Locus 3464

Sequence ID 2L_DroMel_CAF1
Location 10,076,167 – 10,076,282
Length 115
Max. P 0.860440
window5474 window5475 window5476

overview

Window 4

Location 10,076,167 – 10,076,270
Length 103
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 80.62
Mean single sequence MFE -38.42
Consensus MFE -24.52
Energy contribution -24.47
Covariance contribution -0.05
Combinations/Pair 1.30
Mean z-score -1.56
Structure conservation index 0.64
SVM decision value 0.14
SVM RNA-class probability 0.603722
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10076167 103 + 22407834
-----UGACUGCUCC------CGCUGGUCGAGGUUGCCAAUUGGGAGGCCGCGAUGGUCUCCCGAUUCAACGCCGCCGACUGCGUUAGCUGCUGCAGCUUUUUAAUUUGCUGAA
-----.....(((..------(((.(((((.(((....((((((((((((.....))))))))))))....)))..))))))))..))).....((((..........)))).. ( -43.10)
>DroGri_CAF1 2972 112 + 1
GC--UUGGCUGCCACUGCUGCUGCCUGUCGAUGUGGCCAAUUGCGAAGCCGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGCUGCAACUUUUUAAUUUGCUGUA
((--((....((((...((((.(((((....(((((.((((((((....)))))))).).))))...))).)).))))..)).))...)))).((((.........)))).... ( -34.80)
>DroWil_CAF1 9490 106 + 1
GC--CUGACUGUUAC------CGCCCGUCGAUGUGGCCAAUUGUGAGGCCGCAAUUGUCUCGCGAUUCAAUGCCGCUGAUUGCGUUAAAAGUUGCAACUUUUUAAUUUGCUGAA
((--..((((.(((.------(((..((((..(((((.(((((((((((.......)))))))))))....))))))))).))).))).))))))................... ( -30.10)
>DroMoj_CAF1 4648 112 + 1
GU--CUGGCUGCCGCCGCCGCUGCCUGUCGAUGUGGCCAAUUGUGAGGCAGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGUUGCAACUUUUUAAUUUGCUGCA
..--...((((..((((((((...........))))).....(((((((((...)))))))))))).))))((.((((((((....((((((....)))))))))))))).)). ( -39.70)
>DroAna_CAF1 3066 108 + 1
GCUUCUGGCUACUGC------CGCUGGUGGAUGUGGCCAAUUGGGAGGCCGCUAUGGUCUCGCGGUUGAGGGCCGCCGAUUGCGUUAGCAGCUGCAGCUUUUUAAUUUGCUGUU
(((...(((....))------)(((..((.(.(((((((((((.((((((.....)))))).)))))...))))))....).))..)))))).(((((..........))))). ( -43.40)
>DroPer_CAF1 2969 103 + 1
-----UGGCUGCUGC------CGCUUGUCGAUGUGGCCAAUUGUGAGGCCGCAAUUGUCUCGCGGUUCAGCGCCGCUGAUUGCGUUAACAGCUGCAGUUUUUUAAUUUGCUGAA
-----.(((.(((((------(((..(.((((((((((........)))))).)))).)..))))..)))))))((.....)).....((((...((((....)))).)))).. ( -39.40)
>consensus
GC__CUGGCUGCUGC______CGCCUGUCGAUGUGGCCAAUUGUGAGGCCGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGCUGCAACUUUUUAAUUUGCUGAA
.........(((.((......(((..(((...(((((.(((((((((((.......)))))))))))....))))).))).)))......)).))).................. (-24.52 = -24.47 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,076,190 – 10,076,282
Length 92
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -28.12
Consensus MFE -19.41
Energy contribution -18.97
Covariance contribution -0.44
Combinations/Pair 1.26
Mean z-score -1.67
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.860440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10076190 92 + 22407834
UGCCAAUUGGGAGGCCGCGAUGGUCUCCCGAUUCAACGCCGCCGACUGCGUUAGCUGCUGCAGCUUUUUAAUUUGCUGAAAGGA---UAAAUAA-------A
..((((((((((((((.....))))))))))))....((.((..((...))..)).))..((((..........))))...)).---.......-------. ( -29.70)
>DroVir_CAF1 2899 88 + 1
GGCCAAUUGCGAGGCCGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGUUGCAACUUUUUAAUUUGCUGUAAAAA---UU----GA-------
(((((((((((((((.......)))))))))))..).)))((((((((....((((((....))))))))))))))........---..----..------- ( -27.00)
>DroGri_CAF1 3004 88 + 1
GGCCAAUUGCGAAGCCGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGCUGCAACUUUUUAAUUUGCUGUAAAAA---UC----AA-------
(((((((((((....))))))))....((......)))))((((((((....(((((......)))))))))))))........---..----..------- ( -24.60)
>DroWil_CAF1 9516 95 + 1
GGCCAAUUGUGAGGCCGCAAUUGUCUCGCGAUUCAAUGCCGCUGAUUGCGUUAAAAGUUGCAACUUUUUAAUUUGCUGAAAGGAAGUUAAGAAA-------A
((((........))))((((((....((((((.((.......)))))))).....))))))...((((((((((.((....)))))))))))).-------. ( -28.20)
>DroAna_CAF1 3094 98 + 1
GGCCAAUUGGGAGGCCGCUAUGGUCUCGCGGUUGAGGGCCGCCGAUUGCGUUAGCAGCUGCAGCUUUUUAAUUUGCUGUUGGAA---GAAAUGA-AUCAGAA
(((((((((.((((((.....)))))).)))))...))))...((((.((((.......(((((..........))))).....---..)))))-))).... ( -31.94)
>DroPer_CAF1 2992 88 + 1
GGCCAAUUGUGAGGCCGCAAUUGUCUCGCGGUUCAGCGCCGCUGAUUGCGUUAACAGCUGCAGUUUUUUAAUUUGCUGAAAGGA---AAAG-----------
(((.(((((.(((((.(((.((((..((((((.((((...))))))))))...)))).))).))))).))))).))).......---....----------- ( -27.30)
>consensus
GGCCAAUUGCGAGGCCGCAAUUGUCUCGCGGUUCAGCGCCGCAGAUUGCGUUAAAAGCUGCAACUUUUUAAUUUGCUGAAAGAA___UAA___A________
(((.(((((((((((.......)))))))))))....))).....(((((........)))))....................................... (-19.41 = -18.97 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,076,190 – 10,076,282
Length 92
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 78.78
Mean single sequence MFE -23.27
Consensus MFE -15.10
Energy contribution -15.43
Covariance contribution 0.33
Combinations/Pair 1.24
Mean z-score -1.43
Structure conservation index 0.65
SVM decision value 0.27
SVM RNA-class probability 0.663572
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10076190 92 - 22407834
U-------UUAUUUA---UCCUUUCAGCAAAUUAAAAAGCUGCAGCAGCUAACGCAGUCGGCGGCGUUGAAUCGGGAGACCAUCGCGGCCUCCCAAUUGGCA
.-------.......---........((...((((...(((((.((.((....)).))..))))).))))...(((((.((.....)).))))).....)). ( -27.40)
>DroVir_CAF1 2899 88 - 1
-------UC----AA---UUUUUACAGCAAAUUAAAAAGUUGCAACUUUUAACGCAAUCUGCGGCGCUGAACCGCGAGACAAUUGCGGCCUCGCAAUUGGCC
-------..----..---......((((......((((((....))))))..(((.....)))..))))...(....).((((((((....))))))))... ( -23.40)
>DroGri_CAF1 3004 88 - 1
-------UU----GA---UUUUUACAGCAAAUUAAAAAGUUGCAGCUUUUAACGCAAUCUGCGGCGCUGAACCGCGAGACAAUUGCGGCUUCGCAAUUGGCC
-------..----..---......((((......((((((....))))))..(((.....)))..))))...(....).((((((((....))))))))... ( -24.00)
>DroWil_CAF1 9516 95 - 1
U-------UUUCUUAACUUCCUUUCAGCAAAUUAAAAAGUUGCAACUUUUAACGCAAUCAGCGGCAUUGAAUCGCGAGACAAUUGCGGCCUCACAAUUGGCC
.-------..............((((((......((((((....))))))..(((.....)))))..))))..((((.....))))((((........)))) ( -18.90)
>DroAna_CAF1 3094 98 - 1
UUCUGAU-UCAUUUC---UUCCAACAGCAAAUUAAAAAGCUGCAGCUGCUAACGCAAUCGGCGGCCCUCAACCGCGAGACCAUAGCGGCCUCCCAAUUGGCC
.......-.......---........((..........(((((...(((....)))....))))).(((......)))......))((((........)))) ( -23.60)
>DroPer_CAF1 2992 88 - 1
-----------CUUU---UCCUUUCAGCAAAUUAAAAAACUGCAGCUGUUAACGCAAUCAGCGGCGCUGAACCGCGAGACAAUUGCGGCCUCACAAUUGGCC
-----------....---.......................((((.((((..(((..(((((...)))))...))).)))).))))((((........)))) ( -22.30)
>consensus
________U___UUA___UCCUUACAGCAAAUUAAAAAGCUGCAGCUGUUAACGCAAUCAGCGGCGCUGAACCGCGAGACAAUUGCGGCCUCACAAUUGGCC
..........................((((........(((((..........)))))..((((.......)))).......))))((((........)))) (-15.10 = -15.43 +   0.33)

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 10:53:05 2006