Locus 5320

Sequence ID 3L_DroMel_CAF1
Location 14,682,677 – 14,682,944
Length 267
Max. P 0.990995
window8407 window8408 window8409

overview

Window 7

Location 14,682,677 – 14,682,797
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.38
Mean single sequence MFE -32.86
Consensus MFE -28.42
Energy contribution -28.46
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.86
SVM decision value 2.24
SVM RNA-class probability 0.990995
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14682677 120 - 23771897
UGUGGAAAACGGUUCCGAUUCUGACUCGACGGCUGCAAAUUGUCAGCUCAUGAGUUGCAGCUUAGUUGGCUACAAAAAAAAAAAUGGCCAAAAGAGGCGCAAAAAGAGAACAGAGAAACA
..(((((.....))))).((((((((((..((((((.....).)))))..)))))(((.((((..(((((((............)))))))...))))))).........)))))..... ( -33.60)
>DroSec_CAF1 32473 114 - 1
UGUGGAAAACGGUUCCGAUUCUGACUCGACGGCUGCAAAUUGUCCGCUCAUGAGUUGCAGCUCAGUUGGCUA-----AAA-AAAUGGCCAAAAGAGGCGCAAAAAGAGAACAGAGAAACA
..(((((.....))))).(((((.(((((((((........).))).)).....((((..(((..(((((((-----...-...)))))))..)))..))))...)))..)))))..... ( -31.80)
>DroSim_CAF1 33633 115 - 1
UGUGGAAAACGGUUCCGAUUCUGACUCGACGGCUGCAAAUUGUCCGCUCAUGAGUUGCAGCUUAGUUGGCUA-----AAAAAAAUGGCCAAAAGAGGCGCAAAAAGAGAACAGAGAAACA
..(((((.....))))).(((((.(((((((((........).))).)).....((((.((((..(((((((-----.......)))))))...))))))))...)))..)))))..... ( -32.20)
>DroEre_CAF1 32714 115 - 1
UGUGGAAAACGGUUCCGAUUCUGGCUCGACGGCUGCAAAUUGUCCGCUCAUGAGUUGCAGCUUAGUUGGCUA-----AAAAAAAGGGCCAACAGAGGCGCAAAAAGGGAACAGAGAAACA
...........(((((.....((((.((((((((((((..((......))....))))))))..))))))))-----.......(.(((......))).)......)))))......... ( -33.70)
>DroYak_CAF1 33376 115 - 1
UGUGGAAAACGGUUCCGAUUCUGGCUCGACGGCUGCAAAUUGUCCGCUCAUGAGUUGCAGCUUAGUUGGCUA-----AAAAAAAGGGCCAACAGAGGCGCAAAAAGAGAACAGAGAAACA
..(((((.....))))).(((((.(((((((((........).))).)).....((((.((((.(((((((.-----........)))))))..))))))))...)))..)))))..... ( -33.00)
>consensus
UGUGGAAAACGGUUCCGAUUCUGACUCGACGGCUGCAAAUUGUCCGCUCAUGAGUUGCAGCUUAGUUGGCUA_____AAAAAAAUGGCCAAAAGAGGCGCAAAAAGAGAACAGAGAAACA
..(((((.....))))).(((((.(((....(((((((..((......))....)))))((((..((((((..............))))))...)))))).....)))..)))))..... (-28.42 = -28.46 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,682,797 – 14,682,904
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.58
Mean single sequence MFE -24.76
Consensus MFE -22.70
Energy contribution -22.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.92
SVM decision value 1.89
SVM RNA-class probability 0.981558
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14682797 107 - 23771897
UAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA----AGCAGAAGCGAGCUGAAACAAAAAAAUAUUUUUAAA
..(.((((.....))))).((((((((((.((((((((((...........))))))))))...))))((.----.((....))..))...............)))))).. ( -26.00)
>DroSec_CAF1 32587 107 - 1
UAGACCCUCUUAAAGGGCAUAGUAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA----AGCAGAAACGAGCUGAAACAAAAAAAUAUUUUUAAA
..(.((((.....))))).......((((.((((((((((...........))))))))))...))))...----(((........)))...................... ( -23.40)
>DroSim_CAF1 33748 111 - 1
UAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCAAGCAAGCAGAAACGAGCUGAAACAAAAAAAUAUUUUUAAA
..(.((((.....))))).((((((((((.((((((((((...........))))))))))...)))).......(((........)))..............)))))).. ( -24.30)
>DroEre_CAF1 32829 106 - 1
UAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA----AGCAGAAGCGAGCGGAAACAAA-AAAUAUUUUUAAA
..(.((((.....))))).((((((((((.((((((((((...........))))))))))...))))((.----.((....))..))(....)...-.....)))))).. ( -27.90)
>DroYak_CAF1 33491 106 - 1
UAGACCCUCUUAAAGGGCAUAUGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA----AGCAGAAAAGAACUGAAACAAA-AAAUAUUUUUAAA
..(.((((.....))))).......((((.((((((((((...........))))))))))...))))...----..(((.......))).......-............. ( -22.20)
>consensus
UAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA____AGCAGAAACGAGCUGAAACAAAAAAAUAUUUUUAAA
..(.((((.....))))).......((((.((((((((((...........))))))))))...))))((......))................................. (-22.70 = -22.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,682,833 – 14,682,944
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -28.01
Consensus MFE -25.70
Energy contribution -25.38
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -1.41
Structure conservation index 0.92
SVM decision value 1.11
SVM RNA-class probability 0.917409
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14682833 111 - 23771897
GAGCGUAAUUUUUUCGUCGUAAUCCAUUUGGAAAAACAAUUAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
..((..................(((..(((......)))...(.((((.....)))))...))).((((.((((((((((...........))))))))))...)))))). ( -27.80)
>DroSec_CAF1 32623 111 - 1
GAGCGUAACUUUUUCAUCGCAAUCCCUUUGGAAAAACAAUUAGACCCUCUUAAAGGGCAUAGUAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
..((.....(((((((............)))))))...((((..((((.....))))..))))..((((.((((((((((...........))))))))))...)))))). ( -27.60)
>DroSim_CAF1 33788 111 - 1
GAGCGUAACUUUUUCAUCGCAAUCCCUUUGGAAAAACAAUUAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
..(((............)))..(((..(((......)))...(.((((.....)))))...))).((((.((((((((((...........))))))))))...))))... ( -27.00)
>DroEre_CAF1 32864 111 - 1
AAGCGUAACUUUUUCAACAUAAUCCUUUUGGAAAAACAAUUAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
..((..................((((.(((......)))...(.((((.....)))))..)))).((((.((((((((((...........))))))))))...)))))). ( -27.80)
>DroYak_CAF1 33526 111 - 1
UAGCGCAACUUUUUCAACGUAAUCCUUUUGGGAAAACAAUUAGACCCUCUUAAAGGGCAUAUGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
....((...........((((..((((((((((..............))))))))))..))))..((((.((((((((((...........))))))))))...)))))). ( -29.84)
>consensus
GAGCGUAACUUUUUCAUCGUAAUCCCUUUGGAAAAACAAUUAGACCCUCUUAAAGGGCAUAGGAACUGCAACGAAUUCCAUUUACAGCUUUUGGGAUUUGUAGGGCAGGCA
..((.....(((((((............))))))).......(.((((.....))))).......((((.((((((((((...........))))))))))...)))))). (-25.70 = -25.38 +  -0.32)

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 11:47:13 2006