Locus 2437

Sequence ID 3R_DroMel_CAF1
Location 6,772,675 – 6,772,904
Length 229
Max. P 0.720500
window3977 window3978 window3979 window3980

overview

Window 7

Location 6,772,675 – 6,772,795
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.36
Mean single sequence MFE -19.65
Consensus MFE -19.65
Energy contribution -19.65
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 1.00
SVM decision value 0.09
SVM RNA-class probability 0.580831
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6772675 120 - 27905053
GGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUGUCGCAAAACAAACAAUGACGCAUACAAUUUAUAUUUAAUUAUGCGCAAAUUAGUCUGCUCUACCCUCGCACACACACACA
((((((((..........................(((.....)))..........((.((((((....(((....))).)))))))).....).)))))))................... ( -19.50)
>DroSec_CAF1 36925 119 - 1
GGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUGUCGCAAAACAAACAAUGACGCAUACAAUUUAUAUUUAAUUAUGCGCAAAUUAGUCUGCUCUACCCUCGCGCACACACAG-
((((((((..........................(((.....)))..........((.((((((....(((....))).)))))))).....).)))))))..................- ( -19.50)
>DroEre_CAF1 21938 120 - 1
GGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUGUAGCAAAACAAACAAUGACGCAUACAAUUUAUAUUUAAUUAUGCGCAAAUUAGUCUGCUCUACCCCCGCACACACACACA
((((((((..........................(((.....)))..........((.((((((....(((....))).)))))))).....).)))))))................... ( -19.80)
>DroYak_CAF1 34079 120 - 1
GGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUGUAGCAAAACAAACAAUGACGCAUACAAUUUAUAUUUAAUUAUGCGCAAAUUAGUCUGCUCUACCCUCACACACACACACA
((((((((..........................(((.....)))..........((.((((((....(((....))).)))))))).....).)))))))................... ( -19.80)
>consensus
GGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUGUAGCAAAACAAACAAUGACGCAUACAAUUUAUAUUUAAUUAUGCGCAAAUUAGUCUGCUCUACCCUCGCACACACACACA
((((((((..........................(((.....)))..........((.((((((....(((....))).)))))))).....).)))))))................... (-19.65 = -19.65 +   0.00)

alignment

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secondary structure

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Window 8

Location 6,772,715 – 6,772,826
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -30.55
Consensus MFE -23.88
Energy contribution -23.88
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.78
SVM decision value 0.40
SVM RNA-class probability 0.720500
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6772715 111 + 27905053
AAUUAAAUAUAAAUUGUAUGCGUCAUUGUUUGUUUUGCGACAAGCAUUGGGCGUAAAUAUAUUAAAGAAAUUGCUGCUCCUCCAGCACGUUACGUAUACGCCAUGU---------AUGCC
...............((((((((((.((((((((....)))))))).))((((((.................((((......))))(((...))).))))))))))---------)))). ( -29.80)
>DroSec_CAF1 36964 111 + 1
AAUUAAAUAUAAAUUGUAUGCGUCAUUGUUUGUUUUGCGACAAGCAUUGGGCGUAAAUAUAUUAAAGAAAUUGCUGCUCCUCCAGCACGUUACGUAUACGCCAUGU---------AUGCC
...............((((((((((.((((((((....)))))))).))((((((.................((((......))))(((...))).))))))))))---------)))). ( -29.80)
>DroEre_CAF1 21978 111 + 1
AAUUAAAUAUAAAUUGUAUGCGUCAUUGUUUGUUUUGCUACAAGCAUUGGGCGUAAAUAUAUUAAAGAAAUUGCUGCUCCUCCAGCACGUUACGUAUACGCCAUGU---------AUGCC
...............((((((((((.(((((((......))))))).))((((((.................((((......))))(((...))).))))))))))---------)))). ( -29.40)
>DroYak_CAF1 34119 120 + 1
AAUUAAAUAUAAAUUGUAUGCGUCAUUGUUUGUUUUGCUACAAGCAUUGGGCGUAAAUAUAUUAAAGAAAUUGCUGCUCCUCCAGCACAUUACGUAUACGCCAUGUAUACGACGUAUGCC
.......((((..((((((((((((.(((((((......))))))).))((((((.........((....))((((......))))..........))))))))))))))))..)))).. ( -33.20)
>consensus
AAUUAAAUAUAAAUUGUAUGCGUCAUUGUUUGUUUUGCGACAAGCAUUGGGCGUAAAUAUAUUAAAGAAAUUGCUGCUCCUCCAGCACGUUACGUAUACGCCAUGU_________AUGCC
...................((((((.(((((((......))))))).))((((((.................((((......))))((.....)).)))))).............)))). (-23.88 = -23.88 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,772,755 – 6,772,865
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.51
Mean single sequence MFE -31.05
Consensus MFE -25.21
Energy contribution -26.02
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.38
Structure conservation index 0.81
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6772755 110 - 27905053
CAAGUAAAACAAAACUGCAGUGCACUGCAGU-UGCGCGGCGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGAGGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUG
((((((......((((((((....)))))))-)..(.((((((((---------.....(((....)))...))))((((((((......)))))))).........)))))..)))))) ( -33.20)
>DroSec_CAF1 37004 110 - 1
CAAGUAAAACAAAACUCCAGUGCACUGCAGU-UGCGCGGCGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGAGGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUG
((((((........((((((..(......((-((((..(((.((.---------...)).)))...)))))))..))))))(.((.......................)).)..)))))) ( -28.70)
>DroEre_CAF1 22018 105 - 1
CAAGUAAAACAAAACUGCAC-----UGCAGC-UGCGCGACGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGAGGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUG
((((((.........(((..-----.)))((-(((.(..((((((---------.....(((....)))...))))))..)..)))))..........................)))))) ( -26.60)
>DroYak_CAF1 34159 115 - 1
CAAGUAAAACAAAACUGCAG-----UGCAGUUUGCGCGGCGGCAUACGUCGUAUACAUGGCGUAUACGUAAUGUGCUGGAGGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUG
((((((.....(((((((..-----.)))))))..(.(((((((((...(((((((.....)))))))...)))))((((((((......)))))))).........)))))..)))))) ( -35.70)
>consensus
CAAGUAAAACAAAACUGCAG_____UGCAGU_UGCGCGGCGGCAU_________ACAUGGCGUAUACGUAACGUGCUGGAGGAGCAGCAAUUUCUUUAAUAUAUUUACGCCCAAUGCUUG
((((((.......(((((((....))))))).((.((((((.(((...........))).)))..........(((((......)))))..................))).)).)))))) (-25.21 = -26.02 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,772,795 – 6,772,904
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.71
Mean single sequence MFE -31.25
Consensus MFE -20.52
Energy contribution -21.34
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6772795 109 - 27905053
UGGCAAAAAGGACAAA-AAACGGGGCUAAACCAGCGGUGCCAAGUAAAACAAAACUGCAGUGCACUGCAGU-UGCGCGGCGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGA
((((.....(......-...)...))))..(((((.(((((...........((((((((....)))))))-)((...)))))))---------.....((((.......))))))))). ( -32.90)
>DroSec_CAF1 37044 109 - 1
UCGCAAAAAGGACAAA-AAACGGGGCUAAAACAGCGGUGCCAAGUAAAACAAAACUCCAGUGCACUGCAGU-UGCGCGGCGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGA
................-...(((.((.......((((((((.(((........)))...).))))))).((-((((..(((.((.---------...)).)))...)))))))).))).. ( -30.30)
>DroEre_CAF1 22058 104 - 1
UGGCAAAAAGGACAAA-AAACGGGUCUAAAACAGCGGUGCCAAGUAAAACAAAACUGCAC-----UGCAGC-UGCGCGACGGCAU---------ACAUGGCGUAUACGUAACGUGCUGGA
.(((.....((((...-......))))......(((((((..(((........)))))))-----))).))-)((((((((..((---------((.....)))).)))..))))).... ( -29.10)
>DroYak_CAF1 34199 115 - 1
UGGCAAAAAGGACAAAAAAACGGGGCUAAAACAGCGGUGCCAAGUAAAACAAAACUGCAG-----UGCAGUUUGCGCGGCGGCAUACGUCGUAUACAUGGCGUAUACGUAAUGUGCUGGA
((((.....(..........)...))))...((((.(((((.(((........)))((.(-----(((.....)))).)))))))(((((((((((.....)))))))..)))))))).. ( -32.70)
>consensus
UGGCAAAAAGGACAAA_AAACGGGGCUAAAACAGCGGUGCCAAGUAAAACAAAACUGCAG_____UGCAGU_UGCGCGGCGGCAU_________ACAUGGCGUAUACGUAACGUGCUGGA
...............................((((.(((((..((........(((((((....))))))).......))))))).........((...(((....)))...)))))).. (-20.52 = -21.34 +   0.81)

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 10:36:05 2006