Locus 199

Sequence ID 3R_DroMel_CAF1
Location 859,815 – 860,095
Length 280
Max. P 0.866192
window343 window344 window345 window346

overview

Window 3

Location 859,815 – 859,935
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.61
Mean single sequence MFE -36.41
Consensus MFE -32.38
Energy contribution -33.88
Covariance contribution 1.50
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.89
SVM decision value 0.61
SVM RNA-class probability 0.798787
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 859815 120 - 27905053
GGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAAAUAUGUAGGAAAUUAAGCUCACAGGCUCAACAACUUGCUC
(((((((..((((......(((((((.....((((((....)))))).(((.((....))....)))..))))))).......(((..(........)..))).))))..)))..)))). ( -37.10)
>DroSec_CAF1 34598 120 - 1
GGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGCGACCCUUCUCAAAAUAUGUAUGAAAUUAAGCUCACAGGCUCAACAACUUGCUC
(((((((..((((.((...(((((((.....((((((....)))))).........((.(....).)).)))))))...........(((........))).))))))..)))..)))). ( -37.00)
>DroSim_CAF1 33782 120 - 1
GGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAAAUAUGUAUGAAAUUAAGCCUACAGGCUCAACAACUUGCUC
((((..(((((((((...((...(((.....((((((....)))))).....))).)).(....)))).))))))....................((((....))))........)))). ( -37.80)
>DroEre_CAF1 34772 119 - 1
GGCACUGGAGGACAAUCGCAGA-GGGGCAAAAGCCUCAAAGGGGGCUAACGACUUAUGGGGAAACGUGACCCUUCUCAAAAUAUGUGGGAAAUUAAGCUCACAGGCUCAACAACUUGGCC
(((....(((.......(((((-((((((..((((((....))))))............(....).)).))))))).......((((((........)))))).)).......))).))) ( -33.74)
>consensus
GGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAAAUAUGUAGGAAAUUAAGCUCACAGGCUCAACAACUUGCUC
(((((((..((((......(((((((.....((((((....))))))..........(.(....).)..))))))).......((((((........)))))).))))..)))..)))). (-32.38 = -33.88 +   1.50)

alignment

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secondary structure

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Window 4

Location 859,855 – 859,975
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -36.20
Consensus MFE -32.56
Energy contribution -32.88
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.90
SVM decision value 0.85
SVM RNA-class probability 0.866192
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 859855 120 - 27905053
UGCUAUCAAAGCAAUCAAGUGAACAAAGGACAAGGCCUCUGGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAA
((((.....))))....((((..((.(((......))).)).))))(((((((((...((...(((.....((((((....)))))).....))).)).(....)))).))))))..... ( -37.50)
>DroSec_CAF1 34638 120 - 1
UGCUAUCAAAGCAAUCAAGUGUACAAAGGACAAGGCCUCUGGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGCGACCCUUCUCAAA
..........((..((.(((((.((.(((......))).))))))).))..))......(((((((.....((((((....)))))).........((.(....).)).))))))).... ( -38.90)
>DroSim_CAF1 33822 120 - 1
UGCUAUCAAAGCAAUCAAGUGAACAAAGGACAAGGCCUCUGGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAA
((((.....))))....((((..((.(((......))).)).))))(((((((((...((...(((.....((((((....)))))).....))).)).(....)))).))))))..... ( -37.50)
>DroEre_CAF1 34812 119 - 1
UACUAUCAAAGCAAUCAAGUGAACAAAGGACAAGGCCUCUGGCACUGGAGGACAAUCGCAGA-GGGGCAAAAGCCUCAAAGGGGGCUAACGACUUAUGGGGAAACGUGACCCUUCUCAAA
..........((.....((((..((.(((......))).)).)))).((......))))(((-((((((..((((((....))))))............(....).)).))))))).... ( -30.90)
>consensus
UGCUAUCAAAGCAAUCAAGUGAACAAAGGACAAGGCCUCUGGCAUUGGAGGGCACUAACAGAAGGGGCAAAAGCCUCGAAGGGGGCUAACGACCUAUGGGGAAACGUGACCCUUCUCAAA
((((.....))))....................(.(((((......))))).)......(((((((.....((((((....))))))..........(.(....).)..))))))).... (-32.56 = -32.88 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 859,895 – 860,015
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.96
Mean single sequence MFE -43.57
Consensus MFE -37.97
Energy contribution -38.30
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.87
SVM decision value 0.54
SVM RNA-class probability 0.775092
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 859895 120 + 27905053
UUCGAGGCUUUUGCCCCUUCUGUUAGUGCCCUCCAAUGCCAGAGGCCUUGUCCUUUGUUCACUUGAUUGCUUUGAUAGCAUGGAGGGUACGGUAUCGUGGUGAGGGGUUCGAGGUUCGAG
.(((((.(((..((((((((..(..((((((((((....((((((......))))))..........((((.....))))))))))))))......)..).)))))))..))).))))). ( -50.20)
>DroSec_CAF1 34678 117 + 1
UUCGAGGCUUUUGCCCCUUCUGUUAGUGCCCUCCAAUGCCAGAGGCCUUGUCCUUUGUACACUUGAUUGCUUUGAUAGCAUCAAGGGUACGGAAUCGUGGUGAGGGGUUCGAGGUUC---
...(((.(((..((((((((..(..((((((........((((((......)))))).....(((((.(((.....))))))))))))))......)..).)))))))..))).)))--- ( -38.90)
>DroSim_CAF1 33862 117 + 1
UUCGAGGCUUUUGCCCCUUCUGUUAGUGCCCUCCAAUGCCAGAGGCCUUGUCCUUUGUUCACUUGAUUGCUUUGAUAGCAUCGAGGGUACGGAAUCGUGUUGAGGGGUACGAGGUUC---
...(((.(((.(((((((((.(((.((((((((......((((((......)))))).......(((.(((.....))))))))))))))..))).)....)))))))).))).)))--- ( -41.60)
>consensus
UUCGAGGCUUUUGCCCCUUCUGUUAGUGCCCUCCAAUGCCAGAGGCCUUGUCCUUUGUUCACUUGAUUGCUUUGAUAGCAUCGAGGGUACGGAAUCGUGGUGAGGGGUUCGAGGUUC___
...(((.(((..(((((((.((...(((((((((((((.((((((......))))))..)).)))..((((.....))))..)))))))).....))....)))))))..))).)))... (-37.97 = -38.30 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 859,975 – 860,095
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.44
Mean single sequence MFE -37.33
Consensus MFE -30.53
Energy contribution -32.03
Covariance contribution 1.50
Combinations/Pair 0.97
Mean z-score -2.14
Structure conservation index 0.82
SVM decision value 0.39
SVM RNA-class probability 0.718069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 859975 120 - 27905053
ACCGCAGUAGUCCUCCUGUGCACCGAAGAGGAAGUAAGCCGGACUACCGUGGAGGGUACCUCGAACCUCGAACCUCGAACCUCGAACCUCGAACCCCUCACCACGAUACCGUACCCUCCA
...((.(((((((..((.(((.((.....))..)))))..))))))).))(((((((((.((((...(((.....)))...))))...(((............)))....))))))))). ( -38.40)
>DroSec_CAF1 34758 106 - 1
ACCGCAGUAGUCCUCCUGUGCACCGAAGGGGAAGUAAGCCGGACUACCGUGGAGGGUACCUCGAACCUC--------------GAACCUCGAACCCCUCACCACGAUUCCGUACCCUUGA
.((((.(((((((..((.(((.((....))...)))))..))))))).))))(((((((.(((.....)--------------))...(((............)))....)))))))... ( -35.60)
>DroSim_CAF1 33942 106 - 1
ACCGCAGUAGUCCUCCUGUGCACCGAAGGGGAAGUAAGCCGGACUACCGUGGAGGGUACCUCGAACCUC--------------GAACCUCGUACCCCUCAACACGAUUCCGUACCCUCGA
..(((.(((((((..((.(((.((....))...)))))..))))))).)))((((((((.(((.....)--------------))...((((..........))))....)))))))).. ( -38.00)
>consensus
ACCGCAGUAGUCCUCCUGUGCACCGAAGGGGAAGUAAGCCGGACUACCGUGGAGGGUACCUCGAACCUC______________GAACCUCGAACCCCUCACCACGAUUCCGUACCCUCGA
.((((.(((((((..((.(((.((....))...)))))..))))))).))))(((((((.((((...(((((........)))))...)))).....((.....))....)))))))... (-30.53 = -32.03 +   1.50)

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 09:37:08 2006