Locus 7614

Sequence ID 3L_DroMel_CAF1
Location 20,491,978 – 20,492,133
Length 155
Max. P 0.991205
window12372 window12373 window12374 window12375 window12376

overview

Window 2

Location 20,491,978 – 20,492,075
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.88
Mean single sequence MFE -23.65
Consensus MFE -18.20
Energy contribution -18.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.90
Structure conservation index 0.77
SVM decision value -0.04
SVM RNA-class probability 0.512649
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20491978 97 - 23771897
GCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUUUU--GGUGGUUCCA--------UGUGG-------------
(((...(((.((.(((((.((....((((.....(((((.(((((((((....))))))))).)))))..)))).)).))))--))).)))...--------)))..------------- ( -24.50)
>DroVir_CAF1 43034 89 - 1
GCAGAUAACAGC--AAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGAAUUCUU------GGUGAGG-GA---------GAGA-------------
((........))--..(((((..(((....)))..)))))(((((((((....)))))))))....((((...(((..------...))).-..---------))))------------- ( -20.10)
>DroSec_CAF1 34511 98 - 1
GCAGAUAAAAGCACAAAAUGUUGGCAGCCCUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUUUU-CGGUGGUUCCA--------UGGGG-------------
........((((.((((((((..(((....)))..)))))(((((((((....)))))))))......)))))))......(-(.(((....))--------).)).------------- ( -24.40)
>DroMoj_CAF1 41897 103 - 1
GCAGAUAACAGC--AAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGCAUUCUA------GGCAAGGCGA---------GGGAGGAGCAGGAGGCU
(((((((((.((--..(((((..(((....)))..))))).((.....)))).)))))))....((((((((......------.)))))))).---------.......))........ ( -28.70)
>DroAna_CAF1 33034 106 - 1
GCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUUUU-CGGUUGUUCGAACUUCCAAUAGGG-------------
((........))......((((((.(((.(....(((((.(((((((((....))))))))).)))))..))))......((-(((....)))))...))))))...------------- ( -24.10)
>DroPer_CAF1 39228 90 - 1
GCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGGUUAUUCUUUUUGGAGG----A--------------------------
((...(((((........)))))...))(((...(((((.(((((((((....))))))))).)))))...)))..(((((....))))----)-------------------------- ( -20.10)
>consensus
GCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUUUU__GGUGGUUCGA_________GGGG_____________
..(((((.........(((((..(((....)))..)))))(((((((((....)))))))))..)))))................................................... (-18.20 = -18.20 +  -0.00)

alignment

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secondary structure

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Window 3

Location 20,491,995 – 20,492,113
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.98
Mean single sequence MFE -23.32
Consensus MFE -12.23
Energy contribution -14.15
Covariance contribution 1.92
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.52
SVM decision value 0.19
SVM RNA-class probability 0.624707
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20491995 118 + 23771897
AAAAUAAGCCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACAGAAACAGCGACCAC
......((((..(((((.((.(((.((....)).))).)).))))).....))))............(((((((...(((((.....)))))..((((....)))))))))))..... ( -31.80)
>DroVir_CAF1 43047 93 + 1
--AAGAAUUCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGUGCUGCCAACAUUUU--GCUGUUAUCUGCG-------CGCAAUUCUAACAACA--------------
--.(((((((..(((((.((.(((.((....)).))).)).)))))....((((.(..((((....--..))))..).)))-------)).)))))).......-------------- ( -16.00)
>DroEre_CAF1 36492 117 + 1
AAAAUAAGCCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACG-AAACAGCGACCAC
......((((..(((((.((.(((.((....)).))).)).))))).....))))............(((((((.(((((((.....))))).....(....))-))))))))..... ( -26.90)
>DroMoj_CAF1 41924 93 + 1
--UAGAAUGCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGUGCUGCCAACAUUUU--GCUGUUAUCUGCG-------CGCAAUUCUAACAACA--------------
--((((((((..(((((.((.(((.((....)).))).)).)))))....((((.(..((((....--..))))..).)))-------))).))))))......-------------- ( -19.30)
>DroAna_CAF1 33060 118 + 1
AAAAUAAGCCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGUGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCGCUCGCGCAAUUCUGGCAACAGAAACAGCGACCGC
...........................((((((.............(((((..(............)..)))))...(((((.....))))).(((((....)))))))))))..... ( -30.90)
>DroPer_CAF1 39238 92 + 1
AGAAUAACCCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGUGCUGCCAACAUUUUGUGCUGUUAUCUGCUCU--------------------------AGCGACCAC
(((.........(((((.((.(((.((....)).))).)).)))))(((((..(............)..))))).)))((...--------------------------.))...... ( -15.00)
>consensus
AAAAUAAGCCAAGACAUAAUAAAUAACCGCUGUCAUUCAUAAUGUCAACAGUGCUGCCAACAUUUUGUGCUGUUAUCUGCGCC_____CGCAAUUCUGGCAACA_____AGCGACCAC
............(((((.((.(((.((....)).))).)).)))))((((((((............))))))))...(((((.....))))).......................... (-12.23 = -14.15 +   1.92)

alignment

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secondary structure

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Window 4

Location 20,491,995 – 20,492,113
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.98
Mean single sequence MFE -30.90
Consensus MFE -22.72
Energy contribution -24.47
Covariance contribution 1.75
Combinations/Pair 1.07
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 1.19
SVM RNA-class probability 0.927782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20491995 118 - 23771897
GUGGUCGCUGUUUCUGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUU
..(((((((((((((((.(((......((....)))))))))).))))))(((.(((((..(((....)))..)))))(((((((((....)))))))))..)))...))))...... ( -38.50)
>DroVir_CAF1 43047 93 - 1
--------------UGUUGUUAGAAUUGCG-------CGCAGAUAACAGC--AAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGAAUUCUU--
--------------((((((((...(((..-------..))).)))))))--).(((((..(((....)))..)))))(((((((((....)))))))))................-- ( -23.90)
>DroEre_CAF1 36492 117 - 1
GUGGUCGCUGUUU-CGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUU
..((((.......-.((((((....((((((.....))))))..((((........))))))))))......(((((.(((((((((....))))))))).)))))..))))...... ( -35.60)
>DroMoj_CAF1 41924 93 - 1
--------------UGUUGUUAGAAUUGCG-------CGCAGAUAACAGC--AAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGCAUUCUA--
--------------(((((((((..((((.-------...........))--))....))))))))).(((.(((((.(((((((((....))))))))).)))))..))).....-- ( -25.00)
>DroAna_CAF1 33060 118 - 1
GCGGUCGCUGUUUCUGUUGCCAGAAUUGCGCGAGCGGCGCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUU
..(((((((((((((((.(((......((....)))))))))).))))))(((.(((((..(((....)))..)))))(((((((((....)))))))))..)))...))))...... ( -40.00)
>DroPer_CAF1 39238 92 - 1
GUGGUCGCU--------------------------AGAGCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGGUUAUUCU
.((.((...--------------------------.)).))((((((....((((((((..(((....)))..)))))(((((((((....)))))))))......))).)))))).. ( -22.40)
>consensus
GUGGUCGCU_____UGUUGCCAGAAUUGCG_____GGCGCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUUAUGAAUGACAGCGGUUAUUUAUUAUGUCUUGGCUUAUUUU
...............((((((....((((((.....))))))..((((........))))))))))......(((((.(((((((((....))))))))).)))))............ (-22.72 = -24.47 +   1.75)

alignment

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secondary structure

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Window 5

Location 20,492,035 – 20,492,133
Length 98
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 91.49
Mean single sequence MFE -27.82
Consensus MFE -22.94
Energy contribution -23.38
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.82
SVM decision value 2.25
SVM RNA-class probability 0.991205
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20492035 98 + 23771897
AAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACAGA--AACAGCGACCACAACAACCACAUU----------CUGCACAU
...(((.((((((.((....))))))))((((((...(((((.....)))))..((((....))))--)))))))))...............----------........ ( -26.10)
>DroSec_CAF1 34569 100 + 1
AAUGUCAACAGGGCUGCCAACAUUUUGUGCUUUUAUCUGCGCCACUCGCGCAAUUCUGGCAACAGAAGAACAGCGACCACAACAACCAAAUU----------CUGCACAU
.((((...((((((.....((.....))((........)))))..((((....(((((....))))).....))))................----------))).)))) ( -22.20)
>DroSim_CAF1 34540 100 + 1
AAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACAGAAGAACAGCGACCACAACAACCACAUU----------CUGCACAU
...(((.((((((.((....))))))))((((((...(((((.....))))).(((((....))))).)))))))))...............----------........ ( -27.20)
>DroEre_CAF1 36532 97 + 1
AAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACG-A--AACAGCGACCACAACAACCACAUU----------CUGCACAU
...(((.((((((.((....))))))))((((((.(((((((.....))))).....(....))-)--)))))))))...............----------........ ( -21.20)
>DroAna_CAF1 33100 108 + 1
AAUGUCAACAGUGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCGCUCGCGCAAUUCUGGCAACAGA--AACAGCGACCGCAACAACCACAUUGCGGCGCAUUCGGCGCAU
......(((((..(............)..)))))...(((((((.........(((((....))))--)...(((.((((((........)))))))))...))))))). ( -42.40)
>consensus
AAUGUCAACAGGGCUGCCAACAUUUUGUGCUGUUAUCUGCGCCACUCGCGCAAUUCUGGCAACAGA__AACAGCGACCACAACAACCACAUU__________CUGCACAU
...(((.((((((.((....))))))))((((((...(((((.....)))))..((((....))))..)))))))))................................. (-22.94 = -23.38 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,492,035 – 20,492,133
Length 98
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 91.49
Mean single sequence MFE -34.90
Consensus MFE -29.10
Energy contribution -29.50
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.83
SVM decision value 1.60
SVM RNA-class probability 0.966827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20492035 98 - 23771897
AUGUGCAG----------AAUGUGGUUGUUGUGGUCGCUGUU--UCUGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUU
........----------..((((.((((((((((.((....--...)).)))....((((((.....))))))))))))))))).(((((..(((....)))..))))) ( -32.00)
>DroSec_CAF1 34569 100 - 1
AUGUGCAG----------AAUUUGGUUGUUGUGGUCGCUGUUCUUCUGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAAAAGCACAAAAUGUUGGCAGCCCUGUUGACAUU
.(((((..----------.........(((.((((.((.........)).)))).)))(((((.....))))).......))))).(((((..(((....)))..))))) ( -31.50)
>DroSim_CAF1 34540 100 - 1
AUGUGCAG----------AAUGUGGUUGUUGUGGUCGCUGUUCUUCUGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUU
.(((((.(----------((((((..(.....)..))).))))(((((....)))))((((((.....))))))......))))).(((((..(((....)))..))))) ( -32.90)
>DroEre_CAF1 36532 97 - 1
AUGUGCAG----------AAUGUGGUUGUUGUGGUCGCUGUU--U-CGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUU
........----------..((((.((((((((((.((....--.-.)).)))....((((((.....))))))))))))))))).(((((..(((....)))..))))) ( -31.90)
>DroAna_CAF1 33100 108 - 1
AUGCGCCGAAUGCGCCGCAAUGUGGUUGUUGCGGUCGCUGUU--UCUGUUGCCAGAAUUGCGCGAGCGGCGCAGAUAACAGCACAAAAUGUUGGCAGCACUGUUGACAUU
.(((((((..(((((((((((......)))))))).((...(--((((....)))))..)))))..))))))).............(((((..(((....)))..))))) ( -46.20)
>consensus
AUGUGCAG__________AAUGUGGUUGUUGUGGUCGCUGUU__UCUGUUGCCAGAAUUGCGCGAGUGGCGCAGAUAACAGCACAAAAUGUUGGCAGCCCUGUUGACAUU
.(((((.....................(((.((((.((.........)).)))).)))(((((.....))))).......))))).(((((..(((....)))..))))) (-29.10 = -29.50 +   0.40)

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 12:51:45 2006