Locus 1823

Sequence ID 3L_DroMel_CAF1
Location 5,104,677 – 5,104,830
Length 153
Max. P 0.936452
window2846 window2847 window2848

overview

Window 6

Location 5,104,677 – 5,104,795
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Mean single sequence MFE -29.10
Consensus MFE -21.91
Energy contribution -22.47
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.94
Structure conservation index 0.75
SVM decision value 0.64
SVM RNA-class probability 0.807888
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104677 118 + 23771897
GUUU--UCAGCUGCAAGAUCGUCGUCAGCAUCAUCAAUACUUGCACGAUGACUGGGCAAAAAAAACACUUGGCCUCCGUACCAAUCAUAUGUUGGUUUUUAUACCAUCGCCCAGCCCAAA
....--............(((((((..(((...........))))))))))((((((...........((((........))))......(.((((......)))).)))))))...... ( -27.40)
>DroSec_CAF1 297592 118 + 1
GUUUUUUUAGCUGCAAGAUCGUCGUUAUCAUCAUCGAUACUUGCACGAUGACUGGGCAAA--AAACACUUGGCCUCCGUACCAAUCAUAGGUUGGUUUUUAUACCAUCGCCCAGUCCAAA
.........(.((((((((((..(.......)..)))).)))))))...((((((((...--......((((........)))).....(((.(((......)))))))))))))).... ( -34.00)
>DroSim_CAF1 319270 118 + 1
GUUUUUUUACCUGCAAGAUAGUCGUCAUAAUCAUCGAUACUUGCACGAUGACUGGGCAAA--AAACACUUGGCCUCCGUACCAAUCAUAGGUUGGUUUUUAUACCAUCGCCCAGCCCAAA
.........(.((((((...((((..........)))).)))))).).((.((((((...--......((((........)))).....(((.(((......))))))))))))..)).. ( -27.50)
>DroYak_CAF1 309937 113 + 1
GUUU--UCAGCUGCAAGAUCAUCU---CCAUCGUCGAUACUUGCACGAUGACUGGGCUGA--AAACACUUGGCCUCCGUACCAUUCAUAGAUUGGUUUUUAUACCACAGCCCCACCCAAA
(((.--((.(.(((((((((..(.---.....)..))).))))))))).))).((((((.--.......(((........))).........((((......))))))))))........ ( -27.50)
>consensus
GUUU__UCAGCUGCAAGAUCGUCGUCAUCAUCAUCGAUACUUGCACGAUGACUGGGCAAA__AAACACUUGGCCUCCGUACCAAUCAUAGGUUGGUUUUUAUACCAUCGCCCAGCCCAAA
......(((.(((((((...((((..........)))).)))))).).)))((((((............(((........))).........((((......))))..))))))...... (-21.91 = -22.47 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,104,677 – 5,104,795
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -35.17
Consensus MFE -33.42
Energy contribution -32.80
Covariance contribution -0.62
Combinations/Pair 1.23
Mean z-score -1.79
Structure conservation index 0.95
SVM decision value 1.25
SVM RNA-class probability 0.936452
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104677 118 - 23771897
UUUGGGCUGGGCGAUGGUAUAAAAACCAACAUAUGAUUGGUACGGAGGCCAAGUGUUUUUUUUGCCCAGUCAUCGUGCAAGUAUUGAUGAUGCUGACGACGAUCUUGCAGCUGA--AAAC
....((((((((((((((......))))((((....(((((......))))))))).....)))))))))).(((((((((.((((.((.......)).))))))))))..)))--.... ( -35.70)
>DroSec_CAF1 297592 118 - 1
UUUGGACUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU--UUUGCCCAGUCAUCGUGCAAGUAUCGAUGAUGAUAACGACGAUCUUGCAGCUAAAAAAAC
....((((((((((((((......))))........(((((......)))))......--.))))))))))....((((((.((((.((.......)).))))))))))........... ( -37.90)
>DroSim_CAF1 319270 118 - 1
UUUGGGCUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU--UUUGCCCAGUCAUCGUGCAAGUAUCGAUGAUUAUGACGACUAUCUUGCAGGUAAAAAAAC
....((((((((((((((......))))........(((((......)))))......--.))))))))))..(.(((((((((((..........))).)).)))))).)......... ( -34.90)
>DroYak_CAF1 309937 113 - 1
UUUGGGUGGGGCUGUGGUAUAAAAACCAAUCUAUGAAUGGUACGGAGGCCAAGUGUUU--UCAGCCCAGUCAUCGUGCAAGUAUCGACGAUGG---AGAUGAUCUUGCAGCUGA--AAAC
(((.(((.((((((((((......)))).........((((......)))).......--.))))))........((((((.((((.(.....---.).))))))))))))).)--)).. ( -32.20)
>consensus
UUUGGGCUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU__UUUGCCCAGUCAUCGUGCAAGUAUCGAUGAUGAUGACGACGAUCUUGCAGCUAA__AAAC
....((((((((((((((......))))........(((((......))))).........))))))))))....((((((.((((.((.......)).))))))))))........... (-33.42 = -32.80 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,104,715 – 5,104,830
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.56
Mean single sequence MFE -30.58
Consensus MFE -27.34
Energy contribution -26.78
Covariance contribution -0.56
Combinations/Pair 1.19
Mean z-score -1.69
Structure conservation index 0.89
SVM decision value 0.77
SVM RNA-class probability 0.846483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104715 115 - 23771897
AAAUCAAUAAAAGUUA-----AGCUAAACGACGGAACCAUUUUGGGCUGGGCGAUGGUAUAAAAACCAACAUAUGAUUGGUACGGAGGCCAAGUGUUUUUUUUGCCCAGUCAUCGUGCAA
................-----.((...((((((((.....))))((((((((((((((......))))((((....(((((......))))))))).....)))))))))).)))))).. ( -30.60)
>DroSec_CAF1 297632 113 - 1
AAAUCAAUAAAAGUAA-----AGCUAAAGGACGGAACCAUUUUGGACUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU--UUUGCCCAGUCAUCGUGCAA
................-----.......(.((((...(.....)((((((((((((((......))))........(((((......)))))......--.)))))))))).)))).).. ( -29.60)
>DroSim_CAF1 319310 113 - 1
AAAUCAAUAAAAGUAA-----AGCUAAACGACGGAACCAUUUUGGGCUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU--UUUGCCCAGUCAUCGUGCAA
................-----.((...((((((((.....))))((((((((((((((......))))........(((((......)))))......--.)))))))))).)))))).. ( -30.20)
>DroYak_CAF1 309972 118 - 1
GAAUCAAUAAAAGUAAAGUUGAGCUAAGCGAUGGAACCAUUUUGGGUGGGGCUGUGGUAUAAAAACCAAUCUAUGAAUGGUACGGAGGCCAAGUGUUU--UCAGCCCAGUCAUCGUGCAA
...(((((.........)))))((...(((((((.(((......))).((((((((((......)))).........((((......)))).......--.))))))..))))))))).. ( -31.90)
>consensus
AAAUCAAUAAAAGUAA_____AGCUAAACGACGGAACCAUUUUGGGCUGGGCGAUGGUAUAAAAACCAACCUAUGAUUGGUACGGAGGCCAAGUGUUU__UUUGCCCAGUCAUCGUGCAA
......................((...((((.(....)......((((((((((((((......))))........(((((......))))).........)))))))))).)))))).. (-27.34 = -26.78 +  -0.56)

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 10:17:41 2006