Locus 3428

Sequence ID X_DroMel_CAF1
Location 9,156,281 – 9,156,458
Length 177
Max. P 0.979872
window5609 window5610 window5611 window5612

overview

Window 9

Location 9,156,281 – 9,156,388
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.92
Mean single sequence MFE -34.97
Consensus MFE -25.95
Energy contribution -27.07
Covariance contribution 1.12
Combinations/Pair 1.08
Mean z-score -2.34
Structure conservation index 0.74
SVM decision value 1.52
SVM RNA-class probability 0.961019
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9156281 107 + 22224390
GGCGCAGAAAAAAG---GGGG-------UAGGAGGUGGGUUUUU---CGAUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAU
.............(---((((-------(((...(.((((((..---........(((....)))(((((((.....))))))))))))))..((((....)))).....)))))))).. ( -36.30)
>DroSec_CAF1 8949 105 + 1
GGCGCAGAACAAAG---GGGG--------AGCAGGUGGGUU-UU---CGGUUUAGGCCGAAGGGCAUUUUUCAAAUUGAAAAGAGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAU
............((---(((.--------((...(.(((((-((---(.......(((....)))..(((((.....))))))))))))))..((((....)))).....)).))))).. ( -33.90)
>DroSim_CAF1 9977 105 + 1
GGCGCAGAAAAAAG---GGGG--------AGGAGGUGGGUU-UU---CGGUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAU
..............---....--------.((((((((...-((---((((....))))))(((((((((((.....)))))))..))))...((((....)))).....)))))))).. ( -36.40)
>DroYak_CAF1 9465 120 + 1
GGUGCGGAAAAGGGAUUGGGAAACGGGAUUGGGAUUGGGAUUGGGAAUGGAAUUGGCCGAAGGGCAUUUUUCAAUUUGAAAAGUGAGCCCCAAAACCGCAAGGUGCCUAACUACCUCUAU
..........((((.((.(....).))....((.(((((.(((((..........(((....)))(((((((.....)))))))....))))).(((....))).)))))))..)))).. ( -33.30)
>consensus
GGCGCAGAAAAAAG___GGGG________AGGAGGUGGGUU_UU___CGGUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAU
..............................((((((((.........(((......)))..(((((((((((.....)))))))..))))...((((....)))).....)))))))).. (-25.95 = -27.07 +   1.12)

alignment

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secondary structure

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Window 0

Location 9,156,311 – 9,156,421
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.43
Mean single sequence MFE -29.40
Consensus MFE -24.38
Energy contribution -24.98
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.83
SVM decision value 1.85
SVM RNA-class probability 0.979872
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9156311 110 + 22224390
UUUU---CGAUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCC
((((---((((.((((((....)))......)))))))))))(((((((....((((....))))....................)))))))......(((.(-------....).))). ( -28.05)
>DroSec_CAF1 8978 109 + 1
U-UU---CGGUUUAGGCCGAAGGGCAUUUUUCAAAUUGAAAAGAGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCC
.-((---((((....))))))((((.((((((.....))))))...))))...((((....))))........(((.(((((((((.......))))))))).-------...))).... ( -28.20)
>DroSim_CAF1 10006 109 + 1
U-UU---CGGUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAUUAGAUGC-------AAAAGGGUCC
.-((---((((....))))))((((..(((((.....)))))(((((((....((((....))))....................)))))))...........-------......)))) ( -29.65)
>DroEre_CAF1 9298 107 + 1
----CAAUCC--CAAGCCGAAGGGCAUUUUUCAAUUUGAAAAGUUAGCCCCAAAACCGCAAGGUUCCUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCC
----....((--(.((((((.(((((((((((.....)))))))..))))...((((....))))..................))))))..(((.....))).-------....)))... ( -28.00)
>DroYak_CAF1 9505 120 + 1
UUGGGAAUGGAAUUGGCCGAAGGGCAUUUUUCAAUUUGAAAAGUGAGCCCCAAAACCGCAAGGUGCCUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGCAAAAUGCAAAAGGGUCC
(((((..........(((....)))(((((((.....)))))))....))))).(((....)))((((.......((((((...((.....)).))))))(((.....)))...)))).. ( -33.10)
>consensus
U_UU___CGGUAUUGGCCGAAGGGCAUUUUUCAAAUUGAAAAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC_______AAAAGGGUCC
...............(((....)))(((((((.....)))))))..((((...((((....))))..........((((((...((.....)).))))))..............)))).. (-24.38 = -24.98 +   0.60)

alignment

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secondary structure

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Window 1

Location 9,156,311 – 9,156,421
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.43
Mean single sequence MFE -29.65
Consensus MFE -24.20
Energy contribution -24.44
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.82
SVM decision value 0.49
SVM RNA-class probability 0.756518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9156311 110 - 22224390
GGACCCUUUU-------GCAUCUAUUAUGUGAGCCAAUAAAUAGAGGUAGUUAAGAACCUUGCGGUUUUGGGGCUCACUUUUCAAUUUGAAAAAUGCCCUUCGGCCAAUAUCG---AAAA
((.((.....-------((((.......(((((((...((((.(((((........)))))...))))...)))))))(((((.....))))))))).....)))).......---.... ( -29.90)
>DroSec_CAF1 8978 109 - 1
GGACCCUUUU-------GCAUCUAUUAUGUGAGCCAAUAAAUAGAGGUAGUUAAGAACCUUGCGGUUUUGGGGCUCUCUUUUCAAUUUGAAAAAUGCCCUUCGGCCUAAACCG---AA-A
((........-------(((((((((.(((......)))))))))(((........))).)))((((..(((((....(((((.....)))))..)))))..))))....)).---..-. ( -26.90)
>DroSim_CAF1 10006 109 - 1
GGACCCUUUU-------GCAUCUAAUAUGUGAGCCAAUAAAUAGAGGUAGUUAAGAACCUUGCGGUUUUGGGGCUCACUUUUCAAUUUGAAAAAUGCCCUUCGGCCAAUACCG---AA-A
..........-------((((.......(((((((...((((.(((((........)))))...))))...)))))))(((((.....)))))))))..(((((......)))---))-. ( -30.40)
>DroEre_CAF1 9298 107 - 1
GGACCCUUUU-------GCAUCUAUUAUGUGAGCCAAUAAAUAGAGGUAGUUAGGAACCUUGCGGUUUUGGGGCUAACUUUUCAAAUUGAAAAAUGCCCUUCGGCUUG--GGAUUG----
....(((.((-------((.((((((.(((......))))))))).))))..)))..((..((.(....(((((....(((((.....)))))..))))).).))..)--).....---- ( -28.50)
>DroYak_CAF1 9505 120 - 1
GGACCCUUUUGCAUUUUGCAUCUAUUAUGUGAGCCAAUAAAUAGAGGUAGUUAGGCACCUUGCGGUUUUGGGGCUCACUUUUCAAAUUGAAAAAUGCCCUUCGGCCAAUUCCAUUCCCAA
((.((.....(((((((.((........(((((((...((((.(((((.(.....))))))...))))...))))))).........)).))))))).....)))).............. ( -32.53)
>consensus
GGACCCUUUU_______GCAUCUAUUAUGUGAGCCAAUAAAUAGAGGUAGUUAAGAACCUUGCGGUUUUGGGGCUCACUUUUCAAUUUGAAAAAUGCCCUUCGGCCAAUACCG___AA_A
((.((.......................(((((((...((((.(((((........)))))...))))...)))))))(((((.....))))).........)))).............. (-24.20 = -24.44 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,156,348 – 9,156,458
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.37
Mean single sequence MFE -27.37
Consensus MFE -21.48
Energy contribution -22.48
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.78
SVM decision value 0.11
SVM RNA-class probability 0.586032
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9156348 110 + 22224390
AAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCCACUG--UCCU-CGCAAGGGCUCCUCCAUUCGGUGCACUGA
..(((((((....((((....))))....................)))))))....(((.(((-------(..(((((((..((--(...-.))).)))).)))((....))))))))). ( -29.95)
>DroSec_CAF1 9014 111 + 1
AAGAGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCCACUG--UCCACCUCACGAGCUCCUCCAUUCGGUGCACUGC
.((.(..(((...((((....))))..........((((((...((.....)).))))))...-------....)))..).))(--(.((((....(((...))).....)))).))... ( -23.10)
>DroSim_CAF1 10042 111 + 1
AAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAUUAGAUGC-------AAAAGGGUCCACUG--UCCACCUCACGAGCUCCUCCAUUCGGUGCACUGC
.((((..(((...((((....)))).....................((((........)).))-------....)))..))))(--(.((((....(((...))).....)))).))... ( -25.30)
>DroEre_CAF1 9332 111 + 1
AAGUUAGCCCCAAAACCGCAAGGUUCCUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC-------AAAAGGGUCCACUGAGUCCU-UCCACGGGCUCCUCCAUU-GGUGCACUGA
.((((((......((((....)))).))))))...((((((...((.....)).))))))(((-------(....((......((((((.-.....))))))..))...-..)))).... ( -27.90)
>DroYak_CAF1 9545 116 + 1
AAGUGAGCCCCAAAACCGCAAGGUGCCUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGCAAAAUGCAAAAGGGUCCACUG--UCCU-UCCACGGGCUCCUCCAUU-GAUGCACUGA
..(((((((.....(((....))).....................)))))))....(((.((((.((((....(((((((....--....-.....)))).))).))))-..))))))). ( -30.59)
>consensus
AAGUGAGCCCCAAAACCGCAAGGUUCUUAACUACCUCUAUUUAUUGGCUCACAUAAUAGAUGC_______AAAAGGGUCCACUG__UCCU_CCCACGGGCUCCUCCAUUCGGUGCACUGA
.((((.((((...((((....))))..........((((((...((.....)).))))))..............)))).))))...............((.((.......)).))..... (-21.48 = -22.48 +   1.00)

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 10:59:11 2006