Locus 3815

Sequence ID X_DroMel_CAF1
Location 10,139,895 – 10,140,137
Length 242
Max. P 0.996767
window6270 window6271 window6272 window6273 window6274 window6275 window6276

overview

Window 0

Location 10,139,895 – 10,139,986
Length 91
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 90.74
Mean single sequence MFE -24.12
Consensus MFE -16.35
Energy contribution -17.60
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.68
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10139895 91 + 22224390
GUGUGUGUGCCUGCUGCAGCGCACAUUACACACGCACACUCGUACAUUAAAUUUAUGUGCUCGAGUUGGACGCGGUA-AAAAAAAAAGAGUA
(((((((((((((...))).))))).))))).(((.(((((((((((.......))))))..))).))...)))...-.............. ( -26.60)
>DroSec_CAF1 29322 83 + 1
---UGUGUGCCUGCUGCAG--CACAUUACACACGCACACUCAUACAUUAAAUUUAUGUGCUCGAGUUGGACGCG----AACAAAAAAGAGUA
---.((((.((.(((..((--(((((............................)))))))..))).)))))).----.............. ( -16.69)
>DroSim_CAF1 20771 86 + 1
GUAUGUGUGCCUGCUGGAG--CACAUUACACACGCACACUCGUACAUUAAAUUUAUGUGCUCGAGUUGGACGCG----AACAAAAAAGAGUA
((.(((((.((.(((.(((--(((((............................)))))))).))).)))))))----.))........... ( -24.69)
>DroYak_CAF1 21587 90 + 1
GUGUGUGUGUCUGCUGCAG--CACAUUACACACGCACACUCGUACAUUAAAUUUAUGUGCUCGAGUUGGACGCCAAAAAAAAAAAAAGAGUA
((((((((((.(((....)--))....))))))))))((((((((((.......)))))).....((((...))))...........)))). ( -28.50)
>consensus
GUGUGUGUGCCUGCUGCAG__CACAUUACACACGCACACUCGUACAUUAAAUUUAUGUGCUCGAGUUGGACGCG____AAAAAAAAAGAGUA
(((((((((..((.((.....))))...)))))))))((((((((((.......))))))((......)).................)))). (-16.35 = -17.60 +   1.25)

alignment

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secondary structure

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Window 1

Location 10,139,895 – 10,139,986
Length 91
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 90.74
Mean single sequence MFE -22.50
Consensus MFE -18.83
Energy contribution -18.45
Covariance contribution -0.38
Combinations/Pair 1.10
Mean z-score -1.51
Structure conservation index 0.84
SVM decision value 0.20
SVM RNA-class probability 0.632469
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10139895 91 - 22224390
UACUCUUUUUUUUU-UACCGCGUCCAACUCGAGCACAUAAAUUUAAUGUACGAGUGUGCGUGUGUAAUGUGCGCUGCAGCAGGCACACACAC
.............(-(((((((..((.((((.(((...........))).))))))..)))).))))(((((.(((...))))))))..... ( -24.90)
>DroSec_CAF1 29322 83 - 1
UACUCUUUUUUGUU----CGCGUCCAACUCGAGCACAUAAAUUUAAUGUAUGAGUGUGCGUGUGUAAUGUG--CUGCAGCAGGCACACA---
..........((((----((.(.....).))))))..................((((((.((((((.....--.)))).)).)))))).--- ( -22.60)
>DroSim_CAF1 20771 86 - 1
UACUCUUUUUUGUU----CGCGUCCAACUCGAGCACAUAAAUUUAAUGUACGAGUGUGCGUGUGUAAUGUG--CUCCAGCAGGCACACAUAC
(((((......(((----((.(.....).)))))((((.......))))..)))))...((((((....((--(....))).)))))).... ( -22.20)
>DroYak_CAF1 21587 90 - 1
UACUCUUUUUUUUUUUUUGGCGUCCAACUCGAGCACAUAAAUUUAAUGUACGAGUGUGCGUGUGUAAUGUG--CUGCAGCAGACACACACAC
.................(((...)))(((((.(((...........))).)))))(((.((((((....((--(....))).)))))).))) ( -20.30)
>consensus
UACUCUUUUUUGUU____CGCGUCCAACUCGAGCACAUAAAUUUAAUGUACGAGUGUGCGUGUGUAAUGUG__CUGCAGCAGGCACACACAC
...................(((....(((((.(((...........))).))))).)))((((((..(((........))).)))))).... (-18.83 = -18.45 +  -0.38)

alignment

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secondary structure

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Window 2

Location 10,139,986 – 10,140,080
Length 94
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -21.77
Consensus MFE -19.08
Energy contribution -19.08
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.88
SVM decision value 0.34
SVM RNA-class probability 0.696209
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10139986 94 - 22224390
AGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUCUUUUCAUUUUGUGCUCUU
((((((.((((((...))))))...))))))((..(....((....((((((((..............-...)))))))).))....)..))... ( -20.33)
>DroSec_CAF1 29405 94 - 1
AGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUCCUUUCAUUUUGUGCUCUU
((((((.((((((...))))))...))))))((..(((((......))))(((((.............-.....)))))........)..))... ( -22.17)
>DroSim_CAF1 20857 94 - 1
AGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUCCUUUCAUUUUGUGCUCUU
((((((.((((((...))))))...))))))((..(((((......))))(((((.............-.....)))))........)..))... ( -22.17)
>DroYak_CAF1 21677 95 - 1
AGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUUUGUUGUAAAGAGUCUUUAUAUUUUUUUUUACAUUUUCUUUUCAUUUUGUGCUCUG
.(((...)))((((((((((((((........)))))......(((((((((...........))))))))).........)))))))))..... ( -22.40)
>consensus
AGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU_UCAUUUUCCUUUCAUUUUGUGCUCUU
((((((.((((((...))))))...))))))....((((((......)))))).......................................... (-19.08 = -19.08 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,140,004 – 10,140,113
Length 109
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 90.41
Mean single sequence MFE -37.28
Consensus MFE -33.24
Energy contribution -33.55
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -3.69
Structure conservation index 0.89
SVM decision value 2.65
SVM RNA-class probability 0.996058
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10140004 109 + 22224390
GAAAAUGA-AAAUAAAAUAAGACUCCUCUUUACAACAAAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUACCAAGGGGGCGUGGCGAAAAAAGGGGCUG-------CUG
........-..........((...(((((((.(..((((.((((..........))))...))))..)(((((((((.(....))))))))))....)))))))...-------)). ( -32.70)
>DroSec_CAF1 29423 109 + 1
GAAAAUGA-AAAUAAAAUAAGACUCCUCUUUACAACAAAAGGCACUAAGCAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGGAAAAAGGGGCUG-------CUG
........-.................(((((......))))).....((((....((((.((((....(((((((((((...)))))))))))....))))))))))-------)). ( -37.40)
>DroSim_CAF1 20875 109 + 1
GAAAAUGA-AAAUAAAAUAAGACUCCUCUUUACAACAAAAGGCACUAAGCAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGGAAAAAGGGGCUG-------CUG
........-.................(((((......))))).....((((....((((.((((....(((((((((((...)))))))))))....))))))))))-------)). ( -37.40)
>DroYak_CAF1 21695 117 + 1
GAAAAUGUAAAAAAAAAUAUAAAGACUCUUUACAACAAAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCAAAAAAAGAGGCUGAUGGCUGCCG
.....((((((.................))))))......((((.....(((((.(((..((((....(((((((((((...)))))))))))....)))).))))))))..)))). ( -41.63)
>consensus
GAAAAUGA_AAAUAAAAUAAGACUCCUCUUUACAACAAAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGAAAAAAGGGGCUG_______CUG
........................(((((((.(..((((.((((..........))))...))))..)(((((((((((...)))))))))))....)))))))............. (-33.24 = -33.55 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,140,004 – 10,140,113
Length 109
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 90.41
Mean single sequence MFE -38.00
Consensus MFE -34.38
Energy contribution -34.88
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -3.22
Structure conservation index 0.90
SVM decision value 2.75
SVM RNA-class probability 0.996767
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10140004 109 - 22224390
CAG-------CAGCCCCUUUUUUCGCCACGCCCCCUUGGUAGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUC
...-------..((.(((((((..((((((((((...))..))))))))..((((...((((((........))))))....))))))))))).))............-........ ( -33.30)
>DroSec_CAF1 29423 109 - 1
CAG-------CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUC
.((-------((((((((((....((((((((((....)).))))))))....)))).))))....)))).((..((((((......))))))...))..........-........ ( -39.60)
>DroSim_CAF1 20875 109 - 1
CAG-------CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU-UCAUUUUC
.((-------((((((((((....((((((((((....)).))))))))....)))).))))....)))).((..((((((......))))))...))..........-........ ( -39.60)
>DroYak_CAF1 21695 117 - 1
CGGCAGCCAUCAGCCUCUUUUUUUGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUUUGUUGUAAAGAGUCUUUAUAUUUUUUUUUACAUUUUC
.(((........))).........((((((((((....)).))))))))..(((((..((((((........)))))))))))(((((((((...........)))))))))..... ( -39.50)
>consensus
CAG_______CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUUUGUUGUAAAGAGGAGUCUUAUUUUAUUU_UCAUUUUC
...............(((((((..((((((((((....)).))))))))..((((...((((((........))))))....)))))))))))........................ (-34.38 = -34.88 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,140,040 – 10,140,137
Length 97
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 88.11
Mean single sequence MFE -41.43
Consensus MFE -35.44
Energy contribution -35.94
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -4.43
Structure conservation index 0.86
SVM decision value 2.42
SVM RNA-class probability 0.993678
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10140040 97 + 22224390
AAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUACCAAGGGGGCGUGGCGAAAAAAGGGGCUG-------CUGCCUGCCAUUAACAUGAAGAAGAAA
...((((.....((.((.((((.((((....(((((((((.(....))))))))))....))))))))))-------.))..)))).................. ( -34.70)
>DroSec_CAF1 29459 95 + 1
AAAGGCACUAAGCAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGGAAAAAGGGGCUG-------CUGCCUGCCAUUAAUAUGAA--AGAAA
...((((...((((....((((.((((....(((((((((((...)))))))))))....))))))))))-------))...))))...........--..... ( -44.70)
>DroSim_CAF1 20911 95 + 1
AAAGGCACUAAGCAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGGAAAAAGGGGCUG-------CUGCCUGCCAUUAACAUGAA--AGAAA
...((((...((((....((((.((((....(((((((((((...)))))))))))....))))))))))-------))...))))...........--..... ( -44.70)
>DroYak_CAF1 21732 97 + 1
AAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCAAAAAAAGAGGCUGAUGGCUGCCGGCUGCCAUCAACAUGAA-------
...((((.....(((((.(((..((((....(((((((((((...)))))))))))....)))).))))))))((.....))))))...........------- ( -41.60)
>consensus
AAAGGCACUAAACAUUAUGCCCACUUUGCGGGCCACGCCUCCCAAGGGGGCGUGGCGAAAAAAGGGGCUG_______CUGCCUGCCAUUAACAUGAA__AGAAA
...((((...........((((.((((....(((((((((((...)))))))))))....))))))))..............)))).................. (-35.44 = -35.94 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,140,040 – 10,140,137
Length 97
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 88.11
Mean single sequence MFE -40.20
Consensus MFE -33.97
Energy contribution -33.97
Covariance contribution -0.00
Combinations/Pair 1.12
Mean z-score -3.83
Structure conservation index 0.84
SVM decision value 2.56
SVM RNA-class probability 0.995297
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10140040 97 - 22224390
UUUCUUCUUCAUGUUAAUGGCAGGCAG-------CAGCCCCUUUUUUCGCCACGCCCCCUUGGUAGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUU
..................((((((((.-------..((((((((....((((((((((...))..))))))))....)))).))))....))))...))))... ( -33.90)
>DroSec_CAF1 29459 95 - 1
UUUCU--UUCAUAUUAAUGGCAGGCAG-------CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUU
.....--...........((((((((.-------..((((((((....((((((((((....)).))))))))....)))).))))....))))...))))... ( -41.70)
>DroSim_CAF1 20911 95 - 1
UUUCU--UUCAUGUUAAUGGCAGGCAG-------CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUU
.....--...........((((((((.-------..((((((((....((((((((((....)).))))))))....)))).))))....))))...))))... ( -41.70)
>DroYak_CAF1 21732 97 - 1
-------UUCAUGUUGAUGGCAGCCGGCAGCCAUCAGCCUCUUUUUUUGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGUUUAGUGCCUUU
-------.....(((((((((........)))))))))(.((((....((((((((((....)).))))))))....)))).)(((((........)))))... ( -43.50)
>consensus
UUUCU__UUCAUGUUAAUGGCAGGCAG_______CAGCCCCUUUUUCCGCCACGCCCCCUUGGGAGGCGUGGCCCGCAAAGUGGGCAUAAUGCUUAGUGCCUUU
..................((((((((..........((((((((....((((((((((....)).))))))))....)))).))))....))))...))))... (-33.97 = -33.97 +  -0.00)

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 11:09:23 2006