Locus 5794

Sequence ID 3R_DroMel_CAF1
Location 15,120,834 – 15,120,960
Length 126
Max. P 0.951295
window9494 window9495 window9496

overview

Window 4

Location 15,120,834 – 15,120,947
Length 113
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 82.36
Mean single sequence MFE -30.00
Consensus MFE -23.20
Energy contribution -22.62
Covariance contribution -0.58
Combinations/Pair 1.10
Mean z-score -2.30
Structure conservation index 0.77
SVM decision value 0.86
SVM RNA-class probability 0.868616
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15120834 113 - 27905053
GCAGUCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGA--CAUUCA----G
((....)).......(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).)))))))))--))))..----. ( -32.50)
>DroVir_CAF1 54076 111 - 1
GCGAGCGGAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCCAAGCUGUUAAGGGCUUUACU------CGCAGCUAAA--CCUUCAACCAG
(((((..((((((((....))))))(((((((((((((((.........)))))))))))))))..((((..........))))))..))------))).......--........... ( -32.10)
>DroPse_CAF1 51289 110 - 1
GCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAACUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGAGGGCUUUUCCAUUUAGCGUAGA-AGC--CA--CA----G
(((((.(((((((((....))))))(((((((((((((((.........))))))))))))))).)))....)))))....(((((((.(.......).)))-)))--).--..----. ( -31.90)
>DroGri_CAF1 65470 113 - 1
GCGAACGGCGAUAAAAUUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUAAAGGGCUUUACU------CUCAGAUACUGGCACACACACAG
((.....))((((((....))))))..(((((((((((((.........)))))))))))))((.((((....(((...((((.....))------))))).....)))).))...... ( -28.50)
>DroWil_CAF1 35768 113 - 1
GCAGUCAGCGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCCAAGCUGUUAAGGGCUUUUCCAUUUAGAUAGAAUAGA--CAUACU----A
...(((.((.......)).(((((((((((((((((((((.........)))))))))))))))..((((..........))))...........))))))...))--).....----. ( -26.90)
>DroAna_CAF1 44212 113 - 1
GCAGCAACAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGAGGGCUUUUCCAUUUGGCGCAGAUAGA--CGUUCA----G
..................((((((((((((((((((((((.........)))))))))))))))..(((.(((((......)))))........)))...))))))--).....----. ( -28.10)
>consensus
GCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUAAGGGCUUUUCCAUUUAGCGCAGAUAGA__CAUUCA____G
((((.....((((((....))))))(((((((((((((((.........)))))))))))))))))))..(((((......)))))................................. (-23.20 = -22.62 +  -0.58)

alignment

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secondary structure

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Window 5

Location 15,120,867 – 15,120,960
Length 93
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 82.77
Mean single sequence MFE -20.12
Consensus MFE -13.28
Energy contribution -13.34
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.97
Structure conservation index 0.66
SVM decision value 0.77
SVM RNA-class probability 0.847001
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15120867 93 + 27905053
UCAACGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGACUGCUGUUC------ACUCUCGG
..((((((....(((....((((((((((.............))))))))))...((((((....)))))))))....)))))).------........ ( -19.22)
>DroVir_CAF1 54107 91 + 1
UUAACAGCUUGGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUCCGCUCGCUGCGCUGCCAA--------
....((((.(((((.....((((((((((.............))))))))))...((((((....))))))...)))))....))))....-------- ( -19.92)
>DroPse_CAF1 51319 82 + 1
UCAACAGCUUAGGCAAACAUUUGCAAUUACAAGUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUC-----------------
....(((((...(((....((((((((((...(.....)...))))))))))...((((((....))))))))))))))...----------------- ( -18.40)
>DroGri_CAF1 65503 88 + 1
UUUACAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACAAUUUUAUCGCCGUUCGCUGCUC------GCU-----
....((((...(((.....((((((((((.............))))))))))...((((((....)))))))))....))))...------...----- ( -21.12)
>DroMoj_CAF1 54071 94 + 1
UUUGCAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCGCCGCUCGUUGCGCCGCCAAGCA-----
......((((.(((.....((((((((((.............))))))))))...((((((....))))))(.(((.....))).)))))))).----- ( -24.22)
>DroPer_CAF1 47898 82 + 1
UCAACAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUC-----------------
....(((((...(((....((((((((((.............))))))))))...((((((....))))))))))))))...----------------- ( -17.82)
>consensus
UCAACAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUCCGCCCGCUGC_C______________
....((((...........((((((((((.............))))))))))...((((((....)))))).......))))................. (-13.28 = -13.34 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,120,867 – 15,120,960
Length 93
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 82.77
Mean single sequence MFE -28.03
Consensus MFE -20.07
Energy contribution -20.90
Covariance contribution 0.83
Combinations/Pair 1.08
Mean z-score -4.02
Structure conservation index 0.72
SVM decision value 1.41
SVM RNA-class probability 0.951295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15120867 93 - 27905053
CCGAGAGU------GAACAGCAGUCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGA
...((.(.------.(((.((....)).((((((....))))))..(((((((((((((.........))))))))))))))))..))).......... ( -22.80)
>DroVir_CAF1 54107 91 - 1
--------UUGGCAGCGCAGCGAGCGGAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCCAAGCUGUUAA
--------.(((((((...((((((...((((((....))))))..(((((((((((((.........)))))))))))))))))))....))))))). ( -32.50)
>DroPse_CAF1 51319 82 - 1
-----------------GAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAACUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGA
-----------------.((((((.(((((((((....))))))(((((((((((((((.........))))))))))))))).)))....)))))).. ( -25.70)
>DroGri_CAF1 65503 88 - 1
-----AGC------GAGCAGCGAACGGCGAUAAAAUUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUAAA
-----...------..(((((....(((((((((....))))))(((((((((((((((.........)))))))))))))))..)))...)))))... ( -29.20)
>DroMoj_CAF1 54071 94 - 1
-----UGCUUGGCGGCGCAACGAGCGGCGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGCAAA
-----......(((((((.....))(((((((((....))))))(((((((((((((((.........)))))))))))))))..)))...)))))... ( -32.30)
>DroPer_CAF1 47898 82 - 1
-----------------GAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGA
-----------------.((((((.(((((((((....))))))(((((((((((((((.........))))))))))))))).)))....)))))).. ( -25.70)
>consensus
______________G_GCAGCAACCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUAA
................(((((.......((((((....))))))(((((((((((((((.........)))))))))))))))........)))))... (-20.07 = -20.90 +   0.83)

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 12:04:58 2006