Locus 5093

Sequence ID 2R_DroMel_CAF1
Location 16,550,627 – 16,550,756
Length 129
Max. P 0.986315
window8141 window8142 window8143

overview

Window 1

Location 16,550,627 – 16,550,728
Length 101
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 83.61
Mean single sequence MFE -27.54
Consensus MFE -19.56
Energy contribution -19.45
Covariance contribution -0.11
Combinations/Pair 1.18
Mean z-score -2.81
Structure conservation index 0.71
SVM decision value 0.63
SVM RNA-class probability 0.805730
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16550627 101 + 20766785
GCAUUAGUGCUGCGUAGAAUGCAAUUUACGCAGAAACGCCCAGCAGCGCAAAA-----AAAAAAUAGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAG----
.(((((...(((((((((......)))))))))...(((..((((.((((...-----............))))..))))..)))(((....))).))))).....---- ( -28.06)
>DroSec_CAF1 17399 97 + 1
GCAUUAGUGCUGCGUAGAAUGCAAUUUACGCAGAAAUGCCCAGCAGCGCAAAA-----AAA----AGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAG----
.(((((((((((((((((......)))))(((....)))...)))))))....-----...----...........((((((........))))))))))).....---- ( -28.60)
>DroSim_CAF1 20121 96 + 1
GCAUUAGUGCUGCGUAGAAUGCAAUUUACGCAGAAAUGCCCAGCAGCGCAAAA------AA----AGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAG----
.(((((((((((((((((......)))))(((....)))...)))))))....------..----...........((((((........))))))))))).....---- ( -28.60)
>DroEre_CAF1 17490 95 + 1
GCAUUAGUGCUGCGUAAAAUGCAAUUUACGCAGAAACGCCCGGCAGCGCAAGA-------A----AAAGGUGCGAAUGCAAAGCGGUCUAUUGGCAUAAUGAAAAG----
(((((....(((((((((......)))))))))...(((((.....(....).-------.----...)).))))))))......(((....)))...........---- ( -28.30)
>DroYak_CAF1 18398 97 + 1
GCAUUAGUGCUGCGUAAAAUGCAAUUUACGCAGAAAUGCCCAGCAGCGCAAAA-----AAA----AAAGGUGCGAGUGCAAAACGGUCUAUUGGCAUAAUGAAAAG----
.((((.((((((((((((......)))))(((....)))...)))))))....-----...----....((((.((((..........)))).)))))))).....---- ( -26.80)
>DroAna_CAF1 17207 94 + 1
GCGUUAGUGCUGCGUAAAAUGCAAUUUACGCAGAAACCCCCA-CAGAACAGUACCUCUCAC----AAAGGUGAGAAUGCAAAACGGUCUG-----------AGAAGUACA
......((((((((((((......)))))))...........-.....(((.(((((((((----....)))))).........))))))-----------...))))). ( -24.90)
>consensus
GCAUUAGUGCUGCGUAAAAUGCAAUUUACGCAGAAACGCCCAGCAGCGCAAAA_____AAA____AAAGGUGCGAAUGCAAAGCGGUCUAUUGGCAUAAUGAAAAG____
(((((....(((((((((......)))))))))...(((((...........................)).))))))))......(((....)))............... (-19.56 = -19.45 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,550,627 – 16,550,728
Length 101
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 83.61
Mean single sequence MFE -26.68
Consensus MFE -14.89
Energy contribution -14.47
Covariance contribution -0.42
Combinations/Pair 1.20
Mean z-score -3.01
Structure conservation index 0.56
SVM decision value 0.14
SVM RNA-class probability 0.600983
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16550627 101 - 20766785
----CUUUUCAUUAUGCCAAUAGACCGCUUAGCAUUCGCACCUCUAUUUUUU-----UUUUGCGCUGCUGGGCGUUUCUGCGUAAAUUGCAUUCUACGCAGCACUAAUGC
----.....((((((((....(((.(((((((((..((((............-----...)))).)))))))))..)))(((((..........))))).))).))))). ( -27.16)
>DroSec_CAF1 17399 97 - 1
----CUUUUCAUUAUGCCAAUAGACCGCUUAGCAUUCGCACCUCU----UUU-----UUUUGCGCUGCUGGGCAUUUCUGCGUAAAUUGCAUUCUACGCAGCACUAAUGC
----.....((((((((.........((((((((..((((.....----...-----...)))).)))))))).....((((((..........))))))))).))))). ( -26.00)
>DroSim_CAF1 20121 96 - 1
----CUUUUCAUUAUGCCAAUAGACCGCUUAGCAUUCGCACCUCU----UU------UUUUGCGCUGCUGGGCAUUUCUGCGUAAAUUGCAUUCUACGCAGCACUAAUGC
----.....((((((((.........((((((((..((((.....----..------...)))).)))))))).....((((((..........))))))))).))))). ( -26.10)
>DroEre_CAF1 17490 95 - 1
----CUUUUCAUUAUGCCAAUAGACCGCUUUGCAUUCGCACCUUU----U-------UCUUGCGCUGCCGGGCGUUUCUGCGUAAAUUGCAUUUUACGCAGCACUAAUGC
----.....((((((((....(((.((((..(((..((((.....----.-------...)))).)))..))))..)))(((((((......))))))).))).))))). ( -27.30)
>DroYak_CAF1 18398 97 - 1
----CUUUUCAUUAUGCCAAUAGACCGUUUUGCACUCGCACCUUU----UUU-----UUUUGCGCUGCUGGGCAUUUCUGCGUAAAUUGCAUUUUACGCAGCACUAAUGC
----.....((((((((.........(((..(((..((((.....----...-----...)))).)))..))).....((((((((......))))))))))).))))). ( -23.20)
>DroAna_CAF1 17207 94 - 1
UGUACUUCU-----------CAGACCGUUUUGCAUUCUCACCUUU----GUGAGAGGUACUGUUCUG-UGGGGGUUUCUGCGUAAAUUGCAUUUUACGCAGCACUAACGC
....((((.-----------((((.((...(((.(((((((....----)))))))))).)).))))-.))))(((.(((((((((......)))))))))....))).. ( -30.30)
>consensus
____CUUUUCAUUAUGCCAAUAGACCGCUUAGCAUUCGCACCUCU____UUU_____UUUUGCGCUGCUGGGCAUUUCUGCGUAAAUUGCAUUCUACGCAGCACUAAUGC
........................((((...(((..........................)))...)).))(((((.(((((((.(......).)))))))....))))) (-14.89 = -14.47 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,550,663 – 16,550,756
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 91.60
Mean single sequence MFE -22.14
Consensus MFE -21.48
Energy contribution -20.96
Covariance contribution -0.52
Combinations/Pair 1.16
Mean z-score -1.58
Structure conservation index 0.97
SVM decision value 2.04
SVM RNA-class probability 0.986315
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16550663 93 + 20766785
CGCCCAGCAGCGCAAAAAAAAAAUAGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAGCAGUAACAAUGCAGCAGCAACACCUUGA
(((......))).............((((((....((((.....(((....)))..........(((.......)))))))....)))))).. ( -19.60)
>DroSec_CAF1 17435 89 + 1
UGCCCAGCAGCGCAAAAAAA----AGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAGCGGUAACAAUGCAGCAGCAGCACCUUGA
(((.(....).)))......----.(((((((..(((((((........)))))))........((.(((....))).))....))))))).. ( -23.10)
>DroSim_CAF1 20157 88 + 1
UGCCCAGCAGCGCAAAA-AA----AGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAGCGGUAACAAUGCAGCAGCAGCACCUUGA
(((.(....).)))...-..----.(((((((..(((((((........)))))))........((.(((....))).))....))))))).. ( -23.10)
>DroEre_CAF1 17526 87 + 1
CGCCCGGCAGCGCAAGA--A----AAAGGUGCGAAUGCAAAGCGGUCUAUUGGCAUAAUGAAAAGCAGUAAUAAUGCAGCAGCAGCACCUUGA
(((......))).....--.----.(((((((...(((......(((....)))..........(((.......))).)))...))))))).. ( -23.30)
>DroYak_CAF1 18434 89 + 1
UGCCCAGCAGCGCAAAAAAA----AAAGGUGCGAGUGCAAAACGGUCUAUUGGCAUAAUGAAAAGCAGUAAUAAUGCAGCAGCAGCACCUUGA
(((.(....).)))......----.(((((((...(((......(((....)))..........(((.......))).)))...))))))).. ( -21.60)
>consensus
UGCCCAGCAGCGCAAAAAAA____AGAGGUGCGAAUGCUAAGCGGUCUAUUGGCAUAAUGAAAAGCAGUAACAAUGCAGCAGCAGCACCUUGA
(((......))).............(((((((...(((......(((....)))..........(((.......))).)))...))))))).. (-21.48 = -20.96 +  -0.52)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:21 2006