAAGCGCAUGCUCGACUUCUUGUUGUGUUGAACUUGUGAGGAAAAGGCGAAAGAGGGAAAUA
..((((((((...((((((...((((.(((((....))))).-...(..((((((((...(((....)))...))))))))..)))))..)))))).))....))))))........... ( -35.00)
>DroSec_CAF1 26571 120 - 1
CGUUCGCCCCAAAAACAACAAGCAAUAAGUUGGAGGCAAUUAAUGAAUGGCAAGAAGAAGAGCGCAUGCUCGAAUUCUUGUACAGUUCAACAUGUGAGGAAAAGGCAAAAGAGGGAAAUA
(.((((((((((.................)))).)))......(((((.(((((((...((((....))))...)))))))...))))).....................))).)..... ( -29.43)
>DroEre_CAF1 16312 118 - 1
--UGCGCCCCAAAAACAACGCGCAAUAAGUUGGAGGCAAUUAAUGAAUGGCAAGAAGAAGAGCGCAUGCUCGGCUUCUUGUACAGUUGAGCGUGCGAGGAAGAGGCGAAAGAGGGAAACA
--..((((((.....((((.........))))...(((.(((((.....((((((((..((((....))))..))))))))...)))))...)))..))....))))......(....). ( -36.00)
>DroYak_CAF1 27200 118 - 1
--UGCGCCCCAAAAUCAACGCGCAAUAAGUUGGAGGCAAUUAAUGAAUGGCAAGAAGAAGAGCGCAUGCUCGACUUCUUGUACAGUUGAGCGUACGAGGAAGAGGCGAAAGAGGGAAAUA
--..((((.(....((.((((.((((.(((((....)))))........((((((((..((((....))))..))))))))...)))).))))..))....).))))............. ( -34.50)
>consensus
__UGCGCCCCAAAAACAACGAGCAAUAAGUUGGAGGCAAUUAAUGAAUGGCAAGAAGAAGAGCGCAUGCUCGACUUCUUGUACAGUUGAACGUGCGAGGAAAAGGCGAAAGAGGGAAAUA
.......(((.......((((.((((.(((((....)))))........((((((((..((((....))))..))))))))...)))).))))............(....).)))..... (-23.52 = -25.02 +   1.50)

alignment

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secondary structure

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Window 4

Location 1,994,647 – 1,994,767
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.18
Mean single sequence MFE -36.16
Consensus MFE -31.48
Energy contribution -31.52
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.87
SVM decision value 1.77
SVM RNA-class probability 0.976318
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1994647 120 + 22224390
GUACUCCUAGGGCAUGAGCGAGAGAGUCGAUAUUUGCAUUUCGUAAAAAUGACAAAUGCCUAAUGAGCGUAAAUUGCUGCGCGUGCUUUUGUCAUAUUGCCUCUCACUCUGGCACGUUAA
..........(.((.(((.(((((.(.((((((((((.....)))))..(((((((.((.......(((((......)))))..)).)))))))))))))))))).))))).)....... ( -33.80)
>DroSec_CAF1 26691 120 + 1
AUACUCCUAGGGCAUGAGCGAGAGAGUCGAUAUUUGCAUUUCGUAAAAAUGACAAAUGUCUAAUGAGCGUAAAUUGCUGCGCGUGCUUUUCUCACAUUGCCUCUCGCUCUAGCACGUUAA
...........((..(((((((((.((.(((((((((((((.....))))).))))))))......(((((......)))))(((.......)))...)))))))))))..))....... ( -37.50)
>DroSim_CAF1 20891 120 + 1
NNNNNNNNNGGGCAUGAGCGAGAGAGUCGAUAUUUGCAUUUCGUAAAAAUGACAAAUGCCUAAUGAGCGUAAAUUGCUGCGCGUGCUUUUCUCACAUUGCCUCUCGCUCUGGCACGUUAA
..........(.((.(((((((((.(.((((((((((((((.....))))).))))).........(((((......)))))(((.......))))))))))))))))))).)....... ( -33.70)
>DroEre_CAF1 16430 113 + 1
-------UGGGGCGUGAGCGAGAGAGCCGAUAUUUGCAUUUCGAAAAAAUGACAAAUGCUUAAUGAGCGUAAAUUGCUGCGCGUGCUUUUCUCACAUUGCCUCUCGCUCUGGCUAGUUGA
-------...(((..(((((((((.((...(((((((((((.....))))).))))))........(((((......)))))(((.......)))...)))))))))))..)))...... ( -35.60)
>DroYak_CAF1 27318 112 + 1
-------AGGGGCGUGAGCGAGAGGGUCGAUAUUUGCAUUUCGUAAAAAUGACAAAUGCUUAAUGAGCGUAAAUUGCUGCGCGUGCUU-UCCCACAUUGCCUCUCGCUCUGGCUCGUUUA
-------..((((..((((((((((.(((.((...(((((((((....))))..))))).)).)))(((((......)))))(((...-...)))....))))))))))..))))..... ( -40.20)
>consensus
_______UAGGGCAUGAGCGAGAGAGUCGAUAUUUGCAUUUCGUAAAAAUGACAAAUGCCUAAUGAGCGUAAAUUGCUGCGCGUGCUUUUCUCACAUUGCCUCUCGCUCUGGCACGUUAA
...........((..(((((((((.(.((((((((((((((.....))))).))))).........(((((......)))))(((.......)))))))))))))))))..))....... (-31.48 = -31.52 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,994,647 – 1,994,767
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.18
Mean single sequence MFE -31.50
Consensus MFE -29.32
Energy contribution -29.04
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -1.67
Structure conservation index 0.93
SVM decision value 1.36
SVM RNA-class probability 0.946340
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1994647 120 - 22224390
UUAACGUGCCAGAGUGAGAGGCAAUAUGACAAAAGCACGCGCAGCAAUUUACGCUCAUUAGGCAUUUGUCAUUUUUACGAAAUGCAAAUAUCGACUCUCUCGCUCAUGCCCUAGGAGUAC
.....((((..((((((((((....((((((((.((......(((.......)))......)).)))))))).....(((.((....)).)))..))))))))))...((...)).)))) ( -31.80)
>DroSec_CAF1 26691 120 - 1
UUAACGUGCUAGAGCGAGAGGCAAUGUGAGAAAAGCACGCGCAGCAAUUUACGCUCAUUAGACAUUUGUCAUUUUUACGAAAUGCAAAUAUCGACUCUCUCGCUCAUGCCCUAGGAGUAU
.....(((((.(((((((((((..((((.(.....).))))..))...............((.(((((.((((((...))))))))))).))....)))))))))...((...))))))) ( -30.90)
>DroSim_CAF1 20891 120 - 1
UUAACGUGCCAGAGCGAGAGGCAAUGUGAGAAAAGCACGCGCAGCAAUUUACGCUCAUUAGGCAUUUGUCAUUUUUACGAAAUGCAAAUAUCGACUCUCUCGCUCAUGCCCNNNNNNNNN
.......((..(((((((((((...(((((........((...))........)))))...))(((((.((((((...))))))))))).......)))))))))..))........... ( -31.59)
>DroEre_CAF1 16430 113 - 1
UCAACUAGCCAGAGCGAGAGGCAAUGUGAGAAAAGCACGCGCAGCAAUUUACGCUCAUUAAGCAUUUGUCAUUUUUUCGAAAUGCAAAUAUCGGCUCUCUCGCUCACGCCCCA-------
.......((..(((((((((((..((((.......)))).))(((.......(((.....)))(((((.((((((...)))))))))))....))))))))))))..))....------- ( -31.30)
>DroYak_CAF1 27318 112 - 1
UAAACGAGCCAGAGCGAGAGGCAAUGUGGGA-AAGCACGCGCAGCAAUUUACGCUCAUUAAGCAUUUGUCAUUUUUACGAAAUGCAAAUAUCGACCCUCUCGCUCACGCCCCU-------
.......((..((((((((((...((((.(.-.....).)))).........(((.....)))(((((.((((((...)))))))))))......))))))))))..))....------- ( -31.90)
>consensus
UUAACGUGCCAGAGCGAGAGGCAAUGUGAGAAAAGCACGCGCAGCAAUUUACGCUCAUUAGGCAUUUGUCAUUUUUACGAAAUGCAAAUAUCGACUCUCUCGCUCAUGCCCCA_______
.......((..(((((((((((...((((.....((....)).((.......))))))...))(((((.((((((...))))))))))).......)))))))))..))........... (-29.32 = -29.04 +  -0.28)

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 09:52:25 2006