Locus 5345

Sequence ID X_DroMel_CAF1
Location 13,931,602 – 13,931,856
Length 254
Max. P 0.974476
window8666 window8667 window8668 window8669 window8670

overview

Window 6

Location 13,931,602 – 13,931,697
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.93
Mean single sequence MFE -29.34
Consensus MFE -26.34
Energy contribution -25.98
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.45
Structure conservation index 0.90
SVM decision value 0.31
SVM RNA-class probability 0.683611
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931602 95 + 22224390
AUAUUUGAAGCUAGUUGUGAACCUGAAUCUGGGGGCUGGGGCCAUGCAAUUAGUCUAAUUGCUAAGCAUGCCAGCCGGACUAUUUCCAUUUGCAU-------------------------
......((((.(((((.....(((......)))((((((.((...(((((((...)))))))...))...)))))).))))))))).........------------------------- ( -27.60)
>DroSec_CAF1 11601 95 + 1
AUAUUUGAAGCUAGUUGCGAACCUGAAUCUGGGGGCUGGGGCCAUGCAAUUAGUCUAAUUGCUAAGCAUGCCAGCCGGACUAUUUCCAUUUGCAU-------------------------
...............(((((((((......)))((((((.((...(((((((...)))))))...))...))))))(((.....))).)))))).------------------------- ( -29.40)
>DroSim_CAF1 15177 95 + 1
AUAUUUGAAGCUAGUUGCGAACCUGAAUCUGGGGGUUGGGGCCAUGCAAUUAGUAUAAUUGAUAAGCAUGCCAGCCGGAAUAUUUCCAUUUGCAU-------------------------
...............(((((((((......)))((((((...(((((.((((((...))))))..)))))))))))(((.....))).)))))).------------------------- ( -24.60)
>DroEre_CAF1 13215 97 + 1
ACAUUUGAUGCUAGUUGUGAACCUGAAUCUGGGGGCUGGGGCCAUGCAAUUAGUCUAAUUGCUAAGCAUGCCAGCCGGACUAUUUCCAUUUGCAUU-----------------------C
......(((((....((.((((((......)))((((((.((...(((((((...)))))))...))...)))))).......)))))...)))))-----------------------. ( -28.60)
>DroYak_CAF1 13750 120 + 1
AUAUUUGAAGCUAGUUGUGAACCUGAAUCUGGGGGCUGGGGCCAUGCAAUUAGUCUAAUUGCUAAGCAUGCCAGUCGGACUAUUUCCAUUUGCAUUCGGCCAAAAGCCCAGCCACCAUAC
.........(((.........((.......))(((((..((((((((((.(((((..(((((.......).))))..))))).......))))))..))))...))))))))........ ( -36.50)
>consensus
AUAUUUGAAGCUAGUUGUGAACCUGAAUCUGGGGGCUGGGGCCAUGCAAUUAGUCUAAUUGCUAAGCAUGCCAGCCGGACUAUUUCCAUUUGCAU_________________________
...............(((((((((......)))((((((.((...(((((((...)))))))...))...))))))(((.....))).)))))).......................... (-26.34 = -25.98 +  -0.36)

alignment

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secondary structure

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Window 7

Location 13,931,697 – 13,931,816
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.89
Mean single sequence MFE -26.10
Consensus MFE -21.56
Energy contribution -22.16
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.83
SVM decision value 0.10
SVM RNA-class probability 0.583654
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931697 119 + 22224390
-CCAUCCCCCAUCCAUUCGCCAACCGAAUCUGGCCAAGACAGAUCGAAGAGGCAGCAGGCACAAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
-.................(((...(((.((((.......)))))))....)))..............((((((..((((....)))).....((((........))))......)))))) ( -26.90)
>DroSec_CAF1 11696 114 + 1
----UCCCCCAUCCAUUCGCCAGCCGAAUCUGGCCAAGACAGAUCGAAGAGACAGCAGGC--AAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
----..............(((.(((((.((((.......)))))))........)).)))--.....((((((..((((....)))).....((((........))))......)))))) ( -27.20)
>DroSim_CAF1 15272 114 + 1
----UCCCCCGUCCAUUCGCCAGCCGAAUCUGGCCAAGACAGAUCGAAGAGGCAGCAGGC--AAACCGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
----......(((..((((((((......)))))...((....)))))..)))....((.--...))((((((..((((....)))).....((((........))))......)))))) ( -28.60)
>DroEre_CAF1 13312 117 + 1
CCCAUUCCCCAUCCAUUCCCCAACCGAAUCUGGCCAAGACAGAUCGAAGAGGCAGCAGGC--A-ACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
..................((....(((.((((.......)))))))....))...(((..--.-.)))(((((..((((....)))).....((((........))))......))))). ( -25.10)
>DroYak_CAF1 13870 118 + 1
CCCAUACCCCUUUCAUUCCCCAUCCAAAUCUGGCCAAGACAGAUCGAAGAGGCAGCAGGC--AAACUGGCGCUAAUCGUUCGAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
........(((......((.(.((...(((((.......))))).)).).))....))).--.....((((((..((((....)))).....((((........))))......)))))) ( -22.70)
>consensus
_CCAUCCCCCAUCCAUUCGCCAACCGAAUCUGGCCAAGACAGAUCGAAGAGGCAGCAGGC__AAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCC
..................(((...(((.((((.......)))))))..(......).))).......((((((..((((....)))).....((((........))))......)))))) (-21.56 = -22.16 +   0.60)

alignment

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secondary structure

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Window 8

Location 13,931,697 – 13,931,816
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.89
Mean single sequence MFE -41.66
Consensus MFE -35.06
Energy contribution -35.58
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.89
Structure conservation index 0.84
SVM decision value 1.62
SVM RNA-class probability 0.967914
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931697 119 - 22224390
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUUGUGCCUGCUGCCUCUUCGAUCUGUCUUGGCCAGAUUCGGUUGGCGAAUGGAUGGGGGAUGG-
((((((.(((((.((((((((...........)))))))).))))).))))))(((........))).(((((((.((((((((..(((......)))..).).)))))).))))).))- ( -42.30)
>DroSec_CAF1 11696 114 - 1
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUU--GCCUGCUGUCUCUUCGAUCUGUCUUGGCCAGAUUCGGCUGGCGAAUGGAUGGGGGA----
((((((.(((((.((((((((...........)))))))).))))).)))))).....--..((.((((((.(((((....))...(((((......)))))))).)))))).)).---- ( -42.90)
>DroSim_CAF1 15272 114 - 1
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCGGUUU--GCCUGCUGCCUCUUCGAUCUGUCUUGGCCAGAUUCGGCUGGCGAAUGGACGGGGGA----
((((((.(((((.((((((((...........)))))))).))))).))))))((...--.)).....((((.((.((.((((..((((......)))))))).)).)).))))..---- ( -42.80)
>DroEre_CAF1 13312 117 - 1
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGU-U--GCCUGCUGCCUCUUCGAUCUGUCUUGGCCAGAUUCGGUUGGGGAAUGGAUGGGGAAUGGG
((((((.(((((.((((((((...........)))))))).))))).))))))...-.--.((((...((((.((.((...(((..(((......)))..))).)).)).))))..)))) ( -43.40)
>DroYak_CAF1 13870 118 - 1
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUCGAACGAUUAGCGCCAGUUU--GCCUGCUGCCUCUUCGAUCUGUCUUGGCCAGAUUUGGAUGGGGAAUGAAAGGGGUAUGGG
((((((.(((((.(.((((((...........)))))).).))))).)))))).....--.((((.((((((((((.(((((((...........)))))))...)).)))))))))))) ( -36.90)
>consensus
GGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUU__GCCUGCUGCCUCUUCGAUCUGUCUUGGCCAGAUUCGGCUGGCGAAUGGAUGGGGGAUGG_
((((((.(((((.((((((((...........)))))))).))))).))))))(((........))).((((.((.((.((((..((((......)))))))).)).)).))))...... (-35.06 = -35.58 +   0.52)

alignment

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secondary structure

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Window 9

Location 13,931,736 – 13,931,856
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.20
Mean single sequence MFE -32.46
Consensus MFE -27.58
Energy contribution -27.98
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.85
SVM decision value 1.73
SVM RNA-class probability 0.974476
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931736 120 + 22224390
AGAUCGAAGAGGCAGCAGGCACAAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUUUAGUUCCAUUUUCAGAAUCCGAAAGGGGUCCAG
.(((((((((((.(((((((.......((((((..((((....)))).....((((........))))......))))))..))))...))))).))))).....((....))))))... ( -34.10)
>DroSec_CAF1 11732 118 + 1
AGAUCGAAGAGACAGCAGGC--AAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUUUAGUUUCAUUUUCAGAAUCCGAAAGGGGACCAG
.(.((...(((((...((((--.....((((((..((((....)))).....((((........))))......))))))..))))...)))))..........(((....))))).).. ( -31.80)
>DroSim_CAF1 15308 118 + 1
AGAUCGAAGAGGCAGCAGGC--AAACCGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUUUAGUUUCAUUUUCAGAAUCCGAAAGGGGACCAG
.((....((((((....((.--...))((((((..((((....)))).....((((........))))......))))))..))))))....))..........(((....)))...... ( -31.80)
>DroEre_CAF1 13352 117 + 1
AGAUCGAAGAGGCAGCAGGC--A-ACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUGUGGUUCCAUUUUCAGAAACCGAAAGAGGCCCAG
........(.(((.((((((--.-...((((((..((((....)))).....((((........))))......))))))..))))))((((.(.......).)))).......)))).. ( -34.40)
>DroYak_CAF1 13910 118 + 1
AGAUCGAAGAGGCAGCAGGC--AAACUGGCGCUAAUCGUUCGAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUUUAGUUCCAUUUUCAGAAACCGAAAGAGGACCAG
.......((((((...((..--...))((((((..((((....)))).....((((........))))......))))))..)))))).(.(((.(((((.......))))).))).).. ( -30.20)
>consensus
AGAUCGAAGAGGCAGCAGGC__AAACUGGCGCUAAUCGUUCAAACGAAAUCAGCAACAAUUCAUUUGCACAACAAGCGCCCAGCCUUUAGUUCCAUUUUCAGAAUCCGAAAGGGGACCAG
.....(((((((.(((((((.......((((((..((((....)))).....((((........))))......))))))..))))...))))).)))))....(((....)))...... (-27.58 = -27.98 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,931,736 – 13,931,856
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.20
Mean single sequence MFE -37.90
Consensus MFE -32.42
Energy contribution -32.94
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.78
Structure conservation index 0.86
SVM decision value 1.41
SVM RNA-class probability 0.951059
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13931736 120 - 22224390
CUGGACCCCUUUCGGAUUCUGAAAAUGGAACUAAAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUUGUGCCUGCUGCCUCUUCGAUCU
..((.((..((((((...))))))..))......((((..((((((.(((((.((((((((...........)))))))).))))).)))))).......))))....)).......... ( -35.00)
>DroSec_CAF1 11732 118 - 1
CUGGUCCCCUUUCGGAUUCUGAAAAUGAAACUAAAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUU--GCCUGCUGUCUCUUCGAUCU
..((((...((((((...))))))..((.((...((((..((((((.(((((.((((((((...........)))))))).))))).)))))).....--))))...)).))...)))). ( -38.10)
>DroSim_CAF1 15308 118 - 1
CUGGUCCCCUUUCGGAUUCUGAAAAUGAAACUAAAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCGGUUU--GCCUGCUGCCUCUUCGAUCU
..((((...((((((...))))))..........((((..((((((.(((((.((((((((...........)))))))).))))).))))))((...--.))....))))....)))). ( -36.40)
>DroEre_CAF1 13352 117 - 1
CUGGGCCUCUUUCGGUUUCUGAAAAUGGAACCACAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGU-U--GCCUGCUGCCUCUUCGAUCU
..((((.......((((((.......)))))).(((((..((((((.(((((.((((((((...........)))))))).))))).))))))...-.--)))))..))))......... ( -45.30)
>DroYak_CAF1 13910 118 - 1
CUGGUCCUCUUUCGGUUUCUGAAAAUGGAACUAAAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUCGAACGAUUAGCGCCAGUUU--GCCUGCUGCCUCUUCGAUCU
.((((((..((((((...))))))..)).)))).((((.((((((.......))....((((((.((((((..((((....)))))))))).))))))--))))...))))......... ( -34.70)
>consensus
CUGGUCCCCUUUCGGAUUCUGAAAAUGGAACUAAAGGCUGGGCGCUUGUUGUGCAAAUGAAUUGUUGCUGAUUUCGUUUGAACGAUUAGCGCCAGUUU__GCCUGCUGCCUCUUCGAUCU
.((((((..((((((...))))))..)).)))).((((..((((((.(((((.((((((((...........)))))))).))))).))))))(((........)))))))......... (-32.42 = -32.94 +   0.52)

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 11:45:40 2006