Locus 3854

Sequence ID 3R_DroMel_CAF1
Location 10,503,454 – 10,503,562
Length 108
Max. P 0.842583
window6174 window6175

overview

Window 4

Location 10,503,454 – 10,503,562
Length 108
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 78.61
Mean single sequence MFE -26.22
Consensus MFE -16.66
Energy contribution -18.22
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -1.79
Structure conservation index 0.64
SVM decision value 0.76
SVM RNA-class probability 0.842583
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10503454 108 + 27905053
GACUGCAGCUCGUUCCUGCGCCAUUUGGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCCUC-CGCACUGCA-----CAC-ACUUGAAAACUGCAUCCCCAG
((.(((((.(((....((((((....)))......(((((((.(((.(((.....))).))).)))))))((...-.))...)))-----...-...)))...)))))))..... ( -29.70)
>DroSec_CAF1 152140 106 + 1
GACUGCAGCUCGUUCCUGCGCC-UUUGGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCCUC-CGCACUGCA-----CAC-ACUUCA-AACUGCAUCCCCAG
...(((((..((.....(((((-...)))......(((((((.(((.(((.....))).))).)))))))))...-))..)))))-----...-......-.............. ( -27.20)
>DroSim_CAF1 50064 106 + 1
GACUGCAGCUCGUUCCUGCGCC-UUUGGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCCUC-CACACUGCA-----CAC-ACUUCA-AACUGCAUCCCCAG
((.(((((...((...((((((-...)))......(((((((.(((.(((.....))).))).))))))).....-......)))-----...-))....-..)))))))..... ( -26.20)
>DroEre_CAF1 50486 97 + 1
GACUGCAGCUAGUUCCCGCGCC-UUUAGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCC---------------UCCAC-ACAACA-AGCUGCAUCCCCAG
((.(((((((.(((...((...-....))......(((((((.(((.(((.....))).))).)))))))...---------------.....-..))).-)))))))))..... ( -30.20)
>DroYak_CAF1 50230 112 + 1
GACUGUAGCUAGUUCCUGCGCC-UUUGGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCCCCACACACUCUACACUCCAC-ACUACA-AACUGCAUCCCCAG
((.(((((...((....(((((-...)))......(((((((.(((.(((.....))).))).))))))))).....))...))))).))...-......-.............. ( -25.10)
>DroAna_CAF1 42607 91 + 1
GCUUGCAGU-CG-ACCUGCUCC-UG------------GGGCAUAGUUUGAAUUAUUUAUAAGCUACCCUCGCU-C-UCCACU-CA-----CACCGCCUUA-GCCCCAACCCCCAG
....((((.-..-..))))...-((------------((((.(((((((((....)).))))))).....((.-.-......-..-----....))....-))))))........ ( -18.94)
>consensus
GACUGCAGCUCGUUCCUGCGCC_UUUGGCAUGUAUGAGGGCACCUUCUGAAUUAUUUAUAAGCUGCCCUCGCCUC_CACACUGCA_____CAC_ACUUCA_AACUGCAUCCCCAG
...(((((...........((......))......(((((((.(((.(((.....))).))).))))))).................................)))))....... (-16.66 = -18.22 +   1.56)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 10,503,454 – 10,503,562
Length 108
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -35.27
Consensus MFE -20.58
Energy contribution -22.09
Covariance contribution 1.50
Combinations/Pair 1.20
Mean z-score -1.90
Structure conservation index 0.58
SVM decision value 0.60
SVM RNA-class probability 0.795656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10503454 108 - 27905053
CUGGGGAUGCAGUUUUCAAGU-GUG-----UGCAGUGCG-GAGGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCCAAAUGGCGCAGGAACGAGCUGCAGUC
.((..(((...)))..))...-...-----((((((.((-...(((((((((.(((.............))).)))))))......(((....))))).....)).))))))... ( -37.22)
>DroSec_CAF1 152140 106 - 1
CUGGGGAUGCAGUU-UGAAGU-GUG-----UGCAGUGCG-GAGGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCCAAA-GGCGCAGGAACGAGCUGCAGUC
.......(((((((-((...(-.((-----(((...(((-.....(((((((.(((.............))).))))))).....)))....-.))))).)..)))))))))... ( -38.92)
>DroSim_CAF1 50064 106 - 1
CUGGGGAUGCAGUU-UGAAGU-GUG-----UGCAGUGUG-GAGGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCCAAA-GGCGCAGGAACGAGCUGCAGUC
.......(((((((-((...(-.((-----(((....((-(.(..(((((((.(((.............))).)))))))...)...)))..-.))))).)..)))))))))... ( -39.82)
>DroEre_CAF1 50486 97 - 1
CUGGGGAUGCAGCU-UGUUGU-GUGGA---------------GGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCUAAA-GGCGCGGGAACUAGCUGCAGUC
.......(((((((-..((.(-((...---------------...(((((((.(((.............))).)))))))......((....-.))))).))...)))))))... ( -33.12)
>DroYak_CAF1 50230 112 - 1
CUGGGGAUGCAGUU-UGUAGU-GUGGAGUGUAGAGUGUGUGGGGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCCAAA-GGCGCAGGAACUAGCUACAGUC
(((......))).(-((((((-....(((.....((((.(..((((((((((.(((.............))).)))))))......)))..)-.))))....))).))))))).. ( -34.72)
>DroAna_CAF1 42607 91 - 1
CUGGGGGUUGGGGC-UAAGGCGGUG-----UG-AGUGGA-G-AGCGAGGGUAGCUUAUAAAUAAUUCAAACUAUGCCC------------CA-GGAGCAGGU-CG-ACUGCAAGC
((((((......((-....))(((.-----((-(((...-(-(((.......)))).......))))).)))...)))------------))-)..((((..-..-.)))).... ( -27.80)
>consensus
CUGGGGAUGCAGUU_UGAAGU_GUG_____UGCAGUGCG_GAGGCGAGGGCAGCUUAUAAAUAAUUCAGAAGGUGCCCUCAUACAUGCCAAA_GGCGCAGGAACGAGCUGCAGUC
.......(((((((...............................(((((((.(((.............))).)))))))......(((....))).........)))))))... (-20.58 = -22.09 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:43 2006