Locus 70

Sequence ID 2R_DroMel_CAF1
Location 1,323,012 – 1,323,212
Length 200
Max. P 0.908858
window133 window134 window135 window136

overview

Window 3

Location 1,323,012 – 1,323,132
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.94
Mean single sequence MFE -40.92
Consensus MFE -27.28
Energy contribution -30.04
Covariance contribution 2.76
Combinations/Pair 1.08
Mean z-score -3.53
Structure conservation index 0.67
SVM decision value 1.06
SVM RNA-class probability 0.908858
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1323012 120 + 20766785
AUGGGUGUCCCGGCCACAUGUGCUCGUGUGUGCUGUUGCAUGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUA
...(((.(((((((((((((....)))))).)))..(((((.(((....))))))))......)))).)))((((((((((((...(((((.....)))))..))))).))))))).... ( -45.40)
>DroSec_CAF1 41585 120 + 1
AUGGUUAUCCCGGCCACAUGUGCGCGUGUGUGCUGUUGCAUGUCCGGGAGGAAUGUAUUAAAUGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUA
..((((.(((((((((((((....)))))).)))..(((((.(((....))))))))......))))))))((((((((((((...(((((.....)))))..))))).))))))).... ( -45.80)
>DroSim_CAF1 20608 120 + 1
AUGGUUAUCCCGGCCACAUGUGCUCGUGUGUGCUGUUGCAUGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUA
..((((.(((((((((((((....)))))).)))..(((((.(((....)))))))).....)))).))))((((((((((((...(((((.....)))))..))))).))))))).... ( -45.60)
>DroEre_CAF1 22899 112 + 1
AUGCCAUACCCGGCCACAUGUGCUCGUGUA-------GCCCACGCGGG-GGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGCGACAAUGUAUUA
........(((....((((.(.(((((((.-------....)))))))-.).))))......)))......(((((((.((((...(((((.....)))))..))))..))))))).... ( -32.70)
>DroYak_CAF1 8971 113 + 1
AUGGUUUUCACAGCCAUAUGUGCUCGUGUA-------GCACACACGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUA
..(((((((......((((((.(((((((.-------....)))))))....))))))......)))))))((((((((((((...(((((.....)))))..))))).))))))).... ( -35.10)
>consensus
AUGGUUAUCCCGGCCACAUGUGCUCGUGUGUGCUGUUGCAUGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUA
..((((.((((....((((...((((.((((((....)))))).))))....))))......)))).))))((((((((((((...(((((.....)))))..)))))).)))))).... (-27.28 = -30.04 +   2.76)

alignment

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secondary structure

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Window 4

Location 1,323,012 – 1,323,132
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.94
Mean single sequence MFE -30.34
Consensus MFE -20.33
Energy contribution -20.29
Covariance contribution -0.04
Combinations/Pair 1.20
Mean z-score -2.66
Structure conservation index 0.67
SVM decision value 0.41
SVM RNA-class probability 0.726294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1323012 120 - 20766785
UAAUACAUUGUCACUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCCUUUAAUACAUUCCUCCCGGACAUGCAACAGCACACACGAGCACAUGUGGCCGGGACACCCAU
.....((((((...(((..(((((.....)))))...)))..)))))).......................((((((.(.(((....)))((((........)))))))))))....... ( -28.90)
>DroSec_CAF1 41585 120 - 1
UAAUACAUUGUCACUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCAUUUAAUACAUUCCUCCCGGACAUGCAACAGCACACACGCGCACAUGUGGCCGGGAUAACCAU
.....((((((...(((..(((((.....)))))...)))..)))))).......................(((((((((((.....((......))...)))))..))))))....... ( -29.40)
>DroSim_CAF1 20608 120 - 1
UAAUACAUUGUCACUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCCUUUAAUACAUUCCUCCCGGACAUGCAACAGCACACACGAGCACAUGUGGCCGGGAUAACCAU
.....((((((...(((..(((((.....)))))...)))..)))))).......................((((((.(.(((....)))((((........)))))))))))....... ( -29.00)
>DroEre_CAF1 22899 112 - 1
UAAUACAUUGUCGCUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCCUUUAAUACAUUCC-CCCGCGUGGGC-------UACACGAGCACAUGUGGCCGGGUAUGGCAU
.....((((((...(((..(((((.....)))))...)))..)))))).................(((.((-((((((((.((-------(.....))).)))))))..))).))).... ( -32.90)
>DroYak_CAF1 8971 113 - 1
UAAUACAUUGUCACUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCCUUUAAUACAUUCCUCCCGUGUGUGC-------UACACGAGCACAUAUGGCUGUGAAAACCAU
.....((((((...(((..(((((.....)))))...)))..))))))...................((((..((((((((((-------(.....)))))))))))..).)))...... ( -31.50)
>consensus
UAAUACAUUGUCACUGCAAUUGACAUUUUGUCAAAUGGCAAUACAAUGCGAUUUCCCCUUUAAUACAUUCCUCCCGGACAUGCAACAGCACACACGAGCACAUGUGGCCGGGAAAACCAU
.....((((((...(((..(((((.....)))))...)))..)))))).......................(((((((((((..................)))))..))))))....... (-20.33 = -20.29 +  -0.04)

alignment

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secondary structure

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Window 5

Location 1,323,052 – 1,323,172
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.92
Mean single sequence MFE -31.84
Consensus MFE -27.40
Energy contribution -28.12
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 0.86
SVM decision value 0.62
SVM RNA-class probability 0.801644
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1323052 120 + 20766785
UGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGUACGGGCACAAUGGAGCGA
(((((((((((((((((.....((.....))((((((((((((...(((((.....)))))..))))).))))))).........)))))...))))))....))))))........... ( -33.50)
>DroSec_CAF1 41625 120 + 1
UGUCCGGGAGGAAUGUAUUAAAUGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGA
(((((((((((((((((......((....))((((((((((((...(((((.....)))))..))))).))))))).........)))))...))))))....))))))........... ( -33.30)
>DroSim_CAF1 20648 120 + 1
UGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGA
(((((((((((((((((.....((.....))((((((((((((...(((((.....)))))..))))).))))))).........)))))...))))))....))))))........... ( -33.50)
>DroEre_CAF1 22932 119 + 1
CACGCGGG-GGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGCGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGCGCACAAUGGAGCGA
..((((((-.(((((((.....((.....))(((((((.((((...(((((.....)))))..))))..))))))).........))))))).)))((((((....))....))))))). ( -31.10)
>DroYak_CAF1 9004 120 + 1
CACACGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCAAGCACGGGCACAAUGGAGCGA
.....((((((((((((.....((.....))((((((((((((...(((((.....)))))..))))).))))))).........))))))).)))))..((.(.(......).).)).. ( -27.80)
>consensus
UGUCCGGGAGGAAUGUAUUAAAGGGGAAAUCGCAUUGUAUUGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGA
.((((((((((((((((......((....))((((((((((((...(((((.....)))))..)))))).)))))).........)))))...))))))....)))))............ (-27.40 = -28.12 +   0.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,323,092 – 1,323,212
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -31.16
Consensus MFE -26.38
Energy contribution -26.50
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.39
Structure conservation index 0.85
SVM decision value 0.21
SVM RNA-class probability 0.634369
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1323092 120 + 20766785
UGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGUACGGGCACAAUGGAGCGAUUUGCCAGCUGUCGAACAGAGGUACAAACAAGGACAUCCA
(((...(((((.....)))))..))).................(.(((.(((((((..((((...((((.(((......))))))).))))..))))))).))))......((....)). ( -28.60)
>DroSec_CAF1 41665 120 + 1
UGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGAUUUGCCAGCUGGCGAACAGAGGUACAAACAAGGAUAUCCA
(((...(((((.....)))))..))).................(.(((.(((((((.(((((...((((.(((......))))))).))))).))))))).))))......((....)). ( -33.70)
>DroSim_CAF1 20688 120 + 1
UGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGAUUUGCCAGCUGGCGAACAGAGGUACAAACAAGGAUAUCCA
(((...(((((.....)))))..))).................(.(((.(((((((.(((((...((((.(((......))))))).))))).))))))).))))......((....)). ( -33.70)
>DroEre_CAF1 22971 120 + 1
UGCCAUUUGACAAAAUGUCAAUUGCAGCGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGCGCACAAUGGAGCGAUUUGCCAGCUGCCGAGCAGAGGCAGCAACAAGGAUAUCCA
(((...(((((.....)))))..)))..(((((((((........)))).))))).(((.(((..(((........)))...)))..((((((.......)))))).....)))...... ( -33.30)
>DroYak_CAF1 9044 120 + 1
UGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCAAGCACGGGCACAAUGGAGCGAUUUGCCAGCUGCCGAACAGAGGUUCAAUCAAGGACAUCCA
(((...(((((.....)))))..))).....((((((........))))))(((((...(((...((((.(((......))))))).)))...)))))((.((((......)))).)).. ( -26.50)
>consensus
UGCCAUUUGACAAAAUGUCAAUUGCAGUGACAAUGUAUUAAAAGCUACAUUUGUUCUCCAGCACGGGCACAAUGGAGCGAUUUGCCAGCUGCCGAACAGAGGUACAAACAAGGAUAUCCA
((((..(((((.....))))).((((.......))))............(((((((..((((...((((.(((......))))))).))))..))))))))))).......((....)). (-26.38 = -26.50 +   0.12)

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 09:25:34 2006