Locus 4469

Sequence ID X_DroMel_CAF1
Location 11,824,429 – 11,824,596
Length 167
Max. P 0.765970
window7343 window7344 window7345 window7346 window7347

overview

Window 3

Location 11,824,429 – 11,824,543
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.17
Mean single sequence MFE -52.93
Consensus MFE -28.71
Energy contribution -30.13
Covariance contribution 1.42
Combinations/Pair 1.30
Mean z-score -1.59
Structure conservation index 0.54
SVM decision value 0.11
SVM RNA-class probability 0.587427
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11824429 114 - 22224390
CAGCUGCAGCUGCAGCGGCGGCUCAUCCUUCGGAGGCUCCUGCUCCAGUCG---AAGCAGAAGCUCACGCCGCAGAGGCUCCCGCUGCCGUGGAAGGAGAUGCC---GCACCAGCGGCUG
(((((((.((....)).(((((...((((((.(((.((.(((((.(....)---.))))).))))).(((.((((.((...)).)))).)))))))))...)))---))....))))))) ( -56.60)
>DroSec_CAF1 237 114 - 1
CAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG---AAGCAGAAGCUACCGCCGCAGAGGCUCCCGCUGCCGUGGAAGGAGAUGCC---GCACCAGCGGCUG
(((((((.((....)).(((((...((((((((.((((.(((((.(....)---.))))).)))).))((.((((.((...)).)))).)))).))))...)))---))....))))))) ( -56.40)
>DroSim_CAF1 159 114 - 1
CAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG---AAGGCGAAGCUCCCGCCGCAGAGGCUCCCGCUGCCGUGGAAGGAGAUGCC---GCACCAGCGGCUG
(((((((.((....)).(((((...((((((((..((..((((((.....)---).((((.......))))))))..))..))((....)))).))))...)))---))....))))))) ( -53.20)
>DroEre_CAF1 1755 111 - 1
C------AGCUGCAGCGGCGGCUCAUCCACCGGAGGCACAUGCUCCAGCCGCAGAGGCAGAAGCGCCCGCCGCGGAGGCUCCCGCUGGCGAAGAAGGAGCUGUC---GCACCAGCGGCCG
.------.(((((.((((((((((.(((...)))(((....(((.(.(((.....))).).))))))((((((((......)))).))))......))))))))---))....))))).. ( -51.50)
>DroYak_CAF1 231 108 - 1
C------AGCUGCAGCGGCGGCUCAUCCUCCGGAGCCACCUGCUCCAGUCG---AAGCCGAAGCUCCCGCCGCUGAAGCUCCCGCUGGCGACGAAGGAGCUGCC---GCACCAGCAGCUG
(------((((((.(((((((((..((..(.(((((.....))))).)..)---)))))..((((((((.((((..(((....))))))).))..)))))))))---))....))))))) ( -55.40)
>DroAna_CAF1 10465 96 - 1
C---GGCGGCUGCGGCUGC------------GA---AUCCGGCUUCAGUAG---AGGCG---GCUCCGGCAGAAGGGGCGGCGCCGGCAGGAGAAGGAGAAGCCCCUGCAACCGUUGUUG
(---(((((.(((((..((------------..---.(((..((((.((..---.((((---(((((.......)))))..)))).)).))))..)))...))..))))).))))))... ( -44.50)
>consensus
C___UGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG___AAGCAGAAGCUCCCGCCGCAGAGGCUCCCGCUGCCGUGGAAGGAGAUGCC___GCACCAGCGGCUG
......(((((((.(((((((..........((((.......)))).........(((....))).))))))).....((((..((.....))..))))..............))))))) (-28.71 = -30.13 +   1.42)

alignment

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secondary structure

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Window 4

Location 11,824,466 – 11,824,571
Length 105
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 85.70
Mean single sequence MFE -49.34
Consensus MFE -32.84
Energy contribution -36.44
Covariance contribution 3.60
Combinations/Pair 1.06
Mean z-score -2.21
Structure conservation index 0.67
SVM decision value 0.47
SVM RNA-class probability 0.749712
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11824466 105 + 22224390
AGCCUCUGCGGCGUGAGCUUCUGCUU---CGACUGGAGCAGGAGCCUCCGAAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCUGCCUCCAUUUCCUGAUUGAU
.(((.....)))(.((((((((((((---(....)))))))))).))))..((((.((((.((.((((((((....)))))))).)).).)))....))))....... ( -49.30)
>DroSec_CAF1 274 105 + 1
AGCCUCUGCGGCGGUAGCUUCUGCUU---CGACUGGAGCAGGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCAGCCUCCAUUUCCUGAUUGAU
.(((.....)))((..((((((((((---(....)))))))))))..))((((((.(.((.((.((((((((....)))))))).)).))))))...)))........ ( -53.90)
>DroSim_CAF1 196 105 + 1
AGCCUCUGCGGCGGGAGCUUCGCCUU---CGACUGGAGCAGGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCUGCAGCCUCCACUUCCUGAUUGAU
.(((.....)))((..(((((..(((---(....))))..)))))..))(((((..(((.....(((((((((((....))))))))))))))..)))))........ ( -49.60)
>DroEre_CAF1 1792 102 + 1
AGCCUCCGCGGCGGGCGCUUCUGCCUCUGCGGCUGGAGCAUGUGCCUCCGGUGGAUGAGCCGCCGCUGCAGCU------GCUGCCGCCGUCUCCAUUUCCUGAGUGAU
.......(((((((..((..((((....(((((.((..(((.((((...)))).)))..))))))).))))..------))..)))))))...(((((...))))).. ( -43.30)
>DroYak_CAF1 268 99 + 1
AGCUUCAGCGGCGGGAGCUUCGGCUU---CGACUGGAGCAGGUGGCUCCGGAGGAUGAGCCGCCGCUGCAGCU------GCUGCCGCUGUCUCCACUUCCUGGGUGAU
.....(((((((((((((....))))---.(.(((.(((.((((((((........))))))))))).)))).------.)))))))))....((((.....)))).. ( -50.60)
>consensus
AGCCUCUGCGGCGGGAGCUUCUGCUU___CGACUGGAGCAGGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCAGCCUCCAUUUCCUGAUUGAU
.(((.....)))(((.((((((((((.........)))))))))).)))(((((..((((.((.((((((((....)))))))).)).).)))..)))))........ (-32.84 = -36.44 +   3.60)

alignment

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secondary structure

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Window 5

Location 11,824,466 – 11,824,571
Length 105
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 85.70
Mean single sequence MFE -46.90
Consensus MFE -31.68
Energy contribution -33.12
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -2.15
Structure conservation index 0.68
SVM decision value 0.48
SVM RNA-class probability 0.751095
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11824466 105 - 22224390
AUCAAUCAGGAAAUGGAGGCAGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUUCGGAGGCUCCUGCUCCAGUCG---AAGCAGAAGCUCACGCCGCAGAGGCU
.......((((....(((.(.((.((((((((....)))))))).))).))).))))..(..((((.(((((.(....)---.))))).))))..)(((.....))). ( -47.60)
>DroSec_CAF1 274 105 - 1
AUCAAUCAGGAAAUGGAGGCUGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG---AAGCAGAAGCUACCGCCGCAGAGGCU
........(((...(((((((((.((((((((....)))))))).))))))..))))))((.((((.(((((.(....)---.))))).)))).))(((.....))). ( -54.30)
>DroSim_CAF1 196 105 - 1
AUCAAUCAGGAAGUGGAGGCUGCAGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG---AAGGCGAAGCUCCCGCCGCAGAGGCU
.....((.(((...(((((((((.((((((((....)))))))).))))))..)))))).))(((..((((((.....)---).((((.......))))))))..))) ( -49.30)
>DroEre_CAF1 1792 102 - 1
AUCACUCAGGAAAUGGAGACGGCGGCAGC------AGCUGCAGCGGCGGCUCAUCCACCGGAGGCACAUGCUCCAGCCGCAGAGGCAGAAGCGCCCGCCGCGGAGGCU
....(((.......(....)(((((..((------..((((.(((((((........))((((.(....))))).)))))....))))..))..)))))...)))... ( -42.80)
>DroYak_CAF1 268 99 - 1
AUCACCCAGGAAGUGGAGACAGCGGCAGC------AGCUGCAGCGGCGGCUCAUCCUCCGGAGCCACCUGCUCCAGUCG---AAGCCGAAGCUCCCGCCGCUGAAGCU
.((((.......))))...(((((((.((------....))(((..(((((..((..(.(((((.....))))).)..)---))))))..)))...)))))))..... ( -40.50)
>consensus
AUCAAUCAGGAAAUGGAGGCAGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCCUGCUCCAGUCG___AAGCAGAAGCUCCCGCCGCAGAGGCU
.((..................((((((((....)))))))).(((((((..........((((.(....)))))..........((....))..))))))).)).... (-31.68 = -33.12 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,824,503 – 11,824,596
Length 93
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 85.35
Mean single sequence MFE -39.68
Consensus MFE -28.98
Energy contribution -30.78
Covariance contribution 1.80
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.73
SVM decision value 0.48
SVM RNA-class probability 0.753758
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11824503 93 + 22224390
GGAGCCUCCGAAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCUGCCUCCAUUUCCUGAUUGAUUUCGGUGGCCCGCUUGCUCUGAAGA---
((.(((.((((((((.(.((.((.((((((((....)))))))).)).))))))...((......)).))))).)))))..............--- ( -40.60)
>DroSec_CAF1 311 92 + 1
GGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCAGCCUCCAUUUCCUGAUUGAUUUCGGUGGCCCGCUUGCUCUGAAA----
((.(((.((((((((.(.((.((.((((((((....)))))))).)).))))))...((......)).))))).))))).............---- ( -40.10)
>DroSim_CAF1 233 96 + 1
GGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCUGCAGCCUCCACUUCCUGAUUGAUUUCGGUGGCCCGCUUGCUCUGCAGAAAG
((.(((.(((((((..(((.....(((((((((((....))))))))))))))..))))).((......)))).)))))((.......))...... ( -44.30)
>DroEre_CAF1 1832 90 + 1
UGUGCCUCCGGUGGAUGAGCCGCCGCUGCAGCU------GCUGCCGCCGUCUCCAUUUCCUGAGUGAUUUCGGUGGCCCGCUUGCUCUGAAAAGAU
..(((...((((((.....))))))..)))((.------((.(((((((....(((((...)))))....)))))))..))..))(((....))). ( -33.00)
>DroYak_CAF1 305 89 + 1
GGUGGCUCCGGAGGAUGAGCCGCCGCUGCAGCU------GCUGCCGCUGUCUCCACUUCCUGGGUGAUUUCGGUGGCCCGCUUGCUCUGCAAU-AA
((((((((........))))))))((.(((((.------((..(((..(((((((.....)))).)))..)))..))..)).)))...))...-.. ( -40.40)
>consensus
GGAGCCUCCGGAGGAUGAGCCGCCGCUGCAGCUGCAGCUGCAGCCGCAGCCUCCAUUUCCUGAUUGAUUUCGGUGGCCCGCUUGCUCUGAAAA_A_
((.(((.((((((((.(.((.((.((((((((....)))))))).)).))))))...((......)).))))).)))))................. (-28.98 = -30.78 +   1.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,824,503 – 11,824,596
Length 93
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 85.35
Mean single sequence MFE -37.92
Consensus MFE -29.56
Energy contribution -31.04
Covariance contribution 1.48
Combinations/Pair 1.08
Mean z-score -1.79
Structure conservation index 0.78
SVM decision value 0.52
SVM RNA-class probability 0.765970
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11824503 93 - 22224390
---UCUUCAGAGCAAGCGGGCCACCGAAAUCAAUCAGGAAAUGGAGGCAGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUUCGGAGGCUCC
---..............(((((.((((........((((....(((.(.((.((((((((....)))))))).))).))).)))))))).))))). ( -43.00)
>DroSec_CAF1 311 92 - 1
----UUUCAGAGCAAGCGGGCCACCGAAAUCAAUCAGGAAAUGGAGGCUGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCC
----.............(((((.((((......)).(((...(((((((((.((((((((....)))))))).))))))..)))))))).))))). ( -45.30)
>DroSim_CAF1 233 96 - 1
CUUUCUGCAGAGCAAGCGGGCCACCGAAAUCAAUCAGGAAGUGGAGGCUGCAGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCC
......((.......))(((((.((((......)).(((...(((((((((.((((((((....)))))))).))))))..)))))))).))))). ( -44.20)
>DroEre_CAF1 1832 90 - 1
AUCUUUUCAGAGCAAGCGGGCCACCGAAAUCACUCAGGAAAUGGAGACGGCGGCAGC------AGCUGCAGCGGCGGCUCAUCCACCGGAGGCACA
...............(((((((.(((......(((........)))...(((((...------.)))))..))).))))).(((...))).))... ( -27.90)
>DroYak_CAF1 305 89 - 1
UU-AUUGCAGAGCAAGCGGGCCACCGAAAUCACCCAGGAAGUGGAGACAGCGGCAGC------AGCUGCAGCGGCGGCUCAUCCUCCGGAGCCACC
..-.((((...))))(((((((.(((...............((....))(((((...------.)))))..))).))))).(((...))))).... ( -29.20)
>consensus
_U_UUUUCAGAGCAAGCGGGCCACCGAAAUCAAUCAGGAAAUGGAGGCAGCGGCUGCAGCUGCAGCUGCAGCGGCGGCUCAUCCUCCGGAGGCUCC
.........((((....(((((.(((.......(((.....))).....((((((((....))))))))..))).))))).(((...))).)))). (-29.56 = -31.04 +   1.48)

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 11:25:53 2006