Locus 876

Sequence ID 3R_DroMel_CAF1
Location 2,955,569 – 2,955,708
Length 139
Max. P 0.878662
window1392 window1393 window1394

overview

Window 2

Location 2,955,569 – 2,955,683
Length 114
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -32.27
Consensus MFE -28.10
Energy contribution -28.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.87
SVM decision value 0.35
SVM RNA-class probability 0.699436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2955569 114 - 27905053
AAUUGAAAAAAAUACA-AAAAGUGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGUCGAGUUU-GACG
..............((-((...(((...((((((((((((.......)))))..........(((..((((....))))..)))........)))))))....)))..)))-)... ( -32.80)
>DroVir_CAF1 4052 114 - 1
ACAUAAGAAAAAGGCA-AAAAGUAACAUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGGAGCACUC-GGCG
.............((.-....((..(..((((((((((((.......)))))..........(((..((((....))))..)))........)))))))...)..))....-.)). ( -31.10)
>DroPse_CAF1 6090 111 - 1
----UCAAAUUUUGCAAAAAAGCGAGCUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGUGGGUAUG-UCAG
----......(((((......)))))..((((((((((((.......)))))..........(((..((((....))))..)))........)))))))............-.... ( -31.10)
>DroYak_CAF1 4583 114 - 1
A-AGAAUAUAAAAGCAAAAAAGUUAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGCUUGUGCC-AAUG
.-...........(((...((((.....((((((((((((.......)))))..........(((..((((....))))..)))........)))))))...)))).))).-.... ( -33.40)
>DroMoj_CAF1 4062 115 - 1
AUGCAGAAAAAGUGCAAAAAAGUACAAUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCAUGUU-CUCACGGUCG
.((.((((...((((......))))...((((((((((((.......)))))..........(((..((((....))))..)))........)))))))....))-))))...... ( -34.10)
>DroAna_CAF1 4685 114 - 1
AAAUAAAAAAUAGCAA-AAAAGCGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGUUGUACUC-UAGA
..........(((...-...((((....((((((((((((.......)))))..........(((..((((....))))..)))........)))))))..)))).....)-)).. ( -31.10)
>consensus
A_AUAAAAAAAAUGCA_AAAAGUGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAUGCUAACCAUUACACCACCGACGCCACGUUGCUCUC_GACG
............................((((((((((((.......)))))..........(((..((((....))))..)))........)))))))................. (-28.10 = -28.10 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,955,608 – 2,955,708
Length 100
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -21.92
Consensus MFE -14.50
Energy contribution -14.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value 0.38
SVM RNA-class probability 0.714924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2955608 100 + 27905053
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAGUUCACUUUU-UGUAUUUU-UUUCAAUUCUU--UAC------GGCAUAU-UA-AUUUUUUAUU
.((((((((....(((.((((((.(((((.......))))).....((((........)-))).....-..)))))))))--...------)))).))-))-.......... ( -20.80)
>DroSec_CAF1 5344 100 + 1
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAGUUCGCUUUU-UGCAUUUU-UUUUAUUUUUC--UAC------AGCAACA-UA-UUUUUUAAUU
...(((((.......((.((((..(((((.......))))).)))))).....((....-.)).....-...........--...------.))))).-..-.......... ( -23.20)
>DroSim_CAF1 5357 101 + 1
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAUUUCGCUUUU-UGCAUUUUUUUUUAUUUUUC--UAC------AGCAACU-UA-UUUUUUUAUU
..((((((.......((.((((..(((((.......))))).)))))).....((....-.)).................--...------.))))))-..-.......... ( -23.20)
>DroEre_CAF1 5370 107 + 1
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAGUUCGCUUUU-UGCAUUUU-UUUUCUUUGUU--UCCUAGCGGAGCAAAA-UACAAGUGGUAUU
....((((.......((.((((..(((((.......))))).))))))..((((((...-.(((....-.......))).--....))))))))))((-(((.....))))) ( -26.30)
>DroYak_CAF1 4622 102 + 1
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAGUUAACUUUUUUGCUUUUA-UAUUCU-UGUUUCUCCUA-------AAAA-UACAAAUGGUAUU
.....((((.........((((..(((((.......))))).))))((((.........)))).....-......-...........-------....-.......)))).. ( -18.50)
>DroMoj_CAF1 4101 96 + 1
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAUUGUACUUUUUUGCACUUU-UUCUGCAUU--------------GAAUAUGUA-UUUAUUUAUU
...............(((((((..(((((.......))))).))))(((..(.....)..))).....-...)))..(--------------(((((....-..)))))).. ( -19.50)
>consensus
AUAGUUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCGACGCAGUUCACUUUU_UGCAUUUU_UUUUAUUUUUU__UAC______AGCAAAA_UA_AUUUUUUAUU
...............((.((((..(((((.......))))).))))))................................................................ (-14.50 = -14.50 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,955,608 – 2,955,708
Length 100
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -23.13
Consensus MFE -15.53
Energy contribution -14.75
Covariance contribution -0.78
Combinations/Pair 1.27
Mean z-score -1.99
Structure conservation index 0.67
SVM decision value 0.90
SVM RNA-class probability 0.878662
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2955608 100 - 27905053
AAUAAAAAAU-UA-AUAUGCC------GUA--AAGAAUUGAAA-AAAAUACA-AAAAGUGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
..........-..-...((((------...--(((..((((..-........-...((....)).......(((((.......))))).))))...)))....))))..... ( -20.00)
>DroSec_CAF1 5344 100 - 1
AAUUAAAAAA-UA-UGUUGCU------GUA--GAAAAAUAAAA-AAAAUGCA-AAAAGCGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
..........-..-.((((((------(((--(..........-...(((((-..........))))).((((.((........)).))))..))))......))))))... ( -21.70)
>DroSim_CAF1 5357 101 - 1
AAUAAAAAAA-UA-AGUUGCU------GUA--GAAAAAUAAAAAAAAAUGCA-AAAAGCGAAAUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
..........-..-(((((((------(((--(..............(((((-..........))))).((((.((........)).))))..))))......))))))).. ( -22.90)
>DroEre_CAF1 5370 107 - 1
AAUACCACUUGUA-UUUUGCUCCGCUAGGA--AACAAAGAAAA-AAAAUGCA-AAAAGCGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
....(((.((((.-(((((((((....)))--...........-.....)))-))).))))...((((.((((.((........)).)))).)).)).))).((....)).. ( -25.19)
>DroYak_CAF1 4622 102 - 1
AAUACCAUUUGUA-UUUU-------UAGGAGAAACA-AGAAUA-UAAAAGCAAAAAAGUUAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
....(((((((((-((((-------(.(......))-))))))-))))((((.....((.....))((.((((.((........)).)))).))))))))).((....)).. ( -24.20)
>DroMoj_CAF1 4101 96 - 1
AAUAAAUAAA-UACAUAUUC--------------AAUGCAGAA-AAAGUGCAAAAAAGUACAAUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
..........-......(((--------------((.((((..-...((((......))))........((((.((........)).))))..)))))))))((....)).. ( -24.80)
>consensus
AAUAAAAAAA_UA_AUUUGCU______GUA__AAAAAAUAAAA_AAAAUGCA_AAAAGCGAACUGCGUCGGCCGGGAAUCGAACCCGGGUCAACUGCUUGGAAGGCAACUAU
................................................(((......)))....((((.((((.((........)).)))).)).)).....((....)).. (-15.53 = -14.75 +  -0.78) 

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 09:54:23 2006