Locus 5348

Sequence ID 3R_DroMel_CAF1
Location 14,023,549 – 14,023,668
Length 119
Max. P 0.999933
window8716 window8717 window8718 window8719

overview

Window 6

Location 14,023,549 – 14,023,647
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -32.90
Consensus MFE -29.74
Energy contribution -30.66
Covariance contribution 0.92
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.90
SVM decision value 2.91
SVM RNA-class probability 0.997697
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14023549 98 + 27905053
UCCCUUCUCCCUCGUUCCACUCAGGUGAGUGAGGAGCAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCU
...((((((.((((..((.....)))))).))))))...((((((.((..((.((((....)))).))..))))))))....((((((....)))))) ( -32.30)
>DroSec_CAF1 8647 98 + 1
UCCCUCCUCCCUCGUUCCACUCAGGUGAGUGGGGAACAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCU
((((..((((((.(.......)))).)))..))))....((((((.((..((.((((....)))).))..))))))))....((((((....)))))) ( -35.10)
>DroSim_CAF1 8553 98 + 1
UCCCUCCUCCCUCGUUCCACUCAGGUGAGUGAGGAACAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCU
..((((((((((.(.......)))).))).)))).....((((((.((..((.((((....)))).))..))))))))....((((((....)))))) ( -32.90)
>DroEre_CAF1 8628 98 + 1
UCCCUCCUACCUCGUUCCGCACAGGUGAGUGAGGAGUAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUUCUACCU
..((((((((((.((.....)))))).)).)))).((..((((((.((..((.((((....)))).))..))))))))..))((((((....)))))) ( -33.40)
>DroYak_CAF1 8581 97 + 1
UUCCCCCUACCUCGUUCCGCACAGGUGAGUGAG-UGUAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUUCACAUUGUACACAGGUAGGUUGCUACCU
......(((((((((((.((....)))))))))-.))))((((((.((..((.((((....)))).))..))))))))....((((((....)))))) ( -30.80)
>consensus
UCCCUCCUCCCUCGUUCCACUCAGGUGAGUGAGGAGCAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCU
...((((((.((((..((.....)))))).))))))...((((((.((..((.((((....)))).))..))))))))....((((((....)))))) (-29.74 = -30.66 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,023,549 – 14,023,647
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.67
Mean single sequence MFE -31.90
Consensus MFE -25.64
Energy contribution -26.80
Covariance contribution 1.16
Combinations/Pair 1.03
Mean z-score -1.52
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.646460
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14023549 98 - 27905053
AGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGCUCCUCACUCACCUGAGUGGAACGAGGGAGAAGGGA
((((((....))))))....(((.(((((.((..(((....)))..)).))).)).)))((.((((((((((....)))))......))))).))... ( -30.60)
>DroSec_CAF1 8647 98 - 1
AGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGUUCCCCACUCACCUGAGUGGAACGAGGGAGGAGGGA
((((((....))))))....(((.(((((.((..(((....)))..)).))).)).)))((.((((((((((....)))))......))))).))... ( -32.30)
>DroSim_CAF1 8553 98 - 1
AGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGUUCCUCACUCACCUGAGUGGAACGAGGGAGGAGGGA
((((((....))))))....(((.(((((.((..(((....)))..)).))).)).)))...((((((.(((.(((..(.....).)))))))))))) ( -32.10)
>DroEre_CAF1 8628 98 - 1
AGGUAGAAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUACUCCUCACUCACCUGUGCGGAACGAGGUAGGAGGGA
((((((....))))))(((.(((.(((((.((..(((....)))..)).))).)).))).)))(((((.((.((((((.....)).))))))))))). ( -34.60)
>DroYak_CAF1 8581 97 - 1
AGGUAGCAACCUACCUGUGUACAAUGUGAACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUACA-CUCACUCACCUGUGCGGAACGAGGUAGGGGGAA
......(..((((((((((((....((((.((..(((....)))....))..))))....))))-).(((......))).......)))))))..).. ( -29.90)
>consensus
AGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGCUCCUCACUCACCUGAGUGGAACGAGGGAGGAGGGA
((((((....))))))....(((.(((((.((..(((....)))..)).))).)).)))...((((((.(((.((.....))...))).))))))... (-25.64 = -26.80 +   1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,023,571 – 14,023,668
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 95.05
Mean single sequence MFE -33.08
Consensus MFE -29.84
Energy contribution -30.84
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.90
SVM decision value 2.06
SVM RNA-class probability 0.986872
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14023571 97 + 27905053
AGGUGAGUGAGGAGCAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCUAAAAGCCUAAAGGCCAGCGGG
......((.(((((((........)))))))(((((...(((((.((((.....))))..((((((....))))))..)))))...))))).))... ( -36.90)
>DroSec_CAF1 8669 97 + 1
AGGUGAGUGGGGAACAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCUAAAAGCCUAAAGGCCAGCAGG
....(((((....((.....))..)))))(((((((...(((((.((((.....))))..((((((....))))))..)))))...))))))).... ( -32.70)
>DroSim_CAF1 8575 97 + 1
AGGUGAGUGAGGAACAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCUAAAAGCCUAAAGGCCAGCGGG
.(((..(.((((...(((((....)).)))...)))).)(((((.((((.....))))..((((((....))))))..))))).....)))...... ( -32.30)
>DroEre_CAF1 8650 97 + 1
AGGUGAGUGAGGAGUAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUUCUACCUAAAUGCCUAAAGGCCAGCGGG
......((.(((((((........)))))))(((((...(((...((((.....))))..((((((....))))))....)))...))))).))... ( -32.40)
>DroYak_CAF1 8603 96 + 1
AGGUGAGUGAG-UGUAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUUCACAUUGUACACAGGUAGGUUGCUACCUAACAGCCUUAAGGCCAGCGGG
.(.((.((..(-(((..((((((.((..((.((((....)))).))..))))))))))))((((((....)))))).)).(((....))))).)... ( -31.10)
>consensus
AGGUGAGUGAGGAGCAGACAGUGAUGCUCUUGGCCUCUCGGCUUAGUACACAUUGUACACAGGUAGGUUGCUACCUAAAAGCCUAAAGGCCAGCGGG
......((.(((((((........)))))))(((((...(((((.((((.....))))..((((((....))))))..)))))...))))).))... (-29.84 = -30.84 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,023,571 – 14,023,668
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 95.05
Mean single sequence MFE -32.80
Consensus MFE -29.74
Energy contribution -30.54
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -3.23
Structure conservation index 0.91
SVM decision value 4.65
SVM RNA-class probability 0.999933
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14023571 97 - 27905053
CCCGCUGGCCUUUAGGCUUUUAGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGCUCCUCACUCACCU
.....((((((((.(((((.(((((((....))))))).((((.....)))).))))).)))))))).(((((........)))))........... ( -36.50)
>DroSec_CAF1 8669 97 - 1
CCUGCUGGCCUUUAGGCUUUUAGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGUUCCCCACUCACCU
.....((((((((.(((((.(((((((....))))))).((((.....)))).))))).)))))))).(((((........)))))........... ( -34.10)
>DroSim_CAF1 8575 97 - 1
CCCGCUGGCCUUUAGGCUUUUAGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGUUCCUCACUCACCU
.....((((((((.(((((.(((((((....))))))).((((.....)))).))))).)))))))).(((((........)))))........... ( -34.10)
>DroEre_CAF1 8650 97 - 1
CCCGCUGGCCUUUAGGCAUUUAGGUAGAAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUACUCCUCACUCACCU
...((((((((((.(((...(((((((....))))))).((((.....))))...))).)))))))...)))......................... ( -32.00)
>DroYak_CAF1 8603 96 - 1
CCCGCUGGCCUUAAGGCUGUUAGGUAGCAACCUACCUGUGUACAAUGUGAACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUACA-CUCACUCACCU
...(((((((((..((((..(((((((....)))))))........(....)..))))..))))))...))).............-........... ( -27.30)
>consensus
CCCGCUGGCCUUUAGGCUUUUAGGUAGCAACCUACCUGUGUACAAUGUGUACUAAGCCGAGAGGCCAAGAGCAUCACUGUCUGCUCCUCACUCACCU
...((((((((((.(((((.(((((((....))))))).((((.....)))).))))).)))))))...)))......................... (-29.74 = -30.54 +   0.80)

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 11:52:36 2006