Locus 2850

Sequence ID 2L_DroMel_CAF1
Location 8,167,843 – 8,168,001
Length 158
Max. P 0.744922
window4533 window4534

overview

Window 3

Location 8,167,843 – 8,167,944
Length 101
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 78.76
Mean single sequence MFE -23.02
Consensus MFE -8.78
Energy contribution -9.66
Covariance contribution 0.88
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.38
SVM decision value 0.46
SVM RNA-class probability 0.744922
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8167843 101 + 22407834
AAAAAAGGGGCAAAGGUAUAAAAAAAAAAUA-AAAGUGAAUCAUAAAAAACGGGA---------AGCGAAACUAGCUGCUCCUGCCUGCUCCUUUGCCCGAAUGCAUCAGC
.......(((((((((...............-...(((...)))......(((((---------(((.......)))..)))))......)))))))))............ ( -23.50)
>DroSec_CAF1 7709 94 + 1
AAAAAAG-GGAAAAGGUAUAAAAAACA------AAGUGAAUCAUAAAAAACGGGA---------GGCGA-ACUAGCAGCUCCUACCUGCUCCUUCGGCCGAAUGCAUCAGC
.....((-(((..((((..........------..((............))((((---------(((..-....))..)))))))))..)))))..((.....))...... ( -17.00)
>DroSim_CAF1 8233 95 + 1
AAAAAAG-GGCAAAGGUAUAAAAAACA------AAGUGAAUCAUAAAAAACGGGA---------GGCGAAACUAGCUGCUCCUGCCUGCUCCUUUGCUCGAAUGCAUCAGC
......(-((((((((...........------..(((...)))......(((((---------(((.......))..))))))......)))))))))............ ( -21.70)
>DroEre_CAF1 8196 94 + 1
A---AAG-GGCAAAGACAUAAAAAGUCCAUGUGAAGUAAACCAUAAAAAAGGGGA---------AGCGAAACUAGCUGCUCC----UGUUCCUUUGCCCGAAUGCAUCAGC
.---..(-(((((((..............((((........))))....(((((.---------(((.......))).))))----)....))))))))............ ( -25.90)
>DroYak_CAF1 7907 104 + 1
AA--AAG-GGCAAAGAUAUAAAAGGUCCACGUGAAGUAAACCAUAAAAAACGGGAAAACGGGGUAGCGAAACUAGAUGCUAC----UGUUCCUUUGCCCGAAUGCAUCAGC
..--..(-(((((((........(.(((.(((....((.....))....))))))...)..(((((((........))))))----)....))))))))............ ( -27.00)
>consensus
AAAAAAG_GGCAAAGGUAUAAAAAACA_A____AAGUGAAUCAUAAAAAACGGGA_________AGCGAAACUAGCUGCUCCU_CCUGCUCCUUUGCCCGAAUGCAUCAGC
......(.((((((((................................................(((.......)))((........)).)))))))))............ ( -8.78 =  -9.66 +   0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,167,904 – 8,168,001
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.35
Mean single sequence MFE -32.23
Consensus MFE -12.19
Energy contribution -13.58
Covariance contribution 1.39
Combinations/Pair 1.05
Mean z-score -2.14
Structure conservation index 0.38
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8167904 97 - 22407834
AGG-----------GCAAGAAGCAAACUGG-CAUA-----------GCUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGGGCAAAGGAGCAGGCAGGAGCAGCUAG
...-----------((.....))...((((-(...-----------(((((((((((((((.....))))))....((((.((((.....)))).))))......))))))))).))))) ( -37.30)
>DroSec_CAF1 7763 97 - 1
AGG-----------GCAAGAAGCAAGUUGG-CAUA-----------GCUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGGCCGAAGGAGCAGGUAGGAGCUGCUAG
..(-----------((.....((......)-)..(-----------(((((((((((((((.....))))))....(((((((((.....)))))))))......))))))))))))).. ( -39.20)
>DroSim_CAF1 8288 97 - 1
AGG-----------GCAAGAAGCAAAAUGG-CAUA-----------GCUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGAGCAAAGGAGCAGGCAGGAGCAGCUAG
..(-----------((.....((......)-)...-----------((((((((((.((..(((.....(((.....)))(((((.....)).)))...))))))))))))))).))).. ( -33.70)
>DroEre_CAF1 8254 92 - 1
-GG-----------ACAGGGAGCAAAACGG-CGUA-----------GAUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGGGCAAAGGAACA----GGAGCAGCUAG
-..-----------..............((-(...-----------..(((((((((((((.....))))))....((((.((((.....)))).))))))..))----)))...))).. ( -22.40)
>DroYak_CAF1 7975 95 - 1
-CG-----------GCGAGGAGCCAAACGG-CAUU------GC--UGCUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGGGCAAAGGAACA----GUAGCAUCUAG
-..-----------....((((((....))-)..(------((--((((....((((((((.....))))))....((((.((((.....)))).))))))...)----))))))))).. ( -27.80)
>DroAna_CAF1 9285 116 - 1
GGGGGAGUGUGAGAGGAAAGAGCGAAAGGAAGACAGCUCCUGCUAUGCUCCUCCUAUGCUGUCCAUUAACAAACAAUUUUGCUGAUGCAUUCGGCCCAAAGAACC----GAAACAGUUAG
(((((((((((..((((....((............))))))..)))))))))))...(((((.(((((.((((....)))).)))))..(((((.........))----))))))))... ( -33.00)
>consensus
AGG___________GCAAGAAGCAAAAUGG_CAUA___________GCUCCUGCCUUGUUGUCCAUUAACAAACAAUUUGGCUGAUGCAUUCGGGCAAAGGAACA____GGAGCAGCUAG
..............................................(((((....((((((.....))))))....((((.((((.....)))).))))..........)))))...... (-12.19 = -13.58 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:53 2006