Locus 313

Sequence ID 3R_DroMel_CAF1
Location 1,213,925 – 1,214,074
Length 149
Max. P 0.963946
window526 window527 window528

overview

Window 6

Location 1,213,925 – 1,214,042
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.05
Mean single sequence MFE -35.48
Consensus MFE -31.00
Energy contribution -31.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.87
SVM decision value 1.56
SVM RNA-class probability 0.963946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1213925 117 - 27905053
--AAUGCAUUCAGCCGUUA-AAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCUUUAGGCCACACGGUCCGGUUGAAACGUCCCGUUUGUCCC
--......((((((((...-....(((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))))))))))................ ( -40.11)
>DroVir_CAF1 4334 111 - 1
CAUAAAAAA--------AA-AAACGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCCCGUUGUAAAGCGGCGUUUGUUGC
.........--------..-(((((((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))(((((....))))).))))..... ( -38.20)
>DroGri_CAF1 4747 109 - 1
--AAUACAA--------AU-CUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCCUGUUGUAAAGCGCCGUUAGUCGC
--..(((((--------..-....(((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))...)))))..(((.(....).))) ( -35.70)
>DroEre_CAF1 5695 105 - 1
---------------CUUAUAAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCUUUAGGCCACACGGUCCCGUUGAAACGUCACGUUUGUCCC
---------------.........(((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))......(((((...)))))..... ( -32.30)
>DroWil_CAF1 2733 109 - 1
--AAUAUAAUC---------AUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCUUUAGGCCACACGGUCCUUUUGCAUCGAACAGUUACUUUC
--.........---------....(((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))........................ ( -31.00)
>DroAna_CAF1 4702 113 - 1
--AGUAAAUU--GCA--GA-AGACGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCUUUAGGCCACACGGUCCUGUUGAAACGUCACGUUUGUUCC
--........--(((--((-.((((((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))..((....)))))...)))))... ( -35.60)
>consensus
__AAUAAAA________AA_AAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCCUUUAGGCCACACGGUCCUGUUGAAACGUCCCGUUUGUCCC
........................(((((((...(((((((((.(((.......))).)))).)))))...((((........))))..)))))))........................ (-31.00 = -31.00 +   0.00)

alignment

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secondary structure

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Window 7

Location 1,213,965 – 1,214,074
Length 109
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 74.43
Mean single sequence MFE -26.17
Consensus MFE -17.90
Energy contribution -17.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.97
Structure conservation index 0.68
SVM decision value 0.07
SVM RNA-class probability 0.567507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1213965 109 + 27905053
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAUU-UAACGGCUGAAUGCAUU--UUUUGCACCGACUGGCUUGUUUAAACUUCUCU
(((((((.((((((.(((((....)))))...(((((.......)))))..((((((...-...))))))..((((..--...))))))))).).))))))).......... ( -35.90)
>DroVir_CAF1 4374 89 + 1
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGUUU-UU--------UUUUUUAUGUUUC--------------UUUUCAAUUUUUUU
.(((..((((..(((((.((((((.(.......).)))))))))))))))...)))....-..--------.............--------------.............. ( -17.90)
>DroGri_CAF1 4787 87 + 1
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAG-AU--------UUGUAUU--UUUU--------------UUUCUAAAUUGCAC
.(((..((((..(((((.((((((.(.......).)))))))))))))))...)))....-..--------.((((.(--((..--------------.....))).)))). ( -19.20)
>DroSim_CAF1 4980 109 + 1
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAUU-UACCGGCUAAAUGCAUU--UUUUGCAUCAAGUCGGUUGUUUAAACUUCUUU
.(((..((((..(((((.((((((.(.......).)))))))))))))))...)))(((.-.(((((((..(((((..--...)))))..))))))).)))........... ( -33.70)
>DroYak_CAF1 5756 110 + 1
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAUUAUAACUGCUAAGUGCAUU--UUUUGCAAUAAGUGGACCGUUCUAACUUUUUU
.((((.(((.((((((((..((((....))))..))))))))))).))))((((((.(((...(((....)))(((..--...)))....))).))))))............ ( -31.90)
>DroMoj_CAF1 4786 87 + 1
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGUAU-CA--------UACUUUU--UUUU--------------UUUUUAAUUUUCAG
.((((.(((((.(((((.((((((.(.......).)))))))))))....)).))).)))-).--------.......--....--------------.............. ( -18.40)
>consensus
GGAUAAGGCGUCGGACUUCGAAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAUU_UA________UUGCAUU__UUUU______________GUUUUAACUUUUUU
.(((..((((..(((((.((((((.(.......).)))))))))))))))...)))........................................................ (-17.90 = -17.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,213,965 – 1,214,074
Length 109
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 74.43
Mean single sequence MFE -20.62
Consensus MFE -15.10
Energy contribution -15.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.98
Structure conservation index 0.73
SVM decision value 0.51
SVM RNA-class probability 0.763054
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1213965 109 - 27905053
AGAGAAGUUUAAACAAGCCAGUCGGUGCAAAA--AAUGCAUUCAGCCGUUA-AAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
.(((..(((...........(((((((((...--..))))))..((.(((.-....))).))))).(((((((((.(((.......))).)))).))))))))..))).... ( -23.70)
>DroVir_CAF1 4374 89 - 1
AAAAAAAUUGAAAA--------------GAAACAUAAAAAA--------AA-AAACGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
..............--------------.............--------..-........(((...(((((((((.(((.......))).)))).)))))..)))....... ( -15.10)
>DroGri_CAF1 4787 87 - 1
GUGCAAUUUAGAAA--------------AAAA--AAUACAA--------AU-CUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
..............--------------....--.......--------..-........(((...(((((((((.(((.......))).)))).)))))..)))....... ( -15.10)
>DroSim_CAF1 4980 109 - 1
AAAGAAGUUUAAACAACCGACUUGAUGCAAAA--AAUGCAUUUAGCCGGUA-AAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
.(((...........((((.((.((((((...--..)))))).)).)))).-........(((...(((((((((.(((.......))).)))).)))))..)))))).... ( -28.50)
>DroYak_CAF1 5756 110 - 1
AAAAAAGUUAGAACGGUCCACUUAUUGCAAAA--AAUGCACUUAGCAGUUAUAAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
......(((...((((((.....(((((.((.--.......)).))))).......))))))....(((((((((.(((.......))).)))).))))))))......... ( -26.00)
>DroMoj_CAF1 4786 87 - 1
CUGAAAAUUAAAAA--------------AAAA--AAAAGUA--------UG-AUACGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
..............--------------....--.......--------.(-(((.(..(((....(((((((((.(((.......))).)))).))))).))).).)))). ( -15.30)
>consensus
AAAAAAGUUAAAAA______________AAAA__AAUACAA________UA_AAUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUUCGAAGUCCGACGCCUUAUCC
............................................................(((...(((((((((.(((.......))).)))).)))))..)))....... (-15.10 = -15.10 +  -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 09:40:09 2006