Locus 3698

Sequence ID 2R_DroMel_CAF1
Location 12,275,423 – 12,275,526
Length 103
Max. P 0.962843
window6010 window6011

overview

Window 0

Location 12,275,423 – 12,275,526
Length 103
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 74.28
Mean single sequence MFE -29.80
Consensus MFE -19.37
Energy contribution -20.23
Covariance contribution 0.86
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.65
SVM decision value 1.54
SVM RNA-class probability 0.962843
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12275423 103 + 20766785
AACGUUUGGUAAAGGGGUCUUAGA-UAUUCCCACUCACCUGCAAUAAGUUUCUCGCUGGCCUGCAGCUGAUCCACAGCCAUCUCCGUGGUGGAUCCAUUACGAU
......((((...((((.......-...))))..(((.(((((...(((.....)))....))))).)))......))))....(((((((....))))))).. ( -26.40)
>DroVir_CAF1 167461 90 + 1
UGGAUUGC-------------CUC-UAGGCGAGCUUACCUGCAAUCAGCUUCUCGCUGGCCUGCAAUUGAUCCACGGCCAUCUCCGUGGUGGAACCAUUGCGAU
.((.((((-------------(..-..)))))((......))..(((((.....)))))))((((((.(.(((((.((.......)).))))).).)))))).. ( -29.60)
>DroGri_CAF1 171979 84 + 1
AGCGUUUG-------------AUU-------UGCUUACCUGCAAUGAGCUUCUCGCUGGCCUGCAGCUGAUCCACGGCCAUUUCGGUGGUGGAACCAUUGCGAU
((((....-------------...-------))))....(((((((........((((.....))))...(((((.(((.....))).)))))..))))))).. ( -28.10)
>DroSim_CAF1 132928 91 + 1
----------AAGGGAGUUAGAU--UAU-UCCACUCACCUGCAAUGAGUUUCUCGCUGGCCUGCAGCUGAUCCACAGCCAUCUCCGUUGUGGAUCCAUUGCGAU
----------.(((((((..((.--...-)).)))).)))((((((........((((.....)))).((((((((((.......))))))))))))))))... ( -34.20)
>DroEre_CAF1 145471 104 + 1
CACGUUUGGUAAAAGAGCGUUAGAUGAUCCACACUCACCUGCAAUGAGUUUCUCGCUGGCCUGCAGCUGAUCCACAGCCAUCUCCGUUGUGGAUCCAUUGCGAU
.((((((.......)))))).((.(((.......))).))((((((........((((.....)))).((((((((((.......))))))))))))))))... ( -31.60)
>DroYak_CAF1 141053 104 + 1
CACGUUUGUUAAAAGCUUCAUAGAUUAUCCCCACUUACCUGCAAUGAGUUUCUCGCUGGCCUGCAGCUGAUCCACAGCCAUUUCCGUUGUGGAUCCAUUGCGAU
...((((.....)))).......................(((((((........((((.....)))).((((((((((.......))))))))))))))))).. ( -28.90)
>consensus
AACGUUUG__AAA_G_GU__UAGA_UAU_CCCACUCACCUGCAAUGAGUUUCUCGCUGGCCUGCAGCUGAUCCACAGCCAUCUCCGUGGUGGAUCCAUUGCGAU
.......................................(((((((........((((.....)))).(((((((.((.......)).)))))))))))))).. (-19.37 = -20.23 +   0.86)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,275,423 – 12,275,526
Length 103
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 74.28
Mean single sequence MFE -30.25
Consensus MFE -19.56
Energy contribution -19.92
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -1.55
Structure conservation index 0.65
SVM decision value 1.01
SVM RNA-class probability 0.899326
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12275423 103 - 20766785
AUCGUAAUGGAUCCACCACGGAGAUGGCUGUGGAUCAGCUGCAGGCCAGCGAGAAACUUAUUGCAGGUGAGUGGGAAUA-UCUAAGACCCCUUUACCAAACGUU
...(((((((((((((..((....))...))))))).((((.....))))........)))))).((((((.(((....-.......))).))))))....... ( -30.00)
>DroVir_CAF1 167461 90 - 1
AUCGCAAUGGUUCCACCACGGAGAUGGCCGUGGAUCAAUUGCAGGCCAGCGAGAAGCUGAUUGCAGGUAAGCUCGCCUA-GAG-------------GCAAUCCA
...((..........((((((......)))))).....((((((..((((.....)))).))))))....))..(((..-..)-------------))...... ( -30.00)
>DroGri_CAF1 171979 84 - 1
AUCGCAAUGGUUCCACCACCGAAAUGGCCGUGGAUCAGCUGCAGGCCAGCGAGAAGCUCAUUGCAGGUAAGCA-------AAU-------------CAAACGCU
...((..((((.((((..((.....))..)))))))).((((((...(((.....)))..))))))....)).-------...-------------........ ( -23.30)
>DroSim_CAF1 132928 91 - 1
AUCGCAAUGGAUCCACAACGGAGAUGGCUGUGGAUCAGCUGCAGGCCAGCGAGAAACUCAUUGCAGGUGAGUGGA-AUA--AUCUAACUCCCUU----------
...((((((((((((((.((....))..)))))))).((((.....))))........))))))(((.(((((((-...--.))).))))))).---------- ( -33.50)
>DroEre_CAF1 145471 104 - 1
AUCGCAAUGGAUCCACAACGGAGAUGGCUGUGGAUCAGCUGCAGGCCAGCGAGAAACUCAUUGCAGGUGAGUGUGGAUCAUCUAACGCUCUUUUACCAAACGUG
...((((((((((((((.((....))..)))))))).((((.....))))........)))))).(((((((((((.....)).))))))....)))....... ( -35.30)
>DroYak_CAF1 141053 104 - 1
AUCGCAAUGGAUCCACAACGGAAAUGGCUGUGGAUCAGCUGCAGGCCAGCGAGAAACUCAUUGCAGGUAAGUGGGGAUAAUCUAUGAAGCUUUUAACAAACGUG
...((((((((((((((.((....))..)))))))).((((.....))))........))))))((((..(((((.....)))))...))))............ ( -29.40)
>consensus
AUCGCAAUGGAUCCACAACGGAGAUGGCUGUGGAUCAGCUGCAGGCCAGCGAGAAACUCAUUGCAGGUAAGUGGG_AUA_UAUA__AC_C_UUU__CAAACGUG
...(((...(((((((..((....))...)))))))...)))..(((.((((........)))).))).................................... (-19.56 = -19.92 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:10 2006