Locus 8228

Sequence ID 3L_DroMel_CAF1
Location 21,628,577 – 21,628,827
Length 250
Max. P 0.996786
window13455 window13456 window13457 window13458 window13459

overview

Window 5

Location 21,628,577 – 21,628,684
Length 107
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 96.09
Mean single sequence MFE -18.28
Consensus MFE -14.80
Energy contribution -15.36
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.81
SVM decision value 0.85
SVM RNA-class probability 0.865549
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21628577 107 + 23771897
AACAUAUAUGUACAGUAAUUAUUGGUU-UUUGACAAUAAAUGUAAAUUCGAUUAAGUUUCGAAAGGGUAGAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAU
.....................(((((.-..((((............(((((.......)))))..((((....))))(....)............))))))))).... ( -19.60)
>DroSec_CAF1 5035 107 + 1
AACAUAUAUGUACAGUAAUUAUUGGUU-UUUGACAAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAU
.....................(((((.-..((((............(((((.......)))))..((((....))))(....)............))))))))).... ( -17.00)
>DroSim_CAF1 5073 107 + 1
AACAUAUAUGUACAGUAAUUAUUGGUU-UUUGACAAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAU
.....................(((((.-..((((............(((((.......)))))..((((....))))(....)............))))))))).... ( -17.00)
>DroEre_CAF1 4185 107 + 1
AACAUAUAUGUACAGUAAUUAUUGGUU-UUUGACAAUAAAUGUAAAUUCAAUUAUGUUUCGAAAAGGUAAAAGUACCGGAAACAAAACCAAAAGAGUCAACCAAUAAU
.................(((((((((.-..((((.((((.((......)).))))(((((.....((((....)))).)))))............))))))))))))) ( -19.50)
>DroYak_CAF1 14964 108 + 1
AACAUAUAUGUACAGUAAUUAUUGGUUUUUUGACAAUAAAUGUAAAUUCAAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAGCCAAAAGAGUCAACCAAUAAU
.................(((((((((....((((..(((.((......)).))).(((((.....((((....)))).)))))............))))))))))))) ( -18.30)
>consensus
AACAUAUAUGUACAGUAAUUAUUGGUU_UUUGACAAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAU
.....................(((((....((((............(((((.......)))))..((((....))))(....)............))))))))).... (-14.80 = -15.36 +   0.56)

alignment

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secondary structure

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Window 6

Location 21,628,577 – 21,628,684
Length 107
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 96.09
Mean single sequence MFE -18.19
Consensus MFE -15.34
Energy contribution -15.06
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -1.55
Structure conservation index 0.84
SVM decision value 0.50
SVM RNA-class probability 0.760902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21628577 107 - 23771897
AUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUCUACCCUUUCGAAACUUAAUCGAAUUUACAUUUAUUGUCAAA-AACCAAUAAUUACUGUACAUAUAUGUU
((((.((((((((...(((((((..(((((.((((....)))).....)))))..)))))))............))))..-.)))).))))................. ( -16.76)
>DroSec_CAF1 5035 107 - 1
AUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUUGUCAAA-AACCAAUAAUUACUGUACAUAUAUGUU
((((.((((((((...(((((((..(((((.((((....)))).....)))))..)))))))............))))..-.)))).))))................. ( -17.56)
>DroSim_CAF1 5073 107 - 1
AUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUUGUCAAA-AACCAAUAAUUACUGUACAUAUAUGUU
((((.((((((((...(((((((..(((((.((((....)))).....)))))..)))))))............))))..-.)))).))))................. ( -17.56)
>DroEre_CAF1 4185 107 - 1
AUUAUUGGUUGACUCUUUUGGUUUUGUUUCCGGUACUUUUACCUUUUCGAAACAUAAUUGAAUUUACAUUUAUUGUCAAA-AACCAAUAAUUACUGUACAUAUAUGUU
(((((((((((((...((..(((.((((((.((((....)))).....)))))).)))..))............))))..-.)))))))))................. ( -20.26)
>DroYak_CAF1 14964 108 - 1
AUUAUUGGUUGACUCUUUUGGCUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUUGAAUUUACAUUUAUUGUCAAAAAACCAAUAAUUACUGUACAUAUAUGUU
((((((((((.....(((((((...(((((.((((....)))).....))))).....(((((....)))))..)))))))))))))))))................. ( -18.80)
>consensus
AUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUUGUCAAA_AACCAAUAAUUACUGUACAUAUAUGUU
((((.((((((((...(((((((..(((((.((((....)))).....)))))..)))))))............))))....)))).))))................. (-15.34 = -15.06 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,628,610 – 21,628,722
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 94.11
Mean single sequence MFE -16.60
Consensus MFE -16.20
Energy contribution -16.16
Covariance contribution -0.04
Combinations/Pair 1.11
Mean z-score -1.30
Structure conservation index 0.98
SVM decision value 1.22
SVM RNA-class probability 0.931829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21628610 112 + 23771897
AAUAAAUGUAAAUUCGAUUAAGUUUCGAAAGGGUAGAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAUGAAAGAGGUUCCGAAUGAUUGAUGAACAUGAAGGUAAU
.....((((....(((((((...((((....((((....))))(....)..((((.......(((........)))....)))).)))))))))))...))))......... ( -18.50)
>DroSec_CAF1 5068 112 + 1
AAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAUGAAAAAGGUUCCGAAUGAUUGAUGAACAUGAAGGUAAU
.....((((....(((((((...((((....((((....))))(....)..((((.......(((........)))....)))).)))))))))))...))))......... ( -15.90)
>DroSim_CAF1 5106 112 + 1
AAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAUGAAAAAGGUUCCGAAUGAUUGAUGAACAUGAAGGUAAU
.....((((....(((((((...((((....((((....))))(....)..((((.......(((........)))....)))).)))))))))))...))))......... ( -15.90)
>DroEre_CAF1 4218 112 + 1
AAUAAAUGUAAAUUCAAUUAUGUUUCGAAAAGGUAAAAGUACCGGAAACAAAACCAAAAGAGUCAACCAAUAAUGAAAGAGGUGCCGAGUGAUUGAUGAACAUAAAGGUAAU
.....((((....(((((((((((((.....((((....)))).)))))...(((.......(((........)))....))).....))))))))...))))......... ( -16.80)
>DroYak_CAF1 14998 112 + 1
AAUAAAUGUAAAUUCAAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAGCCAAAAGAGUCAACCAAUAAUGAAAUAGGUUCCGAGUGAUUGAUGAACAUAAGGGUAAU
.....((((....(((((((...((((....((((....))))(....)..((((.......(((........)))....)))).)))))))))))...))))......... ( -15.90)
>consensus
AAUAAAUGUAAAUUCGAUUAAGUUUCGAAAAGGUAAAAAUACCGGAAACAAAACCAAAAGAGUCAACCAGCAAUGAAAAAGGUUCCGAAUGAUUGAUGAACAUGAAGGUAAU
.....((((....(((((((...((((....((((....))))(....)..((((.......(((........)))....)))).)))))))))))...))))......... (-16.20 = -16.16 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,628,610 – 21,628,722
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 94.11
Mean single sequence MFE -16.89
Consensus MFE -15.62
Energy contribution -15.78
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.88
Structure conservation index 0.92
SVM decision value 2.75
SVM RNA-class probability 0.996786
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21628610 112 - 23771897
AUUACCUUCAUGUUCAUCAAUCAUUCGGAACCUCUUUCAUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUCUACCCUUUCGAAACUUAAUCGAAUUUACAUUUAUU
.........((((...(((((((....(((.....))).....)))))))....(((((((..(((((.((((....)))).....)))))..)))))))...))))..... ( -17.90)
>DroSec_CAF1 5068 112 - 1
AUUACCUUCAUGUUCAUCAAUCAUUCGGAACCUUUUUCAUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUU
.........((((...(((((((....(((.....))).....)))))))....(((((((..(((((.((((....)))).....)))))..)))))))...))))..... ( -18.70)
>DroSim_CAF1 5106 112 - 1
AUUACCUUCAUGUUCAUCAAUCAUUCGGAACCUUUUUCAUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUU
.........((((...(((((((....(((.....))).....)))))))....(((((((..(((((.((((....)))).....)))))..)))))))...))))..... ( -18.70)
>DroEre_CAF1 4218 112 - 1
AUUACCUUUAUGUUCAUCAAUCACUCGGCACCUCUUUCAUUAUUGGUUGACUCUUUUGGUUUUGUUUCCGGUACUUUUACCUUUUCGAAACAUAAUUGAAUUUACAUUUAUU
.........((((...(((((((....................)))))))....((..(((.((((((.((((....)))).....)))))).)))..))...))))..... ( -14.85)
>DroYak_CAF1 14998 112 - 1
AUUACCCUUAUGUUCAUCAAUCACUCGGAACCUAUUUCAUUAUUGGUUGACUCUUUUGGCUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUUGAAUUUACAUUUAUU
...........((((((((((((....(((.....))).....))))))).............(((((.((((....)))).....))))).....)))))........... ( -14.30)
>consensus
AUUACCUUCAUGUUCAUCAAUCAUUCGGAACCUCUUUCAUUGCUGGUUGACUCUUUUGGUUUUGUUUCCGGUAUUUUUACCUUUUCGAAACUUAAUCGAAUUUACAUUUAUU
.........((((...(((((((....(((.....))).....)))))))....(((((((..(((((.((((....)))).....)))))..)))))))...))))..... (-15.62 = -15.78 +   0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,628,722 – 21,628,827
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -24.60
Consensus MFE -22.26
Energy contribution -21.98
Covariance contribution -0.28
Combinations/Pair 1.09
Mean z-score -1.40
Structure conservation index 0.90
SVM decision value 0.60
SVM RNA-class probability 0.795232
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21628722 105 + 23771897
GAAAAAAUUACAGAUACCACACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGGGUCGUGAGCGUGUCGAGAAUUUUUUGAUUACGUUUGACAAGGUUUGAA
..........(((((.((.((((..((.((.(((......))))).))..)))).))(((..(((((((((((((...)))))).))))))))))...))))).. ( -24.70)
>DroSec_CAF1 5180 105 + 1
GAAAAAAUUACAGAUACCACACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGGGUCGUGAGCGUGUCGAGAAUUUUUUGAUUACGUUUGACAAGGUUUGAA
..........(((((.((.((((..((.((.(((......))))).))..)))).))(((..(((((((((((((...)))))).))))))))))...))))).. ( -24.70)
>DroSim_CAF1 5218 105 + 1
GAAAAAAUUACAGAUACCACACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGGGUCGUGAGCGUGUCGAGAAUUUUUUGAUUACGUUUGACAAGGUUUGAA
..........(((((.((.((((..((.((.(((......))))).))..)))).))(((..(((((((((((((...)))))).))))))))))...))))).. ( -24.70)
>DroEre_CAF1 4330 105 + 1
GAAAAAAUUACAGAAACCACACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGAGUCGUGAGCGUGUCGAGAAUUUUUUGAUUAUGUUUGACAAGGUUUGAG
.............(((((.((((..((.((.(((......))))).))..))))...(((..(((((((((((((...)))))).))))))))))..)))))... ( -20.70)
>DroYak_CAF1 15110 105 + 1
GAAAAAAUUACAGAUACCGCACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGAGUCGUGAGCGUGUCGAGAAUUUUUUGAUUACGUUCGACAAGGUUUGAG
..........(((((..((((((..((.((.(((......))))).))..)))))).(((..(((((((((((((...)))))).))))))))))...))))).. ( -28.20)
>consensus
GAAAAAAUUACAGAUACCACACGAAUGGAUUAUGAAAUGACAUAUGCAAGUGUGCGGGUCGUGAGCGUGUCGAGAAUUUUUUGAUUACGUUUGACAAGGUUUGAA
..........(((((.((((((...((.((.(((......))))).)).))))).).(((..(((((((((((((...)))))).))))))))))...))))).. (-22.26 = -21.98 +  -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 13:09:56 2006