Locus 1828

Sequence ID 3L_DroMel_CAF1
Location 5,126,150 – 5,126,292
Length 142
Max. P 0.847755
window2855 window2856 window2857

overview

Window 5

Location 5,126,150 – 5,126,265
Length 115
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 78.02
Mean single sequence MFE -29.41
Consensus MFE -15.78
Energy contribution -15.84
Covariance contribution 0.06
Combinations/Pair 1.25
Mean z-score -2.07
Structure conservation index 0.54
SVM decision value 0.69
SVM RNA-class probability 0.823059
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5126150 115 + 23771897
CCGGCCAGGUCGAUGGCCACUUUCUUUCCCCGCAGUUCAUUAAUGGGUUUACGUUCACAAUGGGGCGUUAAAACACCCCAUAAUUCCUUGACGCCCAUUUA-AAUAAGCUAAACAA
..(((((......)))))...............((((.((((((((((...........((((((.((....)).))))))...........)))))))..-))).))))...... ( -30.85)
>DroVir_CAF1 3788 113 + 1
CCGGCCAGAUCUAUGGCGACCUUCUUGCCGCGGAGUUCACAUAUUGGCUUUCGCUCAGCAUGUGGCGUUAAGAUGCUCCACAGUUCCUUAACGCCCAUUUA-AU-UAU-UAAACAC
..((((((.((..((((((.....))))))..))(....)...))))))..........(((.(((((((((..(((....)))..))))))))))))...-..-...-....... ( -32.10)
>DroEre_CAF1 3676 115 + 1
CCGGCCAGGUCAAUGGCCACUUUCUUUCCGCGCAGCUCAUUAAUAGGCUUACGUUCACAAUGGGGCGUCAAAACUCCCCAUAAUUCCUUGACGCCCAUUUA-AAUGAACUAAAUAA
..(((((......)))))...............((((........))))...(((((.....(((((((((................))))))))).....-..)))))....... ( -31.19)
>DroYak_CAF1 3706 115 + 1
CCGGCCAGGUCAAUAGCAACUUUCUUUCCUCGCAGUUCGUUAAUGGGUUUACGUUCACAAUGGGGCGUCAAAACUCCCCACAAUUCCUUGACGCCCAUUUA-AAUAAACUAAAUAA
...((.(((..................))).))((((..(((((((((............(((((.((....)).)))))............)))))))..-))..))))...... ( -23.82)
>DroAna_CAF1 3684 116 + 1
CCGGCCAGAUCGAUGGCCACCUUCUUGCCUCGCAGCUCACUAAUGGGCUUCCGCUCGCAGUGAGGGGUUAAAACAGUCCAUAGCUCCUUAACACCCAUUCAAAAUAAAAUAAAUAA
..(((((......))))).(((((((((..((.((((((....))))))..))...)))).)))))(((((...(((.....)))..)))))........................ ( -30.00)
>DroPer_CAF1 2420 113 + 1
CCGGCCAAAUCAAUGGCCACUUUCUUGCCGCGAAGCUCAUUUAUCGGCUUGCGCUCAGCAUGAGGGGUUAAAACUGUCCAAAGUUCUUUUACACCCAUAAA--ACAAU-GAAACAA
..(((((......))))).(((...(((.((((((((........))))).)))...))).)))(((((((((((......)))...)))).)))).....--.....-....... ( -28.50)
>consensus
CCGGCCAGAUCAAUGGCCACUUUCUUGCCGCGCAGCUCAUUAAUGGGCUUACGCUCACAAUGGGGCGUUAAAACUCCCCAUAAUUCCUUGACGCCCAUUUA_AAUAAACUAAACAA
..(((((......)))))...............((((........))))..........(((.((((((((................))))))))))).................. (-15.78 = -15.84 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,126,190 – 5,126,292
Length 102
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 82.40
Mean single sequence MFE -23.78
Consensus MFE -14.86
Energy contribution -16.00
Covariance contribution 1.14
Combinations/Pair 1.17
Mean z-score -2.95
Structure conservation index 0.62
SVM decision value 0.78
SVM RNA-class probability 0.847755
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5126190 102 + 23771897
UAAUGGGUUUACGUUCACAAUGGGGCGUUAAAACACCCCAUAAUUCCUUGACGCCCAUUUAAAUAAGCUAAACAAAAACC--CCGCGAGAAAUUCGCAACAAAU
....((((((.(((.....)))(((((((((................)))))))))...................)))))--).(((((...)))))....... ( -24.19)
>DroVir_CAF1 3828 101 + 1
AUAUUGGCUUUCGCUCAGCAUGUGGCGUUAAGAUGCUCCACAGUUCCUUAACGCCCAUUUAAU-UAU-UAAACACUAAAUUAGCGCGUUAAUUUCAAAACGAG-
..((((((...(((.....(((.(((((((((..(((....)))..)))))))))))).((((-(..-.........)))))))).))))))...........- ( -21.50)
>DroSec_CAF1 3721 102 + 1
UAAUGGGUUUGCGUUCACAAUGGGGCGUCAAAACACCCCAUAAUUCCUUGACGCCCAUUUAAAUAAGCUAGACAGAAACC--CCGCGAAAUAUUCGCAACAAAU
....((((((((..........(((((((((................)))))))))..........)).......)))))--).((((.....))))....... ( -27.05)
>DroSim_CAF1 3750 102 + 1
UAAUGGGCUUGCGUUCACAAUGGGGCGUCAAAACACCCCAUAAUUCCUUUACGCCCAUUUAAAUAAGCUAAACAGAAACC--CCGCGAGAAAUCCGCAACAAAU
.(((((((...........((((((.((....)).))))))...........))))))).....................--..((((....).)))....... ( -24.05)
>DroEre_CAF1 3716 102 + 1
UAAUAGGCUUACGUUCACAAUGGGGCGUCAAAACUCCCCAUAAUUCCUUGACGCCCAUUUAAAUGAACUAAAUAAAAACC--CCGCGCGAAAUUCGCAACAAAU
............(((((.....(((((((((................))))))))).......)))))............--....(((.....)))....... ( -23.59)
>DroYak_CAF1 3746 102 + 1
UAAUGGGUUUACGUUCACAAUGGGGCGUCAAAACUCCCCACAAUUCCUUGACGCCCAUUUAAAUAAACUAAAUAAAAACC--CCGCGAGAAAUUAUCAACAAAU
....((((((.(((.....)))(((((((((................)))))))))...................)))))--)(....)............... ( -22.29)
>consensus
UAAUGGGCUUACGUUCACAAUGGGGCGUCAAAACACCCCAUAAUUCCUUGACGCCCAUUUAAAUAAGCUAAACAAAAACC__CCGCGAGAAAUUCGCAACAAAU
.(((((((...........((((((.((....)).))))))...........))))))).........................(((.......)))....... (-14.86 = -16.00 +   1.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,126,190 – 5,126,292
Length 102
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 82.40
Mean single sequence MFE -31.95
Consensus MFE -18.46
Energy contribution -19.63
Covariance contribution 1.17
Combinations/Pair 1.25
Mean z-score -2.84
Structure conservation index 0.58
SVM decision value 0.54
SVM RNA-class probability 0.775672
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5126190 102 - 23771897
AUUUGUUGCGAAUUUCUCGCGG--GGUUUUUGUUUAGCUUAUUUAAAUGGGCGUCAAGGAAUUAUGGGGUGUUUUAACGCCCCAUUGUGAACGUAAACCCAUUA
......(((((.....)))))(--(((((.((((((((((((....))))))...........(((((((((....)))))))))..)))))).)))))).... ( -36.70)
>DroVir_CAF1 3828 101 - 1
-CUCGUUUUGAAAUUAACGCGCUAAUUUAGUGUUUA-AUA-AUUAAAUGGGCGUUAAGGAACUGUGGAGCAUCUUAACGCCACAUGCUGAGCGAAAGCCAAUAU
-..(((((....(((((.((((((...)))))))))-)).-...)))))((((((((((..((....))..))))))))))......((.((....)))).... ( -27.60)
>DroSec_CAF1 3721 102 - 1
AUUUGUUGCGAAUAUUUCGCGG--GGUUUCUGUCUAGCUUAUUUAAAUGGGCGUCAAGGAAUUAUGGGGUGUUUUGACGCCCCAUUGUGAACGCAAACCCAUUA
.......((((.....))))((--(((((((.....((((((....))))))....))))))..((((((((....))))))))((((....)))).))).... ( -33.70)
>DroSim_CAF1 3750 102 - 1
AUUUGUUGCGGAUUUCUCGCGG--GGUUUCUGUUUAGCUUAUUUAAAUGGGCGUAAAGGAAUUAUGGGGUGUUUUGACGCCCCAUUGUGAACGCAAGCCCAUUA
......(((((.....)))))(--(((((.((((((((((((....))))))...........(((((((((....)))))))))..)))))).)))))).... ( -36.00)
>DroEre_CAF1 3716 102 - 1
AUUUGUUGCGAAUUUCGCGCGG--GGUUUUUAUUUAGUUCAUUUAAAUGGGCGUCAAGGAAUUAUGGGGAGUUUUGACGCCCCAUUGUGAACGUAAGCCUAUUA
...(((.(((.....))))))(--(((((.......((((((......(((((((((((..((....))..)))))))))))....))))))..)))))).... ( -31.10)
>DroYak_CAF1 3746 102 - 1
AUUUGUUGAUAAUUUCUCGCGG--GGUUUUUAUUUAGUUUAUUUAAAUGGGCGUCAAGGAAUUGUGGGGAGUUUUGACGCCCCAUUGUGAACGUAAACCCAUUA
.....................(--(((((.......((((((......(((((((((((..(......)..)))))))))))....))))))..)))))).... ( -26.60)
>consensus
AUUUGUUGCGAAUUUCUCGCGG__GGUUUUUGUUUAGCUUAUUUAAAUGGGCGUCAAGGAAUUAUGGGGUGUUUUGACGCCCCAUUGUGAACGUAAACCCAUUA
......(((((.....)))))...(((((.((((((.........((((((((((((((..((....))..)))))))))).)))).)))))).)))))..... (-18.46 = -19.63 +   1.17)

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 10:17:49 2006