Locus 8206

Sequence ID 3R_DroMel_CAF1
Location 22,033,184 – 22,033,376
Length 192
Max. P 0.999992
window13202 window13203 window13204 window13205

overview

Window 2

Location 22,033,184 – 22,033,278
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 94.94
Mean single sequence MFE -31.40
Consensus MFE -29.66
Energy contribution -29.90
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -3.08
Structure conservation index 0.94
SVM decision value 5.20
SVM RNA-class probability 0.999978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22033184 94 + 27905053
AUCGAUGAAGGGCUGUUUUUUUUU---UUCAGCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
......(((((((((.........---..)))))))))((((..........(((((.(((.....)))))))).....(((.....)))))))... ( -32.60)
>DroSec_CAF1 31487 93 + 1
AUCGAUGAGGGGCUGUUUUU-UUU---UUCAGCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
...((((((((((((.....-...---..)))))).(((((..(((..((..(((((.(((.....)))))))).))..)))..)))))..)))))) ( -33.60)
>DroSim_CAF1 23701 92 + 1
AUCGAUGAGGGGCUGUUUUU--UU---UUCAGCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
...((((((((((((.....--..---..)))))).(((((..(((..((..(((((.(((.....)))))))).))..)))..)))))..)))))) ( -33.70)
>DroEre_CAF1 25438 89 + 1
AUCGAUGAGGGGAUGUUUUU--------UCAGCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
...((((((.(.........--------(((((((...))))))).......(((((.(((.....))))))))...............).)))))) ( -29.50)
>DroYak_CAF1 33041 97 + 1
AUCGAUGAGGGGCUGUUUUUUUUUUUGUUCACCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
...((((((((((.............))))......(((((..(((..((..(((((.(((.....)))))))).))..)))..)))))..)))))) ( -27.62)
>consensus
AUCGAUGAGGGGCUGUUUUU_UUU___UUCAGCUCUUCGAGCUGAUUUAUUUGGCCGGCACACACUGUGCGGCUUGUUUGUCCACUUGACGCUCAUC
......(((((((((..............)))))))))((((..........(((((.(((.....)))))))).....(((.....)))))))... (-29.66 = -29.90 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,033,184 – 22,033,278
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 94.94
Mean single sequence MFE -28.66
Consensus MFE -27.78
Energy contribution -27.82
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -3.46
Structure conservation index 0.97
SVM decision value 5.67
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22033184 94 - 27905053
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGCUGAA---AAAAAAAAACAGCCCUUCAUCGAU
((((((((((.....)))......(((((((.....))).))))...........))))((((.((((..---.........)))).)))))))... ( -29.80)
>DroSec_CAF1 31487 93 - 1
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGCUGAA---AAA-AAAAACAGCCCCUCAUCGAU
((((((.(((.....)))......(((((((.....))).))))........(((((((...))))))).---...-...........))))))... ( -29.50)
>DroSim_CAF1 23701 92 - 1
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGCUGAA---AA--AAAAACAGCCCCUCAUCGAU
((((((.(((.....)))......(((((((.....))).))))........(((((((...))))))).---..--...........))))))... ( -29.50)
>DroEre_CAF1 25438 89 - 1
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGCUGA--------AAAAACAUCCCCUCAUCGAU
((((((.(((.....)))......(((((((.....))).))))........(((((((...)))))))--------...........))))))... ( -29.50)
>DroYak_CAF1 33041 97 - 1
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGGUGAACAAAAAAAAAAACAGCCCCUCAUCGAU
((((((.(((.....)))......(((((((.....))).))))........(((.(((...))).)))...................))))))... ( -25.00)
>consensus
GAUGAGCGUCAAGUGGACAAACAAGCCGCACAGUGUGUGCCGGCCAAAUAAAUCAGCUCGAAGAGCUGAA___AAA_AAAAACAGCCCCUCAUCGAU
((((((.(((.....)))......(((((((.....))).))))........(((((((...)))))))...................))))))... (-27.78 = -27.82 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,033,278 – 22,033,376
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.38
Mean single sequence MFE -23.25
Consensus MFE -17.18
Energy contribution -17.32
Covariance contribution 0.14
Combinations/Pair 1.20
Mean z-score -1.50
Structure conservation index 0.74
SVM decision value 0.31
SVM RNA-class probability 0.683721
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22033278 98 + 27905053
ACGUUUGGCUAUUAAGGCCAUUAACACUUCCAGUCUUCUGGCCCCCGACUCUCCUUUUAUCGCCGGCCUUUUGACUUGGUUUCGCUUUUACGGCUAUU----------------------
..((((((((.....)))))..)))....((((((....((((..(((...........)))..))))....))).)))....(((.....)))....---------------------- ( -23.70)
>DroPse_CAF1 96163 116 + 1
ACGUUUGGCUAUUAAGGCCAUUAACACCUCCGCUCAUC---CCCACAACAAUC-UCUCGGUCUCAGCCUUUUGACUUGGUUUCGUUUUUAUGGUUACUUGCCUGGCUGUAGCUUGUUAUA
..((((((((.....)))))..))).............---.....(((((.(-(..(((((..((((.........))))..........(((.....))).))))).)).)))))... ( -20.80)
>DroSec_CAF1 31580 98 + 1
ACGUUUGGCUAUUGAGGCCAUUAACACUUCCAGUCUUCUGGCCCCCGACUCUCCGCUUAUCGCCGGCCUUUUGACUUGGUUUUGUCUUUACGGCUAUU----------------------
.(((.(((((.....)))))...(((...((((((....((((..(((...........)))..))))....))).)))...)))....)))......---------------------- ( -24.30)
>DroSim_CAF1 23793 97 + 1
ACGUUUGGCUAUUAGGGCCAUUAACACUUCCAGUCUUCUGGCC-CCGACUCUCCUCUUAUCGCCGGCCUUUCGACUUGGUUUCGUCUUUACGGCUAUU----------------------
..((((((((.....)))))..)))....((((((....((((-.(((...........)))..))))....))).)))....(((.....)))....---------------------- ( -21.70)
>DroEre_CAF1 25527 97 + 1
ACGUUUGGCUAUUAAGGCCAUUAACACUUCCAGUCUUCUGGCCCCCGACUUUCCUCUUAGCGCCGGCCUUUUGACUUGGUUUCGUUUUUACGGCU-UU----------------------
..((((((((.....)))))..)))....((((((....((((..((.((........))))..))))....))).)))..((((....))))..-..---------------------- ( -24.70)
>DroYak_CAF1 33138 97 + 1
ACGUUUGGCUAUUAAGGCCAUUAACACUUCCAGUCUUCUGGCCCCCGACUUUCCUCUCAGCGCCGGCCUUUUGACUUGGUUUCGUUUUUGCGGCU-UU----------------------
..((((((((.....)))))..)))....((((((....((((..((.((........))))..))))....))).)))..((((....))))..-..---------------------- ( -24.30)
>consensus
ACGUUUGGCUAUUAAGGCCAUUAACACUUCCAGUCUUCUGGCCCCCGACUCUCCUCUUAGCGCCGGCCUUUUGACUUGGUUUCGUUUUUACGGCUAUU______________________
.(((.(((((.....))))).........((((((....((((..((.............))..))))....))).)))..........)))............................ (-17.18 = -17.32 +   0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,033,278 – 22,033,376
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.38
Mean single sequence MFE -25.42
Consensus MFE -17.39
Energy contribution -17.50
Covariance contribution 0.11
Combinations/Pair 1.32
Mean z-score -1.53
Structure conservation index 0.68
SVM decision value 0.19
SVM RNA-class probability 0.627510
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22033278 98 - 27905053
----------------------AAUAGCCGUAAAAGCGAAACCAAGUCAAAAGGCCGGCGAUAAAAGGAGAGUCGGGGGCCAGAAGACUGGAAGUGUUAAUGGCCUUAAUAGCCAAACGU
----------------------....(((((...((((...(((.(((....((((..((((.........))))..))))....))))))...)))).)))))................ ( -24.80)
>DroPse_CAF1 96163 116 - 1
UAUAACAAGCUACAGCCAGGCAAGUAACCAUAAAAACGAAACCAAGUCAAAAGGCUGAGACCGAGA-GAUUGUUGUGGG---GAUGAGCGGAGGUGUUAAUGGCCUUAAUAGCCAAACGU
((((((((.((.(((((.((.......))........((.......))....)))))))..(....-).)))))))).(---..((.((.(((((.......)))))....))))..).. ( -23.60)
>DroSec_CAF1 31580 98 - 1
----------------------AAUAGCCGUAAAGACAAAACCAAGUCAAAAGGCCGGCGAUAAGCGGAGAGUCGGGGGCCAGAAGACUGGAAGUGUUAAUGGCCUCAAUAGCCAAACGU
----------------------....(((.....(((........)))....))).(((......(((....)))(((((((...(((.......)))..)))))))....)))...... ( -26.90)
>DroSim_CAF1 23793 97 - 1
----------------------AAUAGCCGUAAAGACGAAACCAAGUCGAAAGGCCGGCGAUAAGAGGAGAGUCGG-GGCCAGAAGACUGGAAGUGUUAAUGGCCCUAAUAGCCAAACGU
----------------------....(((.....(((........)))....))).((((((.........)))((-(((((...(((.......)))..)))))))....)))...... ( -29.10)
>DroEre_CAF1 25527 97 - 1
----------------------AA-AGCCGUAAAAACGAAACCAAGUCAAAAGGCCGGCGCUAAGAGGAAAGUCGGGGGCCAGAAGACUGGAAGUGUUAAUGGCCUUAAUAGCCAAACGU
----------------------..-.(((((...((((...(((.(((....((((..((((........)).))..))))....))))))...)))).)))))................ ( -23.50)
>DroYak_CAF1 33138 97 - 1
----------------------AA-AGCCGCAAAAACGAAACCAAGUCAAAAGGCCGGCGCUGAGAGGAAAGUCGGGGGCCAGAAGACUGGAAGUGUUAAUGGCCUUAAUAGCCAAACGU
----------------------..-...........................(((((((.((....))...))))(((((((...(((.......)))..)))))))....)))...... ( -24.60)
>consensus
______________________AAUAGCCGUAAAAACGAAACCAAGUCAAAAGGCCGGCGAUAAGAGGAGAGUCGGGGGCCAGAAGACUGGAAGUGUUAAUGGCCUUAAUAGCCAAACGU
..........................(((((...((((...(((.(((....(((((((............)))...))))....))))))...)))).)))))................ (-17.39 = -17.50 +   0.11)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:16 2006