Locus 3689

Sequence ID 2L_DroMel_CAF1
Location 10,748,135 – 10,748,269
Length 134
Max. P 0.999843
window5818 window5819 window5820 window5821

overview

Window 8

Location 10,748,135 – 10,748,237
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.10
Mean single sequence MFE -34.72
Consensus MFE -20.42
Energy contribution -20.45
Covariance contribution 0.03
Combinations/Pair 1.15
Mean z-score -2.70
Structure conservation index 0.59
SVM decision value 1.54
SVM RNA-class probability 0.962680
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10748135 102 + 22407834
CUUGCCACAUCU------GAUG------------UUGCAGCUUUGCAUAAAUAUUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGCCAGCAGC
.((((.......------....------------..(((..((.(((((.....))))).))..)))...((((..((((....).((((((((....)))))))))))..)))))))). ( -31.30)
>DroPse_CAF1 2676 114 + 1
CUUGCCACAUCUGAAGCUGACGCUGACGCUGGGGUUGGGGCUUUGCAUAAGUAUUAUGUUGAAAUGGCUCCAGCAAUGCGGCCGUAACAUGCAACAUGUUGCAUGUUCAGCGGC------
..............(((....)))..(((....(((((((((..(((((.....)))))......)))))))))...)))((((((((((((((....)))))))))..)))))------ ( -42.00)
>DroEre_CAF1 2548 96 + 1
CUUGCCACAUCU------GAUG------------UUGCAGCUUUGCAUAAACACUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC------
...(((.(....------..((------------((((.((((.(((((.....))))).))..((((...))))..)).))))))((((((((....))))))))...).)))------ ( -31.20)
>DroYak_CAF1 2589 96 + 1
CUUGCCACAUCU------GAUG------------UUGCAGCUUUGCAUAAAUAUUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC------
...(((.(....------..((------------((((.((((.(((((.....))))).))..((((...))))..)).))))))((((((((....))))))))...).)))------ ( -31.00)
>DroAna_CAF1 2758 91 + 1
CUUGCCACAUCU------AAAG------------UUGCGAUUUUGCAUAAAUAUUGUGUUGAAAUGCCAACGGCGAUGCGGUAACAACAUGCAACAUGUUGCAUGUGCA-----------
.(((((.((((.------...(------------(((((.(((.(((((.....))))).))).)).))))...)))).)))))..((((((((....))))))))...----------- ( -29.20)
>DroPer_CAF1 2619 108 + 1
CUUGCCACAUCU------GACGCUGACGCUGGGGCUGGGGCUUUGCAUAAGUAUUAUGUUGAAAUGGCUCCAGCAAUGCGGCCGUAACAUGCAACAUGUUGCAUGUUCAGCGGC------
............------..(((((((((....(((((((((..(((((.....)))))......)))))))))...)))......((((((((....))))))))))))))..------ ( -43.60)
>consensus
CUUGCCACAUCU______GAUG____________UUGCAGCUUUGCAUAAAUAUUAUGUUGAAAUGCCUACGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC______
.(((((.(((...............................((.(((((.....))))).))..(((.....)))))).)))))..((((((((....)))))))).............. (-20.42 = -20.45 +   0.03)

alignment

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secondary structure

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Window 9

Location 10,748,135 – 10,748,237
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.10
Mean single sequence MFE -35.25
Consensus MFE -22.48
Energy contribution -22.95
Covariance contribution 0.47
Combinations/Pair 1.09
Mean z-score -3.39
Structure conservation index 0.64
SVM decision value 2.00
SVM RNA-class probability 0.985295
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10748135 102 - 22407834
GCUGCUGGCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAGCUGCAA------------CAUC------AGAUGUGGCAAG
((.....))((..(((((((((....))))))))((((((.((.((((.(((((.(((.......))).))))))))).)).))))------------))..------....)..))... ( -34.20)
>DroPse_CAF1 2676 114 - 1
------GCCGCUGAACAUGCAACAUGUUGCAUGUUACGGCCGCAUUGCUGGAGCCAUUUCAACAUAAUACUUAUGCAAAGCCCCAACCCCAGCGUCAGCGUCAGCUUCAGAUGUGGCAAG
------((((((((((((((((....))))))))).)))).((((..(((((((........((((.....))))................((....))....))))))))))))))... ( -36.60)
>DroEre_CAF1 2548 96 - 1
------GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAGUGUUUAUGCAAAGCUGCAA------------CAUC------AGAUGUGGCAAG
------(((((...((((((((....))))))))((((((.((.((((.(((((((((.......))))))))))))).)).))))------------))..------....)))))... ( -41.20)
>DroYak_CAF1 2589 96 - 1
------GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAGCUGCAA------------CAUC------AGAUGUGGCAAG
------(((((...((((((((....))))))))((((((.((.((((.(((((.(((.......))).))))))))).)).))))------------))..------....)))))... ( -34.90)
>DroAna_CAF1 2758 91 - 1
-----------UGCACAUGCAACAUGUUGCAUGUUGUUACCGCAUCGCCGUUGGCAUUUCAACACAAUAUUUAUGCAAAAUCGCAA------------CUUU------AGAUGUGGCAAG
-----------.((((((((((....))))))).)))..(((((((...(((((....)))))..........(((......))).------------....------.))))))).... ( -26.90)
>DroPer_CAF1 2619 108 - 1
------GCCGCUGAACAUGCAACAUGUUGCAUGUUACGGCCGCAUUGCUGGAGCCAUUUCAACAUAAUACUUAUGCAAAGCCCCAGCCCCAGCGUCAGCGUC------AGAUGUGGCAAG
------((((((((((((((((....))))))))).))))(((..((((((.((........((((.....))))..........)).))))))...)))..------......)))... ( -37.67)
>consensus
______GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAGCCGCAA____________CAUC______AGAUGUGGCAAG
..............((((((((....))))))))....(((((((((((...)))..................(((......)))........................))))))))... (-22.48 = -22.95 +   0.47)

alignment

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secondary structure

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Window 0

Location 10,748,157 – 10,748,269
Length 112
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 74.95
Mean single sequence MFE -33.30
Consensus MFE -16.62
Energy contribution -17.02
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.37
Structure conservation index 0.50
SVM decision value 4.23
SVM RNA-class probability 0.999843
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10748157 112 + 22407834
CUUUGCAUAAAUAUUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGCCAGCAGCAGCAGCUGGCCCAGCAGCAACAACAAAGUCGG-
(((((...........(((((...(((...((((..((((....).((((((((....)))))))))))..))))))).)))))((((......)))).....)))))....- ( -38.80)
>DroPse_CAF1 2716 98 + 1
CUUUGCAUAAGUAUUAUGUUGAAAUGGCUCCAGCAAUGCGGCCGUAACAUGCAACAUGUUGCAUGUUCAGCGGC------------CAG---AAAAACAACAACAAACUACAC
..........(((.(.(((((.....((....)).....(((((((((((((((....)))))))))..)))))------------)..---........))))).).))).. ( -31.30)
>DroEre_CAF1 2570 106 + 1
CUUUGCAUAAACACUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC------AACAGCUGGCCCAGCAGCAGCAGCAAAAGCGG-
.((((((((.....)))((((...((((...)))).((((((....((((((((....)))))))).(((((..------..).)))))))..))).)))).))))).....- ( -34.50)
>DroYak_CAF1 2611 91 + 1
CUUUGCAUAAAUAUUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC------AACAGCUGGCCCAGCAG----------------
................(((((...((((...))))....(((....((((((((....)))))))).(((((..------..).)))))))))))).---------------- ( -30.60)
>DroPer_CAF1 2653 98 + 1
CUUUGCAUAAGUAUUAUGUUGAAAUGGCUCCAGCAAUGCGGCCGUAACAUGCAACAUGUUGCAUGUUCAGCGGC------------CAG---AAAAACAACAACAAGCUACAC
..........(((.(.(((((.....((....)).....(((((((((((((((....)))))))))..)))))------------)..---........))))).).))).. ( -31.30)
>consensus
CUUUGCAUAAAUAUUAUGUUGAAAUGCCUAUGGCAAUGCGGCAACAACAUGCAACAUGUUGCAUGUGCAGCGGC______A_CAGCUGGCCCAGCAGCAACAACAAACUACA_
...(((...........((((...(((.....)))...))))....((((((((....))))))))...)))......................................... (-16.62 = -17.02 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,748,157 – 10,748,269
Length 112
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 74.95
Mean single sequence MFE -33.10
Consensus MFE -17.02
Energy contribution -17.78
Covariance contribution 0.76
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.51
SVM decision value 2.22
SVM RNA-class probability 0.990518
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10748157 112 - 22407834
-CCGACUUUGUUGUUGCUGCUGGGCCAGCUGCUGCUGCUGGCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAG
-....(((((((((((((((.(.((((((.......)))))).).)))...))))))......((((((.((((...........))))...)))))).........)))))) ( -40.00)
>DroPse_CAF1 2716 98 - 1
GUGUAGUUUGUUGUUGUUUUU---CUG------------GCCGCUGAACAUGCAACAUGUUGCAUGUUACGGCCGCAUUGCUGGAGCCAUUUCAACAUAAUACUUAUGCAAAG
(((((((.(((((..((..((---(((------------((((...(((((((((....))))))))).)))))((...)).))))..))..)))))....)).))))).... ( -32.30)
>DroEre_CAF1 2570 106 - 1
-CCGCUUUUGCUGCUGCUGCUGGGCCAGCUGUU------GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAGUGUUUAUGCAAAG
-..((....)).((((((....)).))))...(------((.((.((((((((((....))))))).))).)).)))((((.(((((((((.......))))))))))))).. ( -35.10)
>DroYak_CAF1 2611 91 - 1
----------------CUGCUGGGCCAGCUGUU------GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAG
----------------.((((.(((.......(------((.((.((((((((((....))))))).))).)).)))..)))...))))......((((.....))))..... ( -26.50)
>DroPer_CAF1 2653 98 - 1
GUGUAGCUUGUUGUUGUUUUU---CUG------------GCCGCUGAACAUGCAACAUGUUGCAUGUUACGGCCGCAUUGCUGGAGCCAUUUCAACAUAAUACUUAUGCAAAG
..(((...(((((..((..((---(((------------((((...(((((((((....))))))))).)))))((...)).))))..))..)))))...))).......... ( -31.60)
>consensus
_CCGAGUUUGUUGUUGCUGCUGGGCCAGCUG_U______GCCGCUGCACAUGCAACAUGUUGCAUGUUGUUGCCGCAUUGCCAUAGGCAUUUCAACAUAAUAUUUAUGCAAAG
.......................................((.((.((((((((((....))))))).))).)).)).((((.(((((.(((.......))).))))))))).. (-17.02 = -17.78 +   0.76)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:45 2006