Locus 6479

Sequence ID X_DroMel_CAF1
Location 16,258,078 – 16,258,265
Length 187
Max. P 0.994577
window10578 window10579 window10580 window10581

overview

Window 8

Location 16,258,078 – 16,258,185
Length 107
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 86.99
Mean single sequence MFE -32.50
Consensus MFE -25.49
Energy contribution -25.93
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.78
SVM decision value 0.53
SVM RNA-class probability 0.771068
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258078 107 + 22224390
-----UUUUGGGUUUCCAAUGUUUCCACUGCCAAGUCACGAUGCAGUGGGAGUGGAAGAGAAUGGGUGUAGGAGAAAGAGGAGACGGAGGAGUAGAAUUGGAGCUC--CAUUCU
-----...(((..(((((((.((((((((.(((.((......))..))).)))))))).....................(....)...........)))))))..)--)).... ( -28.80)
>DroSec_CAF1 6405 100 + 1
-----UUUUGGGUUUCCAAUGUUUCCACUGCCAAGUCACGAUGCAGUGGAAGUGGAAGAGAAUGGGUGUAGG---------AGACGGAGGAGUAGAAUUGGAGCUCCCCAUUCU
-----.......((((((...((((((((((...........))))))))))))))))(((((((.....(.---------...)...(((((.........)))))))))))) ( -34.80)
>DroSim_CAF1 6303 109 + 1
-----UUUUGGGUUUCCAAUGUUUCCACUGCCAAGUCACGAUGCAGUGGGAGUGGAAGAGAAUGGGUGUAGGAGAAAGAGGAGACGGAGGAGUAGAAUUGGAGCUCCCCAUUCU
-----.......((((((...((((((((((...........))))))))))))))))(((((((..............(....)...(((((.........)))))))))))) ( -34.30)
>DroEre_CAF1 6492 103 + 1
CCGCUUUUUGGGUUUCCAAUGUUUCCACUGCCAAGUCACGAUGCAGUGGGAAUGGAAGAGAAUGGGUAU---------AGGAGGAGGAGGAGCAGAAGUGGAGCUC--CAUUCU
((.(((((((..((((((...((((((((((...........))))))))))))))))..........)---------)))))).)).(((((.........))))--)..... ( -32.10)
>consensus
_____UUUUGGGUUUCCAAUGUUUCCACUGCCAAGUCACGAUGCAGUGGGAGUGGAAGAGAAUGGGUGUAGG______AGGAGACGGAGGAGUAGAAUUGGAGCUC__CAUUCU
............((((((...((((((((((...........))))))))))))))))((((((((.......................((((.........)))))))))))) (-25.49 = -25.93 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,258,078 – 16,258,185
Length 107
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 86.99
Mean single sequence MFE -24.08
Consensus MFE -18.49
Energy contribution -19.30
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.77
SVM decision value 1.51
SVM RNA-class probability 0.959756
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258078 107 - 22224390
AGAAUG--GAGCUCCAAUUCUACUCCUCCGUCUCCUCUUUCUCCUACACCCAUUCUCUUCCACUCCCACUGCAUCGUGACUUGGCAGUGGAAACAUUGGAAACCCAAAA-----
((((((--(........................................))))))).(((((((.(((...(.....)...))).)))))))...((((....))))..----- ( -20.10)
>DroSec_CAF1 6405 100 - 1
AGAAUGGGGAGCUCCAAUUCUACUCCUCCGUCU---------CCUACACCCAUUCUCUUCCACUUCCACUGCAUCGUGACUUGGCAGUGGAAACAUUGGAAACCCAAAA-----
(((((((((((...........))))...((..---------...))..))))))).(((((.(((((((((...........)))))))))....)))))........----- ( -28.30)
>DroSim_CAF1 6303 109 - 1
AGAAUGGGGAGCUCCAAUUCUACUCCUCCGUCUCCUCUUUCUCCUACACCCAUUCUCUUCCACUCCCACUGCAUCGUGACUUGGCAGUGGAAACAUUGGAAACCCAAAA-----
(((((((((((...........))))...(......)............))))))).(((((((.(((...(.....)...))).)))))))...((((....))))..----- ( -24.70)
>DroEre_CAF1 6492 103 - 1
AGAAUG--GAGCUCCACUUCUGCUCCUCCUCCUCCU---------AUACCCAUUCUCUUCCAUUCCCACUGCAUCGUGACUUGGCAGUGGAAACAUUGGAAACCCAAAAAGCGG
.....(--((((.........)))))..........---------............(((((...(((((((...........)))))))......)))))............. ( -23.20)
>consensus
AGAAUG__GAGCUCCAAUUCUACUCCUCCGUCUCCU______CCUACACCCAUUCUCUUCCACUCCCACUGCAUCGUGACUUGGCAGUGGAAACAUUGGAAACCCAAAA_____
(((((((((((...........))).......................)))))))).(((((((.(((...(.....)...))).)))))))...((((....))))....... (-18.49 = -19.30 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,258,147 – 16,258,265
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.52
Mean single sequence MFE -33.70
Consensus MFE -25.74
Energy contribution -27.80
Covariance contribution 2.06
Combinations/Pair 1.09
Mean z-score -3.79
Structure conservation index 0.76
SVM decision value 1.79
SVM RNA-class probability 0.977493
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258147 118 + 22224390
AAAGAGGAGACGGAGGAGUAGAAUUGGAGCUC--CAUUCUGGCUGAAAUCCAAUCACGACCACAAUCUUUAGCUCAUAAUCAAACUUGAACUCUACACUUUUGCUACUCCUCCUUCUUCG
.....(((((.((((((((((.....(((((.--.(((.(((((((.......))).).))).)))....)))))....(((....)))..............)))))))))).))))). ( -35.60)
>DroSec_CAF1 6472 113 + 1
-------AGACGGAGGAGUAGAAUUGGAGCUCCCCAUUCUGGCUGAAAUCCAAUCACGACCACAAUCUUUAGCUCAUAAUCAAACUUGAACUCUACACUUUUGCUACUCCUCCUCCUUCG
-------.((.((((((((((.....(((((....(((.(((((((.......))).).))).)))....)))))....(((....)))..............))))))))))))..... ( -29.90)
>DroSim_CAF1 6372 117 + 1
AAAGAGGAGACGGAGGAGUAGAAUUGGAGCUCCCCAUUCUGGCUGAAAUCCAAUCACGACCACAAUCUUUAGCUCAUAAUCAAACUUGAACUCUACACUUGA---AUUCCACCACCAUUG
.....((((...(((..(((((....(((((....(((.(((((((.......))).).))).)))....)))))....(((....)))..))))).)))..---.)))).......... ( -21.50)
>DroEre_CAF1 6561 114 + 1
----AGGAGGAGGAGGAGCAGAAGUGGAGCUC--CAUUCUGGCUGAAAUCCAAUCACGACCACAAUCUUUAGCUCAUAAUCAAACUUGAACUCUACACUUUUGCUACUCCUCCUCCAUCC
----.((((((((((.(((((((((((((((.--.(((.(((((((.......))).).))).)))....)))))....(((....)))......)))))))))).)))))))))).... ( -47.80)
>consensus
____AGGAGACGGAGGAGUAGAAUUGGAGCUC__CAUUCUGGCUGAAAUCCAAUCACGACCACAAUCUUUAGCUCAUAAUCAAACUUGAACUCUACACUUUUGCUACUCCUCCUCCAUCG
.....(((((.((((((((((.....(((((....(((.(((((((.......))).).))).)))....)))))....(((....)))..............)))))))))).))))). (-25.74 = -27.80 +   2.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,258,147 – 16,258,265
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.52
Mean single sequence MFE -40.62
Consensus MFE -34.51
Energy contribution -35.33
Covariance contribution 0.81
Combinations/Pair 1.11
Mean z-score -3.32
Structure conservation index 0.85
SVM decision value 2.49
SVM RNA-class probability 0.994577
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258147 118 - 22224390
CGAAGAAGGAGGAGUAGCAAAAGUGUAGAGUUCAAGUUUGAUUAUGAGCUAAAGAUUGUGGUCGUGAUUGGAUUUCAGCCAGAAUG--GAGCUCCAAUUCUACUCCUCCGUCUCCUCUUU
.(.(((.((((((((((....(((...(((((((((((..(((((((.(..........).)))))))..)))))((.......))--))))))..))))))))))))).))).)..... ( -38.90)
>DroSec_CAF1 6472 113 - 1
CGAAGGAGGAGGAGUAGCAAAAGUGUAGAGUUCAAGUUUGAUUAUGAGCUAAAGAUUGUGGUCGUGAUUGGAUUUCAGCCAGAAUGGGGAGCUCCAAUUCUACUCCUCCGUCU-------
...((..((((((((((....(((...(((((((((((..(((((((.(..........).)))))))..)))))...((.....)).))))))..)))))))))))))..))------- ( -40.60)
>DroSim_CAF1 6372 117 - 1
CAAUGGUGGUGGAAU---UCAAGUGUAGAGUUCAAGUUUGAUUAUGAGCUAAAGAUUGUGGUCGUGAUUGGAUUUCAGCCAGAAUGGGGAGCUCCAAUUCUACUCCUCCGUCUCCUCUUU
..((((.((((((((---(........(((((((((((..(((((((.(..........).)))))))..)))))...((.....)).)))))).)))))))))...))))......... ( -30.10)
>DroEre_CAF1 6561 114 - 1
GGAUGGAGGAGGAGUAGCAAAAGUGUAGAGUUCAAGUUUGAUUAUGAGCUAAAGAUUGUGGUCGUGAUUGGAUUUCAGCCAGAAUG--GAGCUCCACUUCUGCUCCUCCUCCUCCU----
(((.(((((((((((((...(((((..(((((((((((..(((((((.(..........).)))))))..)))))((.......))--))))))))))))))))))))))))))).---- ( -52.90)
>consensus
CGAAGGAGGAGGAGUAGCAAAAGUGUAGAGUUCAAGUUUGAUUAUGAGCUAAAGAUUGUGGUCGUGAUUGGAUUUCAGCCAGAAUG__GAGCUCCAAUUCUACUCCUCCGUCUCCU____
....(((((((((((((......((..(((((((((((..(((((((.(..........).)))))))..)))))((.......))..))))))))...)))))))))))))........ (-34.51 = -35.33 +   0.81)

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 12:14:50 2006