Locus 4693

Sequence ID 2L_DroMel_CAF1
Location 13,486,620 – 13,486,734
Length 114
Max. P 0.986961
window7424 window7425 window7426

overview

Window 4

Location 13,486,620 – 13,486,712
Length 92
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 75.70
Mean single sequence MFE -17.08
Consensus MFE -11.94
Energy contribution -12.28
Covariance contribution 0.34
Combinations/Pair 1.43
Mean z-score -2.30
Structure conservation index 0.70
SVM decision value 2.06
SVM RNA-class probability 0.986961
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13486620 92 - 22407834
UAG-CAAAAUAGAAUGUACAAUUUCGUUGAUUCGUGGAUCCAGAGAAACUCAACGGAUCCAUGAAAUCAUCUUUCAAAACUAA--ACUAUAAUCA
...-....((((((((........))))(((((((((((((.(((...)))...))))))))).))))...............--.))))..... ( -20.40)
>DroSec_CAF1 85386 92 - 1
UAG-CAAAAUAAAAUGUACAAUUUCGUUGAUCCGUGGAUCCGGAAAAACUCAACAGAUCCAUGGAACAAUCUAUCAAAACUAA--UCUAUAAUCA
...-.....................((((.((((((((((.(...........).)))))))))).)))).............--.......... ( -18.40)
>DroSim_CAF1 86963 92 - 1
UAG-CAAAGUAAAAUGUACAAUUUCGAUGAUUCGUGGAUCCUGAGAAACUCAACGGAUCCAUGAAACCAUCUUUCAAAACUAA--ACUAUAAUCG
...-....(((.....)))......((((.(((((((((((((((...))))..)))))))))))..))))............--.......... ( -22.50)
>DroEre_CAF1 90090 92 - 1
AAG-CAAAAUAAAGUGUAUAAUUUCGUUGAUCAGUGGAUCCUGCAAAACUCAAAAGAUCCACGGAACAAUCUCUCACAACUAA--AGUACAAUCC
...-..........(((((..(((.((((....(((((((...............)))))))(((......)))..)))).))--)))))).... ( -15.56)
>DroYak_CAF1 87380 92 - 1
AAG-CAAAUUAAAGUGUAUAAUAUCGUUGAUCCCUGGAUCCUGCAAAAUUCAAUAGAUCCACGGAACAGUCUUUCACAACUAA--AGUCUAAUCC
...-.........(((..........(((.(((.((((((...............)))))).))).))).....)))......--.......... ( -12.32)
>DroAna_CAF1 149395 94 - 1
UAGCCAAACUAAUAUCUAAAAUCUGAUUGAUCCAUGGACAUUUGAAGCAAGAAAUAAUCCAUGUACCAGUCGCUAAAAA-UAAGGAUUAAAAUCC
((((.....((.....))......(((((...((((((.((((........))))..))))))...)))))))))....-...((((....)))) ( -13.30)
>consensus
UAG_CAAAAUAAAAUGUACAAUUUCGUUGAUCCGUGGAUCCUGAAAAACUCAACAGAUCCAUGGAACAAUCUUUCAAAACUAA__ACUAUAAUCC
.........................((((.((((((((((...............)))))))))).))))......................... (-11.94 = -12.28 +   0.34)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,486,643 – 13,486,734
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 77.02
Mean single sequence MFE -18.10
Consensus MFE -11.98
Energy contribution -11.32
Covariance contribution -0.66
Combinations/Pair 1.40
Mean z-score -1.46
Structure conservation index 0.66
SVM decision value 0.63
SVM RNA-class probability 0.803860
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13486643 91 + 22407834
AUGAUUUCAUGGAUCCGUUGAGUUUCUCUGGAUCCACGAAUCAACGAAAUUGUACAUUCUAUUUUGCUAAACACGCACUAAGAC-AAACA-AU
.((((((..((((((((..(.....)..)))))))).)))))).....(((((....(((....(((.......)))...))).-..)))-)) ( -19.70)
>DroPse_CAF1 128518 89 + 1
GUUGAUUCAUGGAUCUGUAGCUGAUCUUAGGGUCCAAGGAUCAACCGAUUAGA--AGUCUAUUU--CCAAACACGCACUAGAACCACACAAAU
((((((((.(((((((..((.....))..))))))).)))))))).((.(((.--...)))..)--).......................... ( -19.00)
>DroSec_CAF1 85409 87 + 1
AUUGUUCCAUGGAUCUGUUGAGUUUUUCCGGAUCCACGGAUCAACGAAAUUGUACAUUUUAUUUUGCUAAACACGCACUAAGAC-----A-AU
.(((.(((.((((((((..((...))..)))))))).))).)))............(((((...(((.......))).))))).-----.-.. ( -18.10)
>DroSim_CAF1 86986 91 + 1
AUGGUUUCAUGGAUCCGUUGAGUUUCUCAGGAUCCACGAAUCAUCGAAAUUGUACAUUUUACUUUGCUAAACACGCACUAAGAC-AAACA-AU
(((((((..(((((((..((((...))))))))))).)))))))....(((((...(((((...(((.......))).))))).-..)))-)) ( -20.10)
>DroEre_CAF1 90113 91 + 1
AUUGUUCCGUGGAUCUUUUGAGUUUUGCAGGAUCCACUGAUCAACGAAAUUAUACACUUUAUUUUGCUUAACACGCACUAAAAC-AAACA-AU
.(((.((.(((((((((...........))))))))).)).)))....................(((.......))).......-.....-.. ( -15.20)
>DroYak_CAF1 87403 91 + 1
ACUGUUCCGUGGAUCUAUUGAAUUUUGCAGGAUCCAGGGAUCAACGAUAUUAUACACUUUAAUUUGCUUAACACGCACCAAAAU-AAACA-AC
..((.(((.(((((((.............))))))).))).)).....................(((.......))).......-.....-.. ( -16.52)
>consensus
AUUGUUCCAUGGAUCUGUUGAGUUUCUCAGGAUCCACGGAUCAACGAAAUUGUACAUUUUAUUUUGCUAAACACGCACUAAAAC_AAACA_AU
.....(((.(((((((.............))))))).)))..................................................... (-11.98 = -11.32 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,486,643 – 13,486,734
Length 91
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 77.02
Mean single sequence MFE -22.35
Consensus MFE -13.01
Energy contribution -13.79
Covariance contribution 0.78
Combinations/Pair 1.38
Mean z-score -1.92
Structure conservation index 0.58
SVM decision value 0.91
SVM RNA-class probability 0.880831
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13486643 91 - 22407834
AU-UGUUU-GUCUUAGUGCGUGUUUAGCAAAAUAGAAUGUACAAUUUCGUUGAUUCGUGGAUCCAGAGAAACUCAACGGAUCCAUGAAAUCAU
((-(((..-.(((...(((.......)))....)))....))))).....((((((((((((((.(((...)))...))))))))).))))). ( -26.50)
>DroPse_CAF1 128518 89 - 1
AUUUGUGUGGUUCUAGUGCGUGUUUGG--AAAUAGACU--UCUAAUCGGUUGAUCCUUGGACCCUAAGAUCAGCUACAGAUCCAUGAAUCAAC
......((((.(((.(((((...((((--((......)--))))).))(((((((.((((...))))))))))))))))).))))........ ( -20.90)
>DroSec_CAF1 85409 87 - 1
AU-U-----GUCUUAGUGCGUGUUUAGCAAAAUAAAAUGUACAAUUUCGUUGAUCCGUGGAUCCGGAAAAACUCAACAGAUCCAUGGAACAAU
..-.-----......((((((.((((......))))))))))......((((.((((((((((.(...........).)))))))))).)))) ( -24.60)
>DroSim_CAF1 86986 91 - 1
AU-UGUUU-GUCUUAGUGCGUGUUUAGCAAAGUAAAAUGUACAAUUUCGAUGAUUCGUGGAUCCUGAGAAACUCAACGGAUCCAUGAAACCAU
..-.....-......((((((.((((......))))))))))...........(((((((((((((((...))))..)))))))))))..... ( -24.30)
>DroEre_CAF1 90113 91 - 1
AU-UGUUU-GUUUUAGUGCGUGUUAAGCAAAAUAAAGUGUAUAAUUUCGUUGAUCAGUGGAUCCUGCAAAACUCAAAAGAUCCACGGAACAAU
((-(((.(-..((((.(((.......)))...))))..).)))))...((((.((.(((((((...............))))))).)).)))) ( -18.16)
>DroYak_CAF1 87403 91 - 1
GU-UGUUU-AUUUUGGUGCGUGUUAAGCAAAUUAAAGUGUAUAAUAUCGUUGAUCCCUGGAUCCUGCAAAAUUCAAUAGAUCCACGGAACAGU
((-(((.(-((((((.(((.......)))...))))))).)))))....(((.(((.((((((...............)))))).))).))). ( -19.66)
>consensus
AU_UGUUU_GUCUUAGUGCGUGUUUAGCAAAAUAAAAUGUACAAUUUCGUUGAUCCGUGGAUCCUGAAAAACUCAACAGAUCCAUGAAACAAU
...............((((((.((((......))))))))))......((((.((((((((((...............)))))))))).)))) (-13.01 = -13.79 +   0.78)

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 11:24:51 2006