Locus 5741

Sequence ID 3L_DroMel_CAF1
Location 15,612,193 – 15,612,379
Length 186
Max. P 0.975880
window9103 window9104 window9105

overview

Window 3

Location 15,612,193 – 15,612,306
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -29.02
Consensus MFE -20.62
Energy contribution -20.26
Covariance contribution -0.36
Combinations/Pair 1.36
Mean z-score -1.63
Structure conservation index 0.71
SVM decision value 0.17
SVM RNA-class probability 0.618849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15612193 113 + 23771897
GAAU-------UUUAUAUAUAUCCAUUAAGCUCUGUGCUUAACCGAAUCGUAGAGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGG
....-------.......(((((((((((((.....)))))).........(((((...(((((....))))))))))))))))).((.((((((((.........))))))))....)) ( -29.70)
>DroSec_CAF1 35264 113 + 1
GAAU-------UUUAUACAAAUCCUUUAGGCUCUGUGCUUAAGCGAAUCGGAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGG
....-------..........((.(((((((.....))))))).))(((.((((((...(((((....))))))))))).)))...((.((((((((.........))))))))....)) ( -30.30)
>DroSim_CAF1 35301 120 + 1
GAAUAUUUAUAUUUAUACACAUCCAUUAGGCUCUGUGCUUAAGCGAAUCGCAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUAG
....................(((((....((((((((.((.....)).))))))))...(((((....))))).....)))))......((((((((.........))))))))...... ( -29.60)
>DroEre_CAF1 35380 105 + 1
--------------AUAUUUAUUUAUUGGGCU-UGUGCCUAGCAGAAUCGCAGGGUAUUUGGCGCACUUGAUAAAUCUUGGAUAUGCCUGUGGCUGCUCGCUUAUUGUAGCCAUUUAUGG
--------------..(((((((...((.(((-.((((((.((......)).))))))..))).))...)))))))..........((.((((((((.........))))))))....)) ( -31.30)
>DroYak_CAF1 37764 113 + 1
GAAU-------UUUAUAUUUAUUCAUUCAGCUUUGUGCUAAACUGAAUCGCAGGGUAUAUCGCACACUUGCUGGAUUCUGGAUAUCCCUGCGGCUGCUCGUUUAUUGUACCCAUUUAUGG
....-------.........(((((((.(((.....))).)).))))).((((((.((((((((....))).(....)..)))))))))))((.(((.........))).))........ ( -24.20)
>consensus
GAAU_______UUUAUAUAUAUCCAUUAGGCUCUGUGCUUAACCGAAUCGCAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGG
.....................((..((((((.....))))))..))...(((((((((.(((((....)))))........))).))))))((((((.........))))))........ (-20.62 = -20.26 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,612,226 – 15,612,344
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.65
Mean single sequence MFE -34.88
Consensus MFE -24.02
Energy contribution -24.86
Covariance contribution 0.84
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.570808
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15612226 118 + 23771897
AACCGAAUCGUAGAGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA--UACUCGUGAAAUAUGAGUUUAGUUAUCCACAGGCAA
..((.......(((((...(((((....))))))))))((((((((((.((((((((.........))))))))....))))--.(((((((...))))))).....))))))..))... ( -35.10)
>DroSec_CAF1 35297 118 + 1
AAGCGAAUCGGAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA--UACUCGUGAAAUAUGAGUUUAGUUAUCCACCGGCAA
.......((((.(((((..(((((....))))).(((.((..((((((.((((((((.........))))))))....))))--))..)).))).............))))).))))... ( -39.30)
>DroSim_CAF1 35341 120 + 1
AAGCGAAUCGCAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUAGGAUAUACUCGUGAAAUAUGAGUUUAGUUAUCCACCGGCAA
..((.....((((((....(((((....)))))(((....)))..))))))((((((.........)))))).......(((((.(((((((...))))))).....)))))....)).. ( -34.50)
>DroEre_CAF1 35405 118 + 1
AGCAGAAUCGCAGGGUAUUUGGCGCACUUGAUAAAUCUUGGAUAUGCCUGUGGCUGCUCGCUUAUUGUAGCCAUUUAUGGGA--AACUCGUGAAAUAUGACCUUAGUUAUCCACAGGCAA
......(((.(((((((((.((....)).)))..))))))))).(((((((((((((.........)))))).(((((((..--..).))))))..(((((....)))))..))))))). ( -33.30)
>DroYak_CAF1 37797 118 + 1
AACUGAAUCGCAGGGUAUAUCGCACACUUGCUGGAUUCUGGAUAUCCCUGCGGCUGCUCGUUUAUUGUACCCAUUUAUGGGA--UACUCGUGAAAUAUGACUUUAGUUAUCCACAGGCAA
.......((((((((.((((((((....))).(....)..))))))))))))).((((........(((((((....)))).--)))..(((....(((((....))))).))).)))). ( -32.20)
>consensus
AACCGAAUCGCAGGGUAUAUUGCACACUUGCAAAUUCUUGGAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA__UACUCGUGAAAUAUGAGUUUAGUUAUCCACAGGCAA
.........((.(((....(((((....)))))...)))(((((((((.((((((((.........))))))))....))))...(((((((...))))))).....)))))....)).. (-24.02 = -24.86 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,612,266 – 15,612,379
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.35
Mean single sequence MFE -36.86
Consensus MFE -29.50
Energy contribution -29.94
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.37
Structure conservation index 0.80
SVM decision value 1.76
SVM RNA-class probability 0.975880
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15612266 113 + 23771897
GAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA--UACUCGUGAAAUAUGAGUUUAGUUAUCCACAGGCAAGGGAGA---ACUUGGCCAGUCUCC--CCAGGCCAAUCAAU
((((((((.((((((((.........))))))))....))))--)(((((((...))))))).............(((..((((((---.((.....)))))))--)...))).)))... ( -40.00)
>DroSec_CAF1 35337 118 + 1
GAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA--UACUCGUGAAAUAUGAGUUUAGUUAUCCACCGGCAAGGGAGAACAACUUGGCCAGUCUCCCCCCAGGCCAAUCAAU
((((((((.((((((((.........))))))))....))))--)(((((((...))))))).............(((..((((((.(.....).....)))))).....))).)))... ( -37.40)
>DroSim_CAF1 35381 120 + 1
GAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUAGGAUAUACUCGUGAAAUAUGAGUUUAGUUAUCCACCGGCAAGGGAGAACAACUUGGCCAGUCUCCCCCCAGGCCAAUCAAU
(((.(((((((((((((.........)))))))).....(((((.(((((((...))))))).....))))).......)))))........(((((............))))))))... ( -37.60)
>DroEre_CAF1 35445 113 + 1
GAUAUGCCUGUGGCUGCUCGCUUAUUGUAGCCAUUUAUGGGA--AACUCGUGAAAUAUGACCUUAGUUAUCCACAGGCAAGGGAGA---ACUUGGCCAGUCUCC--CCAGGCCAAUCAAU
(((.(((((((((((((.........)))))).(((((((..--..).))))))..(((((....)))))..))))))).((((((---.((.....)))))))--).......)))... ( -38.20)
>DroYak_CAF1 37837 113 + 1
GAUAUCCCUGCGGCUGCUCGUUUAUUGUACCCAUUUAUGGGA--UACUCGUGAAAUAUGACUUUAGUUAUCCACAGGCAAGGGAGA---ACUUGGCCAGUCUCC--CCAGGCCAAUCAAU
(((.(((((...(((...........(((((((....)))).--)))..(((....(((((....))))).))).))).)))))..---...(((((.......--...))))))))... ( -31.10)
>consensus
GAUAUCCCUGUGGCUGCUCGUUUAUUGUAGCCAUUUAUGGGA__UACUCGUGAAAUAUGAGUUUAGUUAUCCACAGGCAAGGGAGA___ACUUGGCCAGUCUCC__CCAGGCCAAUCAAU
(((.(((((((((((((.........)))))).((((((((.....))))))))......................)).)))))........(((((............))))))))... (-29.50 = -29.94 +   0.44)

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 11:58:28 2006