Locus 1705

Sequence ID 2R_DroMel_CAF1
Location 6,447,446 – 6,447,577
Length 131
Max. P 0.749487
window2847 window2848

overview

Window 7

Location 6,447,446 – 6,447,538
Length 92
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 76.42
Mean single sequence MFE -27.59
Consensus MFE -13.61
Energy contribution -14.48
Covariance contribution 0.86
Combinations/Pair 1.12
Mean z-score -1.97
Structure conservation index 0.49
SVM decision value 0.47
SVM RNA-class probability 0.749487
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6447446 92 - 20766785
UAGA-GCCGCAAA-AACGCAGCCAAC----------GAGCUGCAAUGA--GAGCUGUGAACAUUUCACAAACGGUUUGCAAUUAAUGAGUGCGGACGUUCC----AAAAA
....-((((((..-...(((((....----------..)))))..((.--.((((((.............))))))..)).........))))).).....----..... ( -23.62)
>DroVir_CAF1 14776 107 - 1
UAGAGGCCGCAAAAAACGCAGCGUGCAGCAAGCAGUGAGCAGCGUUCAACGAGCUGCGAACAUUG--CAAACGGUUUGCAAUUAAUGAGUGCCUGCCGCUAUGU-AAUAA
...............(((.((((.((((((..((((..(((((.........)))))..))((((--(((.....)))))))...))..)).)))))))).)))-..... ( -33.70)
>DroPse_CAF1 24614 95 - 1
UAGA-GCCGCAAA-AACGCAGCCAAC----------GAGCUGCAAUGA--GAGCCGUGAACAUUUCACAAACGGUUCGCAAUUAAUGAGUGCGCGAGAGCAUCG-ACCAA
..((-...(((..-...(((((....----------..)))))..((.--(((((((.............))))))).)).........)))((....)).)).-..... ( -27.12)
>DroMoj_CAF1 20150 93 - 1
UAGAGGCCGCAAAAAACGCAGCGCGC--------------AGCGUUCAACGAGCUGCGAACAUUG--CAAACGGUUCGCAAUUAAUGAGUGCCUGCUGCUAUGC-AAUAA
........(((......((((.((((--------------...((((...))))(((((((....--......)))))))........)))))))).....)))-..... ( -25.40)
>DroAna_CAF1 20060 96 - 1
UAGA-GCCGCAAA-AACGCAGCCAAC----------GAGCUGCAAUGA--GAGCUGUGAACAUUUCUCAAACGGUUUGCAAUUAAUGAGUGCGAACGGCCCCCCAAAAAA
....-(((.....-...(((((....----------..)))))..(((--(((.((....)).))))))....(((((((.........))))))))))........... ( -28.60)
>DroPer_CAF1 23118 95 - 1
UAGA-GCCGCAAA-AACGCAGCCAAC----------CAGCUGCAAUGA--GAGCCGUGAACAUUUCACAAACGGUUCGCAAUUAAUGAGUGCGCGAGAGCAUCG-ACCAA
..((-...(((..-...(((((....----------..)))))..((.--(((((((.............))))))).)).........)))((....)).)).-..... ( -27.12)
>consensus
UAGA_GCCGCAAA_AACGCAGCCAAC__________GAGCUGCAAUGA__GAGCUGUGAACAUUUCACAAACGGUUCGCAAUUAAUGAGUGCGCGCGGCCAUCC_AAAAA
.......((((......(((((................))))).......(((((((.............)))))))............))))................. (-13.61 = -14.48 +   0.86)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,447,482 – 6,447,577
Length 95
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 81.68
Mean single sequence MFE -26.87
Consensus MFE -15.23
Energy contribution -15.81
Covariance contribution 0.58
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.57
SVM decision value 0.41
SVM RNA-class probability 0.723449
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6447482 95 - 20766785
-GUCGUGCAAAUGAAUGCAGCGGAAAUGAAAUGAAUUCGUUAGA-GCCGCAAA-AACGCAGCCAAC----------GAGCUGCAAUGA--GAGCUGUGAACAUUUCACAA
-...(((.(((((..((((((((.((((((.....))))))...-.)).....-...(((((....----------..))))).....--..))))))..)))))))).. ( -27.60)
>DroVir_CAF1 14815 108 - 1
UGACGUGCAAAUGAAUGCAACGGAAAUGAAAUGAAUUCGUUAGAGGCCGCAAAAAACGCAGCGUGCAGCAAGCAGUGAGCAGCGUUCAACGAGCUGCGAACAUUG--CAA
...((((((......))).)))..((((((.....)))))).(..(((((..........))).))..)..((((((.(((((.........)))))...)))))--).. ( -30.30)
>DroPse_CAF1 24653 96 - 1
UGACGUGCAAAUGAAUGCAGCGGAAAUUAAAUGAAUUCGUUAGA-GCCGCAAA-AACGCAGCCAAC----------GAGCUGCAAUGA--GAGCCGUGAACAUUUCACAA
....(((.(((((..(((.((((...((.((((....)))).))-.))))...-...(((((....----------..))))).....--.....)))..)))))))).. ( -25.60)
>DroGri_CAF1 5287 87 - 1
UGAUGUGCAAAUGAAUGCAGCGGAAAUGAAAUGAAUUCGUUAGAGGCCGCAAAAAACGCA---------------------GCGUUCAACGAGCUGCGAACAUUG--CAA
.....(((((.((......((((.((((((.....)))))).....))))......((((---------------------((.........))))))..)))))--)). ( -25.30)
>DroMoj_CAF1 20189 94 - 1
UGACGUGCAAAUGAAUGCAGCGGAAAUGAAAUGAAUUCGUUAGAGGCCGCAAAAAACGCAGCGCGC--------------AGCGUUCAACGAGCUGCGAACAUUG--CAA
.....((((......))))((((.((((((.....)))))).....)))).......((((..(((--------------(((.........))))))....)))--).. ( -26.80)
>DroPer_CAF1 23157 96 - 1
UGACGUGCAAAUGAAUGCAGCGGAAAUUAAAUGAAUUCGUUAGA-GCCGCAAA-AACGCAGCCAAC----------CAGCUGCAAUGA--GAGCCGUGAACAUUUCACAA
....(((.(((((..(((.((((...((.((((....)))).))-.))))...-...(((((....----------..))))).....--.....)))..)))))))).. ( -25.60)
>consensus
UGACGUGCAAAUGAAUGCAGCGGAAAUGAAAUGAAUUCGUUAGA_GCCGCAAA_AACGCAGCCAAC__________GAGCUGCAAUCA__GAGCUGCGAACAUUG__CAA
.....((((......))))((((......((((....)))).....))))......((((((..............................))))))............ (-15.23 = -15.81 +   0.58)

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 10:11:13 2006