Locus 7385

Sequence ID 3L_DroMel_CAF1
Location 19,830,873 – 19,831,000
Length 127
Max. P 0.999956
window11995 window11996 window11997 window11998

overview

Window 5

Location 19,830,873 – 19,830,971
Length 98
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 79.28
Mean single sequence MFE -21.92
Consensus MFE -11.81
Energy contribution -13.65
Covariance contribution 1.84
Combinations/Pair 1.14
Mean z-score -1.90
Structure conservation index 0.54
SVM decision value 0.15
SVM RNA-class probability 0.607042
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19830873 98 + 23771897
CCGCUCUCUUUAUCGCUGCAGCGAUAAAGUUCCAACAA----AACAGAAAGAAA--AACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUU
.......(((((((((....))))))))).........----............--((((((.((((((((...((....)).)).))))))......)))))) ( -26.20)
>DroVir_CAF1 15304 89 + 1
UUUCUCGGUCGCUCGGCACGCAGAAAACCUUUCACUGCCCCGCGCACACCCAAAAAAACA---------------CAACAGCCAACCAGGCACAAUCAGCUGUG
.....((((.((.(((...((((...........)))).))).))...............---------------.....(((.....))).......)))).. ( -17.00)
>DroSec_CAF1 14551 98 + 1
CCGCUCUCUUUAUCGCUGCAGCGAAAAAGUUCCAACAA----AACAGAAAGAAA--AACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUU
.......((((.((((....)))).)))).........----............--((((((.((((((((...((....)).)).))))))......)))))) ( -22.10)
>DroSim_CAF1 17794 98 + 1
CCGCUCUCUUUAUCGCUGCAGCGAAAAAGUUCCAACAA----AACAGAAAGAAA--AACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUU
.......((((.((((....)))).)))).........----............--((((((.((((((((...((....)).)).))))))......)))))) ( -22.10)
>DroEre_CAF1 14511 95 + 1
CCGCUCUCUUUAUCGCUGCAGCGAAAAAGUUUCAACAA----AACAGAAAGAAA--AACAGCACGACUGCAA---CAACCGUGUGCCAGUCGCAAUCAGCUGUU
......(((((.((((....))))....((((.....)----)))..)))))..--((((((.((((((..(---((....)))..))))))......)))))) ( -22.30)
>DroYak_CAF1 14423 95 + 1
CCGCUCUCUUUAUCGCUGCAGCGAAGAAGUUCCAACAA----AACAGAAAUAAA--AACAGCACGACUGCAA---CAACCGUGUGCCAGUCGCAAUCAGCUGUU
.......((((.((((....)))).)))).........----............--((((((.((((((..(---((....)))..))))))......)))))) ( -21.80)
>consensus
CCGCUCUCUUUAUCGCUGCAGCGAAAAAGUUCCAACAA____AACAGAAAGAAA__AACAGCACGACUGCAA___CAACCGUGUGCCAGUCGCAAUCAGCUGUU
.......((((.((((....)))).))))...........................((((((.((((((((............)).))))))......)))))) (-11.81 = -13.65 +   1.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,830,873 – 19,830,971
Length 98
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 79.28
Mean single sequence MFE -32.70
Consensus MFE -18.46
Energy contribution -20.43
Covariance contribution 1.97
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.56
SVM decision value 0.95
SVM RNA-class probability 0.887362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19830873 98 - 23771897
AACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUU--UUUCUUUCUGUU----UUGUUGGAACUUUAUCGCUGCAGCGAUAAAGAGAGCGG
((((((((((((((((.((((......)))))))))))))).))))))--.......(((((----((.......(((((((((....)))))))))))))))) ( -36.41)
>DroVir_CAF1 15304 89 - 1
CACAGCUGAUUGUGCCUGGUUGGCUGUUG---------------UGUUUUUUUGGGUGUGCGCGGGGCAGUGAAAGGUUUUCUGCGUGCCGAGCGACCGAGAAA
.(((((..(((......)))..)))))..---------------...((((((((...(((.(((.((.(((((.....))).)))).))).))).)))))))) ( -29.40)
>DroSec_CAF1 14551 98 - 1
AACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUU--UUUCUUUCUGUU----UUGUUGGAACUUUUUCGCUGCAGCGAUAAAGAGAGCGG
((((((((((((((((.((((......)))))))))))))).))))))--...((((((...----((((((.(.(......).).))))))...))))))... ( -33.50)
>DroSim_CAF1 17794 98 - 1
AACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUU--UUUCUUUCUGUU----UUGUUGGAACUUUUUCGCUGCAGCGAUAAAGAGAGCGG
((((((((((((((((.((((......)))))))))))))).))))))--...((((((...----((((((.(.(......).).))))))...))))))... ( -33.50)
>DroEre_CAF1 14511 95 - 1
AACAGCUGAUUGCGACUGGCACACGGUUG---UUGCAGUCGUGCUGUU--UUUCUUUCUGUU----UUGUUGAAACUUUUUCGCUGCAGCGAUAAAGAGAGCGG
((((((((((((((((.(((.....))))---))))))))).))))))--...((((((...----((((((...(......)...))))))...))))))... ( -31.60)
>DroYak_CAF1 14423 95 - 1
AACAGCUGAUUGCGACUGGCACACGGUUG---UUGCAGUCGUGCUGUU--UUUAUUUCUGUU----UUGUUGGAACUUCUUCGCUGCAGCGAUAAAGAGAGCGG
.((.((((...(((((((.....))))))---)..)))).))(((.((--((((((.((((.----.((..((.....)).))..)))).)))))))).))).. ( -31.80)
>consensus
AACAGCUGAUUGCGACUGGCACACGGUUG___UUGCAGUCGUGCUGUU__UUUCUUUCUGUU____UUGUUGGAACUUUUUCGCUGCAGCGAUAAAGAGAGCGG
((((((((((((((((((.....)))))......))))))).))))))...........................((((.((((....)))).))))....... (-18.46 = -20.43 +   1.97)

alignment

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secondary structure

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Window 7

Location 19,830,904 – 19,831,000
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 93.21
Mean single sequence MFE -23.70
Consensus MFE -18.30
Energy contribution -18.78
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -2.42
Structure conservation index 0.77
SVM decision value 1.27
SVM RNA-class probability 0.938491
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19830904 96 + 23771897
CCAACAAAACAGAAAGAAAAACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUUUUGCCCGCUCACUCGCUCUGCUCUCUUGC
.........((((....((((((((.((((((((...((....)).)).))))))......))))))))....((......))))))......... ( -21.60)
>DroSec_CAF1 14582 96 + 1
CCAACAAAACAGAAAGAAAAACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUUUUGCGCGCUCACUCGCUCUGCUCUCUCGC
.........((((..(.((((((((.((((((((...((....)).)).))))))......)))))))).)(((......)))))))......... ( -23.40)
>DroSim_CAF1 17825 96 + 1
CCAACAAAACAGAAAGAAAAACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUUUUGCGCGCUCACUCGCUCUGCUCUCUCGC
.........((((..(.((((((((.((((((((...((....)).)).))))))......)))))))).)(((......)))))))......... ( -23.40)
>DroEre_CAF1 14542 92 + 1
UCAACAAAACAGAAAGAAAAACAGCACGACUGCAA---CAACCGUGUGCCAGUCGCAAUCAGCUGUU-UGCGCGCUCACUCGCUCCGCUCUUUCGC
...........((((((.(((((((.((((((..(---((....)))..))))))......))))))-)(((.((......))..))))))))).. ( -26.70)
>DroYak_CAF1 14454 93 + 1
CCAACAAAACAGAAAUAAAAACAGCACGACUGCAA---CAACCGUGUGCCAGUCGCAAUCAGCUGUUUUAAACGCUCACUCGCUCUGUUCUUUUGC
.(((.(.((((((....((((((((.((((((..(---((....)))..))))))......))))))))....((......)))))))).).))). ( -23.40)
>consensus
CCAACAAAACAGAAAGAAAAACAGCACGACUGCAACAACAACCGUGUGCCAGUCGCAAUCAGCUGUUUUGCGCGCUCACUCGCUCUGCUCUCUCGC
.........((((..(.((((((((.((((((((...((....)).)).))))))......)))))))).)..((......))))))......... (-18.30 = -18.78 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,830,904 – 19,831,000
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 93.21
Mean single sequence MFE -38.74
Consensus MFE -34.76
Energy contribution -34.48
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -3.80
Structure conservation index 0.90
SVM decision value 4.85
SVM RNA-class probability 0.999956
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19830904 96 - 23771897
GCAAGAGAGCAGAGCGAGUGAGCGGGCAAAACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUUUUUCUUUCUGUUUUGUUGG
.(((.((((((((((......))(((.((((((((((((((((((.((((......)))))))))))))).)))))))).))))))))))).))). ( -40.40)
>DroSec_CAF1 14582 96 - 1
GCGAGAGAGCAGAGCGAGUGAGCGCGCAAAACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUUUUUCUUUCUGUUUUGUUGG
.(((.(((((((((((.(....).)))((((((((((((((((((.((((......)))))))))))))).))))))))....)))))))).))). ( -40.90)
>DroSim_CAF1 17825 96 - 1
GCGAGAGAGCAGAGCGAGUGAGCGCGCAAAACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUUUUUCUUUCUGUUUUGUUGG
.(((.(((((((((((.(....).)))((((((((((((((((((.((((......)))))))))))))).))))))))....)))))))).))). ( -40.90)
>DroEre_CAF1 14542 92 - 1
GCGAAAGAGCGGAGCGAGUGAGCGCGCA-AACAGCUGAUUGCGACUGGCACACGGUUG---UUGCAGUCGUGCUGUUUUUCUUUCUGUUUUGUUGA
.(((.(((((((((((.(....).)))(-((((((((((((((((.(((.....))))---))))))))).))))))).....)))))))).))). ( -35.90)
>DroYak_CAF1 14454 93 - 1
GCAAAAGAACAGAGCGAGUGAGCGUUUAAAACAGCUGAUUGCGACUGGCACACGGUUG---UUGCAGUCGUGCUGUUUUUAUUUCUGUUUUGUUGG
.(((.((((((((((......))....((((((((((((((((((.(((.....))))---))))))))).))))))))....)))))))).))). ( -35.60)
>consensus
GCGAGAGAGCAGAGCGAGUGAGCGCGCAAAACAGCUGAUUGCGACUGGCACACGGUUGUUGUUGCAGUCGUGCUGUUUUUCUUUCUGUUUUGUUGG
.(((.((((((((((......))..(.((((((((((((((((((.(((.....)))...)))))))))).)))))))).)..)))))))).))). (-34.76 = -34.48 +  -0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:39 2006