Locus 1725

Sequence ID 3R_DroMel_CAF1
Location 4,951,482 – 4,951,606
Length 124
Max. P 0.784799
window2836 window2837

overview

Window 6

Location 4,951,482 – 4,951,582
Length 100
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -24.20
Consensus MFE -16.70
Energy contribution -16.87
Covariance contribution 0.17
Combinations/Pair 1.14
Mean z-score -1.36
Structure conservation index 0.69
SVM decision value -0.03
SVM RNA-class probability 0.520679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4951482 100 + 27905053
UAAAAUGCUUUGGCGAAGCGCAGCGAAAAUGCU--------AAUUAAUGUGAUUAUGUGGCCAUUUUAA-UGUUAAACAAUUGUUUAACGAUUAGUCAGGCGUGAG-AAC
....((((((((((...(((((.......)))(--------((((.....))))).)).))))..((((-((((((((....))))))).)))))..))))))...-... ( -20.10)
>DroVir_CAF1 70967 98 + 1
GAA--ACC--AACUGAGGCGCAACGAAAAUGCU--------AAUUAAUGUGAUUAUGUUGCCAUUUAAAUUGUUAAACAAUUGUUUAGCGAUUAGUCAGGCGUCAAGAAU
...--...--...(((.((((((((.((.(((.--------.......))).)).))))))......(((((((((((....)))))))))))......)).)))..... ( -23.40)
>DroPse_CAF1 94656 100 + 1
GAAGGCCCAACGGCAAGGCGCAACGAAAAUGCU--------AAUUAAUGUGAUUAUGUGGCCAUUUUAA-UGUUAAACAAUUGUUUAGCGAUUAGUCAGGCGUCAG-AGG
....(((....)))..(((((.((.((((((((--------(....(((....))).))).))))))..-((((((((....))))))))....))...)))))..-... ( -23.50)
>DroGri_CAF1 68612 96 + 1
GAA--CGC--AUCUGAAGCGCAACGAAAUUGCU--------AAUUAAUGUGAUUAUGUUGCCAUUUGGA-UGCUAAACAAUUGUUUAGCGCUUAGUCAGGCGUCAU-AAG
((.--(((--..(((((((((((((.(((..(.--------.......)..))).))))))........-.(((((((....))))))))))...)))))))))..-... ( -31.20)
>DroWil_CAF1 58781 100 + 1
AAUAAGGGCUAACCGAGGCGCAACGAAAAUGCU--------AAUUAAUGUGAUUAUGUGGCCAUUUUAA-UGUUAAACAAUUGUUUAACGAUUAGUCAGGCGUCAG-GGG
............((..(((((.((.((((((((--------(....(((....))).))).))))))..-((((((((....))))))))....))...))))).)-).. ( -22.00)
>DroPer_CAF1 100727 108 + 1
GAAGGCCCAACGGCAAGGCGCAACGAAAAUGCUGCAACGAAAAUUAAUGUGAUUAUGUGGCCAUUUUAA-UGUUAAACAAUUGUUUAGCGAUUAGUCAGGCGUCAG-AGG
....(((....)))..(((((.((.(((((((..((......((....)).....))..).))))))..-((((((((....))))))))....))...)))))..-... ( -25.00)
>consensus
GAA__CCC__AGCCGAGGCGCAACGAAAAUGCU________AAUUAAUGUGAUUAUGUGGCCAUUUUAA_UGUUAAACAAUUGUUUAGCGAUUAGUCAGGCGUCAG_AAG
................((((((.......)))...........................(((...((((.((((((((....)))))))).))))...))))))...... (-16.70 = -16.87 +   0.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,951,513 – 4,951,606
Length 93
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.63
Mean single sequence MFE -12.23
Consensus MFE -9.29
Energy contribution -9.45
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.76
SVM decision value 0.57
SVM RNA-class probability 0.784799
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4951513 93 - 27905053
--UACCUACC----UAGCCAUCGCAUUUUCGUUCUCACGCCUGACUAAUCGUUAAACAAUUGUUUAACAU-UAAAAUGGCCACAUAAUCACAUUAAUUAG
--........----..(((((........(((....)))...........(((((((....)))))))..-....))))).................... ( -12.40)
>DroPse_CAF1 94687 81 - 1
UG------------------UGGGGCGGCUCCUCUGACGCCUGACUAAUCGCUAAACAAUUGUUUAACAU-UAAAAUGGCCACAUAAUCACAUUAAUUAG
((------------------(((((((.(......).)))).........(.(((((....))))).)..-........)))))................ ( -15.60)
>DroSim_CAF1 58820 97 - 1
--UACCUACCCAUCUACCCAUCGUAUUUUCGUUCUCACGCCUGACUAAUCGUUAAACAAUUGUUUAACAU-UAAAAUGGCCACAUAAUCACAUUAAUUAG
--....................................(((....((((.(((((((....)))))))))-))....))).................... ( -11.70)
>DroEre_CAF1 59015 86 - 1
--C--A----------CCCAUCUUAUUUUUGUUCUCACGCCUGACUAAUCGUUAAACAAUUGUUUAACAUUUAAAAUGGCCACAUAAUCACAUUAAUUAG
--.--.----------......................(((....(((..(((((((....)))))))..)))....))).................... ( -11.00)
>DroWil_CAF1 58812 79 - 1
AG------------------UU--UCAUCUCCCCUGACGCCUGACUAAUCGUUAAACAAUUGUUUAACAU-UAAAAUGGCCACAUAAUCACAUUAAUUAG
..------------------..--..............(((....((((.(((((((....)))))))))-))....))).................... ( -11.70)
>DroYak_CAF1 59889 88 - 1
--UGCC----------CCCGUCGUAUUUUUGUUCUCACGCCUGACUAAUCGUUAAACAAUUGUUUAACAUUUAAAAUGGCCACAUAAUCACAUUAAUUAG
--....----------......................(((....(((..(((((((....)))))))..)))....))).................... ( -11.00)
>consensus
__U__C__________CCCAUCGUAUUUUUGUUCUCACGCCUGACUAAUCGUUAAACAAUUGUUUAACAU_UAAAAUGGCCACAUAAUCACAUUAAUUAG
......................................(((.........(((((((....))))))).........))).................... ( -9.29 =  -9.45 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:46 2006