Locus 7126

Sequence ID 2L_DroMel_CAF1
Location 19,980,707 – 19,980,853
Length 146
Max. P 0.991362
window11374 window11375 window11376

overview

Window 4

Location 19,980,707 – 19,980,825
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -26.08
Consensus MFE -21.78
Energy contribution -21.80
Covariance contribution 0.02
Combinations/Pair 1.08
Mean z-score -1.29
Structure conservation index 0.84
SVM decision value 0.00
SVM RNA-class probability 0.535142
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19980707 118 - 22407834
AUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUCAGAAUUGUGUGAUGCCGGGCAGUGAUGUGGGGCAGAAACUUAAAAA
....((((((((..(((((((....)))))))((((((.....((((((...........)))))))))))).))).)))))..((((..(((....)))..))))............ ( -29.30)
>DroSec_CAF1 163611 118 - 1
AUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUUGUGUGAUGCCGGGCAGUGAUGUGGGGCAGAAACUUAAAAA
.(((((((((.........((((((((((((.(.(((((((........))))))).).)))).....))))))))..))))).((((..(((....)))..))))....)))).... ( -28.00)
>DroSim_CAF1 166137 117 - 1
AUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAAGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUUGUGUGAUGCCGGGCAGUGAUGUGGGGCAGAAACUUAAAA-
.(((((((((.........((((((((.((((...(((((((.......)))))))......))))..))))))))..))))).((((..(((....)))..))))....))))...- ( -27.00)
>DroEre_CAF1 161750 106 - 1
AUGGGCUCAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUUGUGUGAUGCCG------------UGGCAGAAACUUAAAAA
...(((((((.((......((((((((((((.(.(((((((........))))))).).)))).....)))))))).)).)))).))).------------................. ( -23.00)
>DroYak_CAF1 162622 106 - 1
AUGGGCUCAUUCGUUUUAUUUCUCAGAAUAAGAGGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUUGUGUGAUGCCG------------GGGCAGAAACUUAAAAA
....((((...((((.((.((((((((((((.(.(((((((........))))))).).)))).....)))))))).))...))))...------------))))............. ( -23.10)
>consensus
AUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUUGUGUGAUGCCGGGCAGUGAUGUGGGGCAGAAACUUAAAAA
.((((.....((((..((.(((((((((((((((((.............)))))))))((.....)).)))))))).)).))))((((..(((....)))..))))....)))).... (-21.78 = -21.80 +   0.02)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,980,747 – 19,980,853
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 96.60
Mean single sequence MFE -24.87
Consensus MFE -21.83
Energy contribution -22.03
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.88
SVM decision value 2.26
SVM RNA-class probability 0.991362
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19980747 106 + 22407834
AAUUCUGAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCCUCUCCUUAUUCUGAGAAAUAAAAUGAAUGUGCCCAUUAGCUUGUGCAAACAGACAGGUGGGGAA
.((((.((((((((((((...........)))))))))))).((((........))))........))))...(((((..(..(((....)))..)..)))))... ( -23.80)
>DroSec_CAF1 163651 106 + 1
AAUUCUCAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCCUCUCCUUAUUCUGAGAAAUAAAAUGAAUGUGCCCAUUAGCUUGUGCAAACAGACAGGUGGGGCA
..((((((((((((((((...........)))))))..............)))))))))............(((((....((((((........)))))).))))) ( -26.43)
>DroSim_CAF1 166176 106 + 1
AAUUCUCAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCUUCUCCUUAUUCUGAGAAAUAAAAUGAAUGUGCCCAUUAGCUUGUGUAAACAGACAGGUGGGGCA
..(((((((((...........(((((((.......))))))).......)))))))))............(((((....((((((........)))))).))))) ( -28.07)
>DroEre_CAF1 161778 106 + 1
AAUUCUCAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCCUCUCCUUAUUCUGAGAAAUAAAAUGAAUGAGCCCAUUAGCUUGUGCAAACAGACAGGUGGGGAA
........((((((((((...........))))))))))(((((.(((...(((((....)....((.(..(((......)))..).))..)))).))).))))). ( -23.10)
>DroYak_CAF1 162650 106 + 1
AAUUCUCAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCCUCCUCUUAUUCUGAGAAAUAAAACGAAUGAGCCCAUUAGCUUGUGCAAACAGACAGGUGGGGAA
..((((((((((((((((...........)))))))..............)))))))))..............(((((..(..(((....)))..)..)))))... ( -22.93)
>consensus
AAUUCUCAGAGGCAAAUAACAUAAGAAAAUAUUUGUUUUUCCUCUCCUUAUUCUGAGAAAUAAAAUGAAUGUGCCCAUUAGCUUGUGCAAACAGACAGGUGGGGAA
..((((((((((((((((...........)))))))..............)))))))))..............(((((..(..(((....)))..)..)))))... (-21.83 = -22.03 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,980,747 – 19,980,853
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 96.60
Mean single sequence MFE -22.70
Consensus MFE -20.40
Energy contribution -20.28
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.90
SVM decision value 1.64
SVM RNA-class probability 0.969051
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19980747 106 - 22407834
UUCCCCACCUGUCUGUUUGCACAAGCUAAUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUCAGAAUU
.........((((((((.((....)).)))))))).((((..(((((((....)))))))((((((.....((((((...........)))))))))))).)))). ( -22.10)
>DroSec_CAF1 163651 106 - 1
UGCCCCACCUGUCUGUUUGCACAAGCUAAUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUU
(((((.....(..(((....)))..)....)))))............((((((((((((.(.(((((((........))))))).).)))).....)))))))).. ( -24.30)
>DroSim_CAF1 166176 106 - 1
UGCCCCACCUGUCUGUUUACACAAGCUAAUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAAGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUU
(((((.....(..(((....)))..)....)))))............((((((((.((((...(((((((.......)))))))......))))..)))))))).. ( -23.30)
>DroEre_CAF1 161778 106 - 1
UUCCCCACCUGUCUGUUUGCACAAGCUAAUGGGCUCAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUU
..........(((((((.((....)).))))))).............((((((((((((.(.(((((((........))))))).).)))).....)))))))).. ( -21.90)
>DroYak_CAF1 162650 106 - 1
UUCCCCACCUGUCUGUUUGCACAAGCUAAUGGGCUCAUUCGUUUUAUUUCUCAGAAUAAGAGGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUU
..........(((((((.((....)).))))))).............((((((((((((.(.(((((((........))))))).).)))).....)))))))).. ( -21.90)
>consensus
UUCCCCACCUGUCUGUUUGCACAAGCUAAUGGGCACAUUCAUUUUAUUUCUCAGAAUAAGGAGAGGAAAAACAAAUAUUUUCUUAUGUUAUUUGCCUCUGAGAAUU
...((((...(..(((....)))..)...))))..............(((((((((((((((((.............)))))))))((.....)).)))))))).. (-20.40 = -20.28 +  -0.12)

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 12:28:06 2006