Locus 2816

Sequence ID 3L_DroMel_CAF1
Location 8,039,512 – 8,039,684
Length 172
Max. P 0.996713
window4396 window4397 window4398

overview

Window 6

Location 8,039,512 – 8,039,604
Length 92
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -9.41
Consensus MFE -9.24
Energy contribution -9.13
Covariance contribution -0.11
Combinations/Pair 1.13
Mean z-score -1.64
Structure conservation index 0.98
SVM decision value 0.65
SVM RNA-class probability 0.813110
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8039512 92 - 23771897
AUCCCACUUCUGACAAAACCUUU-UUUUAUCCCUUUUAUAUUUAUCUGUCUAAUCAAAUAGCUUAUUUAUUCAAGUUAUUUUGGUCAGUUUUU
.......................-.....................(((.((((...((((((((........)))))))))))).)))..... (  -9.50)
>DroEre_CAF1 10539 92 - 1
AUCCCACUUCUGACAAAACCUUU-UUUUCUACAUUUUGUAUUUAUCCGUCUAAUCAAAUAGCUUAUUUAUUCAAGUUAUUUUGGUCGGUUUUU
............((((((.....-.........))))))......(((.((((...((((((((........)))))))))))).)))..... ( -11.84)
>DroYak_CAF1 10972 93 - 1
AUCCCACUUCUGACAAAUCCUUUUUUUUCUACUUUUUAUAUUUAUCUGUCUAAUCAAAUUGCUUAUUUAUUCAAGUUAUUUUGGUCGGUUUUU
...((......((((...............................))))..((((((..((((........))))...)))))).))..... (  -6.88)
>consensus
AUCCCACUUCUGACAAAACCUUU_UUUUCUACAUUUUAUAUUUAUCUGUCUAAUCAAAUAGCUUAUUUAUUCAAGUUAUUUUGGUCGGUUUUU
.............................................(((.((((...((((((((........)))))))))))).)))..... ( -9.24 =  -9.13 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,039,545 – 8,039,644
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 94.16
Mean single sequence MFE -18.60
Consensus MFE -18.00
Energy contribution -18.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.97
SVM decision value 0.18
SVM RNA-class probability 0.623400
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8039545 99 - 23771897
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU-UUUUAUCCCUUUUAUAUUUAUCUGUCUAAUCAAAUA
((((.......))))((((((...))))))(((((.......)))))....((((........-......................)))).......... ( -18.31)
>DroSec_CAF1 10759 99 - 1
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAGACAUUU-UUUUAUCCUUUUUAUAUUUAUCUAUCUAAUCAAAUA
...(((...(((...((((((...))))))(((((.......)))))....)))..)))....-.................................... ( -19.10)
>DroSim_CAF1 10741 98 - 1
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAGAC-UUU-UUUUAUCCUUUUUAUAUUUAUCUAUCUAAUCAAAUA
...(((...(((...((((((...))))))(((((.......)))))....)))..)))-...-.................................... ( -18.60)
>DroEre_CAF1 10572 99 - 1
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU-UUUUCUACAUUUUGUAUUUAUCCGUCUAAUCAAAUA
.(((.(((((.....((((((...))))))(((((.......))))).)))))..........-.....(((.....)))......)))........... ( -18.70)
>DroYak_CAF1 11005 100 - 1
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAUCCUUUUUUUUCUACUUUUUAUAUUUAUCUGUCUAAUCAAAUU
((((.......))))((((((...))))))(((((.......)))))....((((...............................)))).......... ( -18.28)
>consensus
UGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU_UUUUAUCCUUUUUAUAUUUAUCUGUCUAAUCAAAUA
...((.((((.....((((((...))))))(((((.......))))).)))))).............................................. (-18.00 = -18.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,039,569 – 8,039,684
Length 115
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 96.53
Mean single sequence MFE -36.10
Consensus MFE -36.10
Energy contribution -36.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 1.00
SVM decision value 2.74
SVM RNA-class probability 0.996713
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8039569 115 - 23771897
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU-UUUUAUCCCUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......)))))))))))).........-............ ( -36.10)
>DroSec_CAF1 10783 115 - 1
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAGACAUUU-UUUUAUCCUUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......)))))))))))).........-............ ( -36.10)
>DroSim_CAF1 10765 114 - 1
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAGAC-UUU-UUUUAUCCUUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......)))))))))))).....-...-............ ( -36.10)
>DroEre_CAF1 10596 115 - 1
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU-UUUUCUACAUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......)))))))))))).........-............ ( -36.10)
>DroYak_CAF1 11029 116 - 1
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAUCCUUUUUUUUCUACUUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......))))))))))))...................... ( -36.10)
>consensus
GUUACUUUCAUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAAACCUUU_UUUUAUCCUUUU
............(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......))))))))))))...................... (-36.10 = -36.10 +   0.00)

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 10:42:25 2006