Locus 1836

Sequence ID 2L_DroMel_CAF1
Location 5,071,324 – 5,071,549
Length 225
Max. P 0.998152
window2948 window2949 window2950

overview

Window 8

Location 5,071,324 – 5,071,438
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.69
Mean single sequence MFE -42.42
Consensus MFE -23.48
Energy contribution -23.72
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.73
Structure conservation index 0.55
SVM decision value 0.76
SVM RNA-class probability 0.843298
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5071324 114 + 22407834
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUU-GGCG----CCCCAAAAUGGAGCAACCCAUUUAGGGUGGCCCAA-AAAAGGGAGCGCCAAAUGGUGACAAAUCGUUGGCGGA
.((((((....))))))...((((((((........((-((((----((((....(((.((.((((.....)))).))))).-....))).))))))).((....))....))).))))) ( -46.70)
>DroSec_CAF1 630 111 + 1
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUU-GGCG----CCCCCAAAUG-AACAUCUUAU-UAGGGUGGCCCAA-AAAAG-GAGCGCCAAAUGGUGACGAAUCGUUGGAGGA
..(((((....)))))((((((.((((...((((..((-((.(----(((((.((((-(.....))))-).))).)))))))-.....-...))))...((....))..)))).)))))) ( -41.00)
>DroSim_CAF1 1632 112 + 1
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUU-GGCG----CCCCAACAUGGAGCAACCCAU-UAGGGUGGCCCAA-AAAAG-GAGCGCCAAAUGGUGACGAAUCGUUGGAGGA
..(((((....)))))((((((.((((.........((-((((----(((.....(((.((.((((..-..)))).))))).-....)-).))))))).((....))..)))).)))))) ( -46.70)
>DroEre_CAF1 102 112 + 1
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUU-GGCUUCACCCCCUCCAUUCAAC-----AU-UAGGGUGGCCCAAAAAAUG-GAACACCAAAUGGUGACGAAUCGUUGGAGGA
..(((((....)))))((((((.(((....((((((..-...))))))......((((..(-----((-((.((((..(((.....))-)..))))...)))))..))))))).)))))) ( -39.30)
>DroYak_CAF1 1788 108 + 1
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUGCGGGCUCAC----GCCAUUCAAC-----AU-UAGGGUGACCCAA-AAUUG-GAGCGCCAACUGGUGGCGAAUCGUUGGUGGA
.((((((....))))))...((..((((...((((((....))))))----)))...((((-----..-..((....))...-....(-(..(((((.....)))))..)))))))..)) ( -38.40)
>consensus
CAGCAAGUACACUUGCUCCUUCUGCGGCAAGGUGAGUU_GGCG____CCCCAACAUGCAACA_C__AU_UAGGGUGGCCCAA_AAAAG_GAGCGCCAAAUGGUGACGAAUCGUUGGAGGA
..(((((....)))))((((((.((((............................................(((...)))............((((....)))).....)))).)))))) (-23.48 = -23.72 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,071,363 – 5,071,478
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.32
Mean single sequence MFE -33.04
Consensus MFE -13.34
Energy contribution -13.46
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.89
Structure conservation index 0.40
SVM decision value 0.41
SVM RNA-class probability 0.724801
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5071363 115 + 22407834
GCG----CCCCAAAAUGGAGCAACCCAUUUAGGGUGGCCCAA-AAAAGGGAGCGCCAAAUGGUGACAAAUCGUUGGCGGAAUGUUAUCAGUGGACAUUUCUAAAGCAACUCCAUGCACCC
((.----(((.....(((.((.((((.....)))).))))).-....))).))(((((.((((.....)))))))))((((((((.......))))))))....(((......))).... ( -38.80)
>DroSec_CAF1 669 103 + 1
GCG----CCCCCAAAUG-AACAUCUUAU-UAGGGUGGCCCAA-AAAAG-GAGCGCCAAAUGGUGACGAAUCGUUGGAGGAACGUAAUCAGUGGGCAUUUCUAAAGCAA---------CCC
(((----(((((.((((-(.....))))-).))).)))....-...((-(((.(((...((((.(((..((......))..))).))))...))).)))))...))..---------... ( -29.60)
>DroSim_CAF1 1671 113 + 1
GCG----CCCCAACAUGGAGCAACCCAU-UAGGGUGGCCCAA-AAAAG-GAGCGCCAAAUGGUGACGAAUCGUUGGAGGAACGUUAUCAGUGGACAUUUCUAAAGCAACUCCAUUCACCC
(((----(((.....(((.((.((((..-..)))).))))).-....)-).)))).....(((((.((...(((..(((((.(((.......))).)))))..)))...))...))))). ( -33.90)
>DroEre_CAF1 141 104 + 1
GCUUCACCCCCUCCAUUCAAC-----AU-UAGGGUGGCCCAAAAAAUG-GAACACCAAAUGGUGACGAAUCGUUGGAGGAACCUUAUCAAUGGAUAUUUCUAAAGCAACGC---------
((((.....(((((((((..(-----((-((.((((..(((.....))-)..))))...)))))..)))....))))))...........((((....)))))))).....--------- ( -30.00)
>DroYak_CAF1 1828 108 + 1
GGCUCAC----GCCAUUCAAC-----AU-UAGGGUGACCCAA-AAUUG-GAGCGCCAACUGGUGGCGAAUCGUUGGUGGAACGUUAUCAAUGGACAUUUCUAAAGCAACGCCCUAGGCUG
(((....----))).......-----.(-(((((((..(((.-...))-).((((((.....))))...((((((((((....))))))))))...........))..)))))))).... ( -32.90)
>consensus
GCG____CCCCAACAUGCAACA_C__AU_UAGGGUGGCCCAA_AAAAG_GAGCGCCAAAUGGUGACGAAUCGUUGGAGGAACGUUAUCAGUGGACAUUUCUAAAGCAACGCC_U___CCC
((.............................(((...)))..............(((..((((((((..((......))..)))))))).)))...........)).............. (-13.34 = -13.46 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,071,438 – 5,071,549
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 65.05
Mean single sequence MFE -25.69
Consensus MFE -12.19
Energy contribution -12.19
Covariance contribution 0.00
Combinations/Pair 1.38
Mean z-score -2.88
Structure conservation index 0.47
SVM decision value 3.02
SVM RNA-class probability 0.998152
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5071438 111 + 22407834
AUGUUAUCAGUGGACAUUUCUAAAGCAACUCCAUGCACCCAUU-CAAC--------AAGUGGAAUCUUGAAUUAUUGGCCUAAAGUCACCUAGAAAUGUCCAUUUAUAGAAUUCUCUUCG
...((((.((((((((((((((..(((......)))..(((((-....--------.))))).............((((.....))))..)))))))))))))).))))........... ( -27.40)
>DroSec_CAF1 741 90 + 1
ACGUAAUCAGUGGGCAUUUCUAAAGCAA---------CCCAUU-CAAC--------AAGUGGAAUCUUGAUUUAUUGGCC----------UAGAAAUGUCCAUUUAUAGAAUUUCCUA--
........((((((((((((((..((..---------.(((((-....--------.)))))(((....))).....)).----------))))))))))))))..............-- ( -20.50)
>DroSim_CAF1 1744 99 + 1
ACGUUAUCAGUGGACAUUUCUAAAGCAACUCCAUUCACCCAUU-CAAC--------AAGUGGAAUCUUGAUUUAUUGGCC----------UAGAAAUGUCCAUUUAUAGAAUUUCCUA--
...((((.((((((((((((((..((........(((.(((((-....--------.))))).....))).......)).----------)))))))))))))).)))).........-- ( -24.36)
>DroYak_CAF1 1896 100 + 1
ACGUUAUCAAUGGACAUUUCUAAAGCAACGCCCUAGGCUGUGUCGAAUCAGUGUCGGCAAAGCCUCGUGGGU--------------------GAAAUGUUUCUUUGAUUAAUUCCUUUCC
.....(((((.(((((((((.........((((.(((((.((((((.......)))))).)))))...))))--------------------)))))))))..)))))............ ( -30.50)
>consensus
ACGUUAUCAGUGGACAUUUCUAAAGCAACUCCAU_CACCCAUU_CAAC________AAGUGGAAUCUUGAUUUAUUGGCC__________UAGAAAUGUCCAUUUAUAGAAUUCCCUA__
........((((((((((((((................((((................))))(((....)))..................))))))))))))))................ (-12.19 = -12.19 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:26 2006