Locus 150

Sequence ID 2L_DroMel_CAF1
Location 436,535 – 436,711
Length 176
Max. P 0.563881
window234 window235 window236

overview

Window 4

Location 436,535 – 436,654
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -32.02
Consensus MFE -21.54
Energy contribution -23.58
Covariance contribution 2.04
Combinations/Pair 1.19
Mean z-score -1.59
Structure conservation index 0.67
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 436535 119 + 22407834
GGGCUUGGAAUUGAAAAGAAGUGAUUGCAAGUAGUUUUCUGCGAAGUAGUCUAUAGUGAAGGUUUAUCGUC-UAAUAACUUUAUGACAGAGGUAUUACUUCCGCAGAAAUCUCGCCAAUC
(((((((.(((((........))))).)))))((.(((((((((((((((((...((((((..(((.....-)))...))))))......)).))))))).)))))))).))..)).... ( -29.90)
>DroSec_CAF1 13876 120 + 1
GGGUUCGAAAUUGAAGCGAAGUGAUUGCAGGGAGUUUUCUGCGAAGUAGUCUUUAGUGAAGAAGUAACAUCUUAAUAACUUUAUGACAGAGCUAUUACUUCCGCAGAAAUCUCGCCAAUC
.(.((((....)))).).....(((((..(.(((.(((((((((((((((((((.((.(.(((((............))))).).))))))..))))))).)))))))).))).)))))) ( -32.50)
>DroSim_CAF1 12988 120 + 1
GGGUUCGAAAUUGAAGCGAAGUGAUUGCAGGGAGUUUUCUGCGAAGUAGUCUUCAGUGAAGUCGUAUCGUCUUAAUAACUUUAUGACAGAGCUAUUACUUCCGCAGAAAUCUCGCCAAUC
.(.((((....)))).).....(((((..(.(((.(((((((((((((((....(((...((((((..((.......))..))))))...)))))))))).)))))))).))).)))))) ( -34.90)
>DroEre_CAF1 14001 120 + 1
CAGCUUGGAAUCCAAGAGAAAUGAUUGCAAGGAAGUUUCUGCAAAUUAGACUACAAUGGAGUUGUAUCGUCUUAACAACUUCAUGACCGAGAUGCUACUUCCGCAGAAAUCUCGCCAAUC
...((((.((((..........)))).))))((..(((((((.((.(((.((...((((((((((.........)))))))))).....))...))).))..)))))))..))....... ( -29.70)
>DroYak_CAF1 13555 120 + 1
GAGUUUGGAAUUCAAGAGAAAUGAUUGCUAGGAUUUAUGUGCGAAGUAGUGUUUAAUGAAGUUUUAUCGUCUCAGUAACUUCAUGGCCGAGCUAUUACUUCCGCAGAUAUCUCGGCCAUC
((((.....)))).........(((.((..((((...((((.((((((((((((.((((((((....(......).))))))))....)))).))))))))))))...))))..)).))) ( -33.10)
>consensus
GGGUUUGGAAUUGAAGAGAAGUGAUUGCAAGGAGUUUUCUGCGAAGUAGUCUUUAGUGAAGUUGUAUCGUCUUAAUAACUUUAUGACAGAGCUAUUACUUCCGCAGAAAUCUCGCCAAUC
......................(((((....(((.((((((((((((((((((..((((((((((.........))))))))))....)))..))))))).)))))))).)))..))))) (-21.54 = -23.58 +   2.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 436,535 – 436,654
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -27.54
Consensus MFE -18.80
Energy contribution -19.20
Covariance contribution 0.40
Combinations/Pair 1.21
Mean z-score -1.59
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.527377
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 436535 119 - 22407834
GAUUGGCGAGAUUUCUGCGGAAGUAAUACCUCUGUCAUAAAGUUAUUA-GACGAUAAACCUUCACUAUAGACUACUUCGCAGAAAACUACUUGCAAUCACUUCUUUUCAAUUCCAAGCCC
(((((.((((.((((((((.(((((........(((.(((.....)))-)))((.......)).........)))))))))))))....)))))))))...................... ( -24.80)
>DroSec_CAF1 13876 120 - 1
GAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAAAGUUAUUAAGAUGUUACUUCUUCACUAAAGACUACUUCGCAGAAAACUCCCUGCAAUCACUUCGCUUCAAUUUCGAACCC
(((((..(((.(((((((((((((((((..(((...(((....)))..)))))))))))).((......))......)))))))).)))....)))))...................... ( -26.90)
>DroSim_CAF1 12988 120 - 1
GAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAAAGUUAUUAAGACGAUACGACUUCACUGAAGACUACUUCGCAGAAAACUCCCUGCAAUCACUUCGCUUCAAUUUCGAACCC
(((((..(((.(((((((.(((((..((....((((.(((.....))).)))).))..)))))...((((....))))))))))).)))....)))))...................... ( -27.70)
>DroEre_CAF1 14001 120 - 1
GAUUGGCGAGAUUUCUGCGGAAGUAGCAUCUCGGUCAUGAAGUUGUUAAGACGAUACAACUCCAUUGUAGUCUAAUUUGCAGAAACUUCCUUGCAAUCAUUUCUCUUGGAUUCCAAGCUG
(((((.((((((..((((....)))).)))))).....((((((((..((((..(((((.....))))))))).....)))...)))))....)))))......(((((...)))))... ( -31.20)
>DroYak_CAF1 13555 120 - 1
GAUGGCCGAGAUAUCUGCGGAAGUAAUAGCUCGGCCAUGAAGUUACUGAGACGAUAAAACUUCAUUAAACACUACUUCGCACAUAAAUCCUAGCAAUCAUUUCUCUUGAAUUCCAAACUC
.(((((((((.(((.(((....)))))).)))))))))(((.(((..((((.((.......))...............((............)).......)))).))).)))....... ( -27.10)
>consensus
GAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAAAGUUAUUAAGACGAUACAACUUCACUAAAGACUACUUCGCAGAAAACUCCUUGCAAUCACUUCUCUUCAAUUCCAAACCC
(((((..(((.((((((((((..((((((((.........)))))))).((.(......).))............)))))))))).)))....)))))...................... (-18.80 = -19.20 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 436,614 – 436,711
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.20
Mean single sequence MFE -28.88
Consensus MFE -11.50
Energy contribution -12.58
Covariance contribution 1.08
Combinations/Pair 1.18
Mean z-score -1.78
Structure conservation index 0.40
SVM decision value 0.06
SVM RNA-class probability 0.563881
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 436614 97 - 22407834
ACGAACGCGGCUUUAAUGCAAAAAUU------GCCAUUAAUGG-----------------CAAGAAGGAGAACGCUGUCUGAUUGGCGAGAUUUCUGCGGAAGUAAUACCUCUGUCAUAA
......(((.......))).....((------((((....)))-----------------)))((.((((..(((((......))))).......(((....)))....)))).)).... ( -23.30)
>DroSec_CAF1 13956 97 - 1
ACGACGGCGGCUUUAAUGCAAAAACU------ACCAUUAAUGG-----------------CAACAAGGAGAACGCUGUCUGAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAA
..(((((((((......)).....((------.((.....((.-----------------...)).))))..)))))))....(((((((.((..(((....)))..))))).))))... ( -26.70)
>DroSim_CAF1 13068 103 - 1
ACGACGACGGCUUUAAUGCAAAAACCGACGAAACCAUUAAUGG-----------------CAACAAGGAGAACGCUGUCUGAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAA
..(((((((((.((((((................))))))((.-----------------...))........))))))........(((.((..(((....)))..))))).))).... ( -22.49)
>DroEre_CAF1 14081 117 - 1
ACGAUCGUGACUGUAAUGCAA-AAU-GA-UUUACCAUUAAUCGGAACAAGCUUUCUCGUACAACAAACAGAACGCUUUUUGAUUGGCGAGAUUUCUGCGGAAGUAGCAUCUCGGUCAUGA
....((((((((.....((..-(((-(.-.....))))((((((((..(((.((((.((.......)))))).))))))))))).))(((((..((((....)))).))))))))))))) ( -34.80)
>DroYak_CAF1 13635 118 - 1
ACGAUCGUGGCUUUAUUGCAAAAAU-GA-UAUACCAUUAAUCGGAAUAAGCUUCCUUGUUCAACAAAUAGAACGCUUUUUGAUGGCCGAGAUAUCUGCGGAAGUAAUAGCUCGGCCAUGA
.((((.((((..(((((.....)))-))-....))))..))))(((((((....)))))))..((((.((....)).))))(((((((((.(((.(((....)))))).))))))))).. ( -37.10)
>consensus
ACGACCGCGGCUUUAAUGCAAAAAU_GA____ACCAUUAAUGG_________________CAACAAGGAGAACGCUGUCUGAUUGGCGAGAUUUCUGCGGAAGUAAUAGCUCUGUCAUAA
..(((((.((((............................................................(((((......))))).......(((....)))..))))))))).... (-11.50 = -12.58 +   1.08)

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 09:27:31 2006