Locus 7627

Sequence ID 3R_DroMel_CAF1
Location 20,435,901 – 20,436,032
Length 131
Max. P 0.987662
window12310 window12311 window12312 window12313

overview

Window 0

Location 20,435,901 – 20,436,008
Length 107
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 84.10
Mean single sequence MFE -26.73
Consensus MFE -22.65
Energy contribution -22.77
Covariance contribution 0.13
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.85
SVM decision value 1.18
SVM RNA-class probability 0.927618
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20435901 107 + 27905053
ACUGGGUAUUCCCCGGACCGGGCAAAAUGCUAACCAUUUACCGCCCAAAACGACGCC----CCCUGGUUACACCCCCACUCCAAACAUUCCCCCCACUUCCGUGGUGGGCU
.(((((.....)))))...((((.(((((.....)))))...))))........(((----(..(((........)))...............((((....)))).)))). ( -28.70)
>DroSec_CAF1 18391 105 + 1
ACUGGGUAUUCCCCGGACCGGGCAAAAUGCUAACCAUUUACCGCCCAAAACGCCGCC----CCCUGGUUACAACCCCACUCCAAGCAU--CCCCCACUUCCAUGGUGGGCU
.(((((.....)))))...((((.(((((.....)))))...))))........(((----((((((.....................--.........))).)).)))). ( -27.61)
>DroSim_CAF1 18045 105 + 1
ACUGGGUAUUCCCCGGACCGGGCAAAAUGCUAACCAUUUACCGCCCAAAACGCCGCC----CCCUGGUUACAACCCCACUCCAGCCAC--CCCCCACUUCCAUGGUGGGCU
.(((((.....)))))...((((.(((((.....)))))...))))...........----..((((.............))))....--..((((((.....)))))).. ( -27.62)
>DroYak_CAF1 19086 108 + 1
CCUGGGUAUUCCCCGGACCGGGCAAAAUGCUAACCAUUUACCGCCCAAAACGGAACCCACACCCAAACCUCCACCCC-CUUCAACAGC--CUUCCCCCUUCUUGCUGGGCU
..(((((.....(((....((((.(((((.....)))))...))))....))).......)))))............-.......(((--((..(........)..))))) ( -23.00)
>consensus
ACUGGGUAUUCCCCGGACCGGGCAAAAUGCUAACCAUUUACCGCCCAAAACGCCGCC____CCCUGGUUACAACCCCACUCCAACCAC__CCCCCACUUCCAUGGUGGGCU
.(((((.....)))))...((((.(((((.....)))))...))))..............................................((((((.....)))))).. (-22.65 = -22.77 +   0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,435,901 – 20,436,008
Length 107
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 84.10
Mean single sequence MFE -41.38
Consensus MFE -25.29
Energy contribution -25.60
Covariance contribution 0.31
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.61
SVM decision value 0.35
SVM RNA-class probability 0.701507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20435901 107 - 27905053
AGCCCACCACGGAAGUGGGGGGAAUGUUUGGAGUGGGGGUGUAACCAGGG----GGCGUCGUUUUGGGCGGUAAAUGGUUAGCAUUUUGCCCGGUCCGGGGAAUACCCAGU
..(((.((((....)))))))........(((.((((((((((((((...----(.((((......)))).)...))))).)))))...)))).)))(((.....)))... ( -46.90)
>DroSec_CAF1 18391 105 - 1
AGCCCACCAUGGAAGUGGGGG--AUGCUUGGAGUGGGGUUGUAACCAGGG----GGCGGCGUUUUGGGCGGUAAAUGGUUAGCAUUUUGCCCGGUCCGGGGAAUACCCAGU
..(((.((((....)))))))--......(((.((((..((((((((...----.((.((.......)).))...))))).))).....)))).)))(((.....)))... ( -38.30)
>DroSim_CAF1 18045 105 - 1
AGCCCACCAUGGAAGUGGGGG--GUGGCUGGAGUGGGGUUGUAACCAGGG----GGCGGCGUUUUGGGCGGUAAAUGGUUAGCAUUUUGCCCGGUCCGGGGAAUACCCAGU
.((((.((((....)))).))--))((((((.(..((((..((((((...----.((.((.......)).))...))))))..))))..))))))).(((.....)))... ( -42.20)
>DroYak_CAF1 19086 108 - 1
AGCCCAGCAAGAAGGGGGAAG--GCUGUUGAAG-GGGGUGGAGGUUUGGGUGUGGGUUCCGUUUUGGGCGGUAAAUGGUUAGCAUUUUGCCCGGUCCGGGGAAUACCCAGG
.((((..(((..((.......--.)).)))...-.))))......((((((((...(((((..(((((((..(((((.....))))))))))))..))))).)))))))). ( -38.10)
>consensus
AGCCCACCAUGGAAGUGGGGG__AUGGUUGGAGUGGGGUUGUAACCAGGG____GGCGGCGUUUUGGGCGGUAAAUGGUUAGCAUUUUGCCCGGUCCGGGGAAUACCCAGU
.(((..((((....))))...............(((........))).......)))..((..(((((((..(((((.....))))))))))))..))(((....)))... (-25.29 = -25.60 +   0.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,435,941 – 20,436,032
Length 91
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -26.85
Consensus MFE -20.15
Energy contribution -21.14
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -2.41
Structure conservation index 0.75
SVM decision value 2.09
SVM RNA-class probability 0.987662
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20435941 91 + 27905053
CCGCCCAAAACGACGCC----CCCUGGUUACACCCCCACUCCAAACAUUCCCCCCACUUCCGUGGUGGGCU---GCUGUGUUGUGGGCUUGUCUAAUU
..((((...(((((((.----...(((........)))............(((((((....)))).)))..---...))))))))))).......... ( -26.10)
>DroSec_CAF1 18431 89 + 1
CCGCCCAAAACGCCGCC----CCCUGGUUACAACCCCACUCCAAGCAU--CCCCCACUUCCAUGGUGGGCU---GCUGUGUUGUGGGCUUGUCUAAUU
..(((((.(((((....----....(((....)))........((((.--((((((......))).))).)---)))))))).))))).......... ( -29.30)
>DroSim_CAF1 18085 89 + 1
CCGCCCAAAACGCCGCC----CCCUGGUUACAACCCCACUCCAGCCAC--CCCCCACUUCCAUGGUGGGCU---GCUGUGUUGUGGGCUUGUCUAAUU
..(((((.(((((.((.----..((((.............))))....--..((((((.....))))))..---)).))))).))))).......... ( -29.92)
>DroYak_CAF1 19126 95 + 1
CCGCCCAAAACGGAACCCACACCCAAACCUCCACCCC-CUUCAACAGC--CUUCCCCCUUCUUGCUGGGCUGCUGCUAUGUUGUGGGCUUGUCUAAUU
..(((((.((((((...............))).....-...((.((((--((..(........)..)))))).))....))).))))).......... ( -22.06)
>consensus
CCGCCCAAAACGCCGCC____CCCUGGUUACAACCCCACUCCAACCAC__CCCCCACUUCCAUGGUGGGCU___GCUGUGUUGUGGGCUUGUCUAAUU
..(((((.(((((.((........(((.............))).........((((((.....)))))).....)).))))).))))).......... (-20.15 = -21.14 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,435,941 – 20,436,032
Length 91
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -34.65
Consensus MFE -21.86
Energy contribution -22.17
Covariance contribution 0.31
Combinations/Pair 1.20
Mean z-score -2.24
Structure conservation index 0.63
SVM decision value 1.18
SVM RNA-class probability 0.926802
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20435941 91 - 27905053
AAUUAGACAAGCCCACAACACAGC---AGCCCACCACGGAAGUGGGGGGAAUGUUUGGAGUGGGGGUGUAACCAGGG----GGCGUCGUUUUGGGCGG
......(((..(((((..((.(((---(.(((.((((....)))))))...))))))..)))))..)))..((((((----.(...).)))))).... ( -35.10)
>DroSec_CAF1 18431 89 - 1
AAUUAGACAAGCCCACAACACAGC---AGCCCACCAUGGAAGUGGGGG--AUGCUUGGAGUGGGGUUGUAACCAGGG----GGCGGCGUUUUGGGCGG
......((((.(((((..((.(((---(.(((.((((....)))))))--.))))))..))))).))))..((((((----.(...).)))))).... ( -35.90)
>DroSim_CAF1 18085 89 - 1
AAUUAGACAAGCCCACAACACAGC---AGCCCACCAUGGAAGUGGGGG--GUGGCUGGAGUGGGGUUGUAACCAGGG----GGCGGCGUUUUGGGCGG
......((((.(((((....((((---.((((.((((....)))).))--)).))))..))))).))))..((((((----.(...).)))))).... ( -37.10)
>DroYak_CAF1 19126 95 - 1
AAUUAGACAAGCCCACAACAUAGCAGCAGCCCAGCAAGAAGGGGGAAG--GCUGUUGAAG-GGGGUGGAGGUUUGGGUGUGGGUUCCGUUUUGGGCGG
..........(((((.(((.(((((((..(((..(.....).)))...--)))))))...-.....((((.((.......)).))))))).))))).. ( -30.50)
>consensus
AAUUAGACAAGCCCACAACACAGC___AGCCCACCAUGGAAGUGGGGG__AUGGUUGGAGUGGGGUUGUAACCAGGG____GGCGGCGUUUUGGGCGG
..........(((((.(((...((.....(((.((((....))))...............(((........)))))).....))...))).))))).. (-21.86 = -22.17 +   0.31)

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 12:50:37 2006