Locus 9931

Sequence ID 3R_DroMel_CAF1
Location 26,580,014 – 26,580,148
Length 134
Max. P 0.898882
window15831 window15832 window15833

overview

Window 1

Location 26,580,014 – 26,580,115
Length 101
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -27.40
Consensus MFE -15.77
Energy contribution -15.39
Covariance contribution -0.39
Combinations/Pair 1.20
Mean z-score -2.05
Structure conservation index 0.58
SVM decision value 0.87
SVM RNA-class probability 0.870289
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26580014 101 + 27905053
AUGGAG-CAUUGAGGAGAUGCAAACUUUUAUUGCGGACUAAAAUGAACUUCCGCU----CGG------GCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU
.....(-((((.....))))).........(((((((.....(((((((((((((----...------.....)))..))))))))))....((....)))))))))..... ( -24.50)
>DroVir_CAF1 209476 96 + 1
ACACGUUCUU--UGG-AAUGCAAACUUUUAUUGUGGGUUAAAAUGAACUUCCGCU----GG--------CUGCAGC-CGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU
...(((((..--..)-))))..(((((.......)))))...(((((((((((((----(.--------...))).-)))))))))))..((((.((......))))))... ( -27.60)
>DroGri_CAF1 339761 87 + 1
-----------GUGG-AAUGCAAACUUUUAUUGUGGGUUAAAAUGAACUUCCGCU----GG--------CUGCAGC-CGGAAGUUCAUAAUUUCAGCUGAUUUGCAAAAACU
-----------(..(-(..((.(((((.......)))))...(((((((((((((----(.--------...))).-))))))))))).......))...))..)....... ( -26.30)
>DroWil_CAF1 195149 110 + 1
ACACGC-CAUUGAAGA-AUGCAAACUUUUAUUGUGGGUUAAAAUGAACUUCCGCUGCUUCGGAGCUCUGCAGCGAAACGGAAGUUCAUAAUUUCAGCUGAUUUGGAAAAGUU
....((-.(((....)-)))).(((((((...((.((((((((((((((((((.((((.(((....))).))))...)))))))))))..))).)))).))....))))))) ( -30.90)
>DroMoj_CAF1 218300 98 + 1
GCACUCUCAUAGUGG-AAUGCAAACUUUUAUUGUGGGUUAAAAUGAACUUCCGCU----AG--------CUGCAGC-CGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU
.....((((((((((-((.......)))))))))))).....(((((((((((((----..--------....)).-)))))))))))..((((.((......))))))... ( -29.20)
>DroAna_CAF1 170553 100 + 1
ACGCA--CAUCGAGGAGAUGCAAACUUUUAUUGCGGACUAAAAUGAACUUCCGCC----CGG------GCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGAGAAAACU
.(.((--.((((..(((((((((.......))))........(((((((((((((----...------.....)))..)))))))))).)))))...)))).)).)...... ( -25.90)
>consensus
ACACA__CAU_GAGG_AAUGCAAACUUUUAUUGUGGGUUAAAAUGAACUUCCGCU____CG________CAGCAGC_CGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU
..................((((((.((.....((.((.....(((((((((((((..................)))..))))))))))....)).)).))))))))...... (-15.77 = -15.39 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 2

Location 26,580,014 – 26,580,115
Length 101
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -24.60
Consensus MFE -14.29
Energy contribution -14.82
Covariance contribution 0.53
Combinations/Pair 1.09
Mean z-score -2.12
Structure conservation index 0.58
SVM decision value 1.01
SVM RNA-class probability 0.898882
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26580014 101 - 27905053
AGUUUUCGCAAAUCAGCUGAAAUUAUGAACUUCCUUGCCAUUGC------CCG----AGCGGAAGUUCAUUUUAGUCCGCAAUAAAAGUUUGCAUCUCCUCAAUG-CUCCAU
.......(((.....((((((...((((((((((..(((.....------..)----.))))))))))))))))))..((((.......))))..........))-)..... ( -23.20)
>DroVir_CAF1 209476 96 - 1
AGUUUUCGCAAAUCAGCUGAAAUUAUGAACUUCCG-GCUGCAG--------CC----AGCGGAAGUUCAUUUUAACCCACAAUAAAAGUUUGCAUU-CCA--AAGAACGUGU
.......((((((............((((((((((-.(((...--------.)----))))))))))))(((((........)))))))))))...-...--.......... ( -23.30)
>DroGri_CAF1 339761 87 - 1
AGUUUUUGCAAAUCAGCUGAAAUUAUGAACUUCCG-GCUGCAG--------CC----AGCGGAAGUUCAUUUUAACCCACAAUAAAAGUUUGCAUU-CCAC-----------
......(((((((............((((((((((-.(((...--------.)----))))))))))))(((((........))))))))))))..-....----------- ( -23.70)
>DroWil_CAF1 195149 110 - 1
AACUUUUCCAAAUCAGCUGAAAUUAUGAACUUCCGUUUCGCUGCAGAGCUCCGAAGCAGCGGAAGUUCAUUUUAACCCACAAUAAAAGUUUGCAU-UCUUCAAUG-GCGUGU
(((((((.....((....))....((((((((((((((((..((...))..))))...)))))))))))).............))))))).((((-.((.....)-).)))) ( -24.80)
>DroMoj_CAF1 218300 98 - 1
AGUUUUCGCAAAUCAGCUGAAAUUAUGAACUUCCG-GCUGCAG--------CU----AGCGGAAGUUCAUUUUAACCCACAAUAAAAGUUUGCAUU-CCACUAUGAGAGUGC
((((((.((......)).))))))(((((((((((-.(((...--------.)----))))))))))))).....................(((((-((.....).)))))) ( -26.20)
>DroAna_CAF1 170553 100 - 1
AGUUUUCUCAAAUCAGCUGAAAUUAUGAACUUCCUUGCCAUUGC------CCG----GGCGGAAGUUCAUUUUAGUCCGCAAUAAAAGUUUGCAUCUCCUCGAUG--UGCGU
...............((.((....((((((((((..(((.....------...----))))))))))))).....)).)).......((..(((((.....))))--))).. ( -26.40)
>consensus
AGUUUUCGCAAAUCAGCUGAAAUUAUGAACUUCCG_GCCGCAG________CG____AGCGGAAGUUCAUUUUAACCCACAAUAAAAGUUUGCAUU_CCAC_AUG__CGUGU
.......((((((............(((((((((..(((..................))))))))))))(((((........)))))))))))................... (-14.29 = -14.82 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,580,053 – 26,580,148
Length 95
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 94.22
Mean single sequence MFE -25.38
Consensus MFE -21.07
Energy contribution -21.10
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.83
SVM decision value 0.48
SVM RNA-class probability 0.752523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26580053 95 + 27905053
AAAUGAACUUCCGCUCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU-UUCGCCACAUUCGCU-GCACCCCCUCCACGAUCC
..(((((((((((((........)))..)))))))))).....((((.(((..(((((....-)))))...))).)))-)................. ( -25.20)
>DroSec_CAF1 163934 95 + 1
AAAUGAACUUCCGCUCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU-UUCGCCACAUUCGCU-GCUCCCCCUCCACGAUCC
..(((((((((((((........)))..)))))))))).....((((.(((..(((((....-)))))...))).)))-)................. ( -25.20)
>DroSim_CAF1 165820 95 + 1
AAAUGAACUUCCGCUCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU-UUCGCCACAUUCGCU-GCUCCCCCUCCACGAUCC
..(((((((((((((........)))..)))))))))).....((((.(((..(((((....-)))))...))).)))-)................. ( -25.20)
>DroEre_CAF1 178122 95 + 1
AAAUGAACUUCCGCUCGGGCGAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU-UUCGCCACAUUCGCU-GCUCCCCCUCCGCGAUCC
..((((((((((......((....))..)))))))))).....((((.(((..(((((....-)))))...))).)))-)................. ( -25.40)
>DroYak_CAF1 173178 92 + 1
AAAUGAACUUCCGCUCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU-UUCGCCACAUUCGCU-GCUCC---UCCACCAUCC
..(((((((((((((........)))..)))))))))).....((((.(((..(((((....-)))))...))).)))-)....---.......... ( -25.20)
>DroAna_CAF1 170591 93 + 1
AAAUGAACUUCCGCCCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGAGAAAACUUUUCGCCACAUUCGCAGGCUCCCCCGCC----UCC
..(((((((((((((........)))..)))))))))).......((.(((.((.(((.....)))..)).))).))((((......)))----).. ( -26.10)
>consensus
AAAUGAACUUCCGCUCGGGCAAUGGCAAGGAAGUUCAUAAUUUCAGCUGAUUUGCGAAAACU_UUCGCCACAUUCGCU_GCUCCCCCUCCACGAUCC
..(((((((((((((........)))..)))))))))).......((.(((..(((((.....)))))...))).)).................... (-21.07 = -21.10 +   0.03)

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 13:45:09 2006