Locus 960

Sequence ID 2R_DroMel_CAF1
Location 4,106,396 – 4,106,491
Length 95
Max. P 0.958491
window1712 window1713

overview

Window 2

Location 4,106,396 – 4,106,491
Length 95
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 62.86
Mean single sequence MFE -29.42
Consensus MFE -17.19
Energy contribution -17.00
Covariance contribution -0.19
Combinations/Pair 1.27
Mean z-score -1.89
Structure conservation index 0.58
SVM decision value 1.49
SVM RNA-class probability 0.958491
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4106396 95 + 20766785
GGGCAGCAGGUUGGUGUUGUGGCUUGGCCACCGCCAGGGCCACGAAGGUAGCGAAAAGCUU--UGAAAAGAUUU-UAAAAAAA----------UAUGGAAUUUUUAAA
((((.....((((.(.((((((((((((....)))).)))))))).).)))).....))))--...((((((((-((......----------..))))))))))... ( -26.30)
>DroVir_CAF1 11690 75 + 1
GGGCAGCUGGCGGAUGCUGUGGCUUGGCCAGAGCCAGCGCCAGGCAGGAGGCGAGCAGCUGCA---GGAGCACA-AAGU-----------------------------
..(((((((.((..(.((((((((((((....))))).)))..)))).)..))..))))))).---........-....----------------------------- ( -32.20)
>DroSec_CAF1 10500 96 + 1
GGGCAGCAGGUUGGUGCUGGGGCUUGGCCACCGCCAGGGCCACGAAGGUAGCGAAAAGCUA-GUGAAAAGAUUA-CAAAUAUA----------UAUAUUAUUCGUAAA
...(((((......)))))((.((((((....)))))).))(((((..((((.....))))-((((.....)))-).......----------.......)))))... ( -29.30)
>DroSim_CAF1 14281 94 + 1
GGGCAGCAGGUUGGUGCUGGGGCUUGGCCACCGCCAGGGCCACGAAGGUAGCGAAAAGCUA-GUGAAAAGAUAA-CAAAUAUA----------UUGA--AUUCGUAAA
...(((((......)))))((.((((((....)))))).))((((((.((((.....))))-.)..........-(((.....----------))).--.)))))... ( -27.90)
>DroWil_CAF1 14709 94 + 1
GGGCAGCUUGCUGAUGCUGUGGCUUGGCCAAAGUCAAUGCCAGGCAGGAGACGAACAGGAG-CUGAAAAGGGGACGCAAGGGUUUGUUAUCC-----------A--UG
...((((((.(((.((((.(((((((((....))))).))))))))(....)...))))))-)))....(....)....((((.....))))-----------.--.. ( -32.40)
>DroYak_CAF1 3452 107 + 1
GGGCAGCAGGUUGGUGCUGGGGCUUGGCCACCGCCAGAGCCACGAAAGUAGCGAAAAGCUGUGUAAGGAGAUUA-GGAAUAAGUGUUUAAUUGUAUUGAAUUCAUAAA
..(((((...(((.((((..((((((((....)))).)))).....)))).)))...))))).....(((.(((-(..((((........)))).)))).)))..... ( -28.40)
>consensus
GGGCAGCAGGUUGGUGCUGGGGCUUGGCCACCGCCAGGGCCACGAAGGUAGCGAAAAGCUG_GUGAAAAGAUUA_CAAAUAAA__________UAU___AUUCAUAAA
...((((........)))).((((((((....))))).)))........(((.....)))................................................ (-17.19 = -17.00 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 3

Location 4,106,396 – 4,106,491
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 62.86
Mean single sequence MFE -21.47
Consensus MFE -12.26
Energy contribution -13.07
Covariance contribution 0.81
Combinations/Pair 1.12
Mean z-score -1.51
Structure conservation index 0.57
SVM decision value 0.87
SVM RNA-class probability 0.870947
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4106396 95 - 20766785
UUUAAAAAUUCCAUA----------UUUUUUUA-AAAUCUUUUCA--AAGCUUUUCGCUACCUUCGUGGCCCUGGCGGUGGCCAAGCCACAACACCAACCUGCUGCCC
((((((((.......----------..))))))-)).........--.(((.....)))......(((((..((((....)))).))))).................. ( -18.80)
>DroVir_CAF1 11690 75 - 1
-----------------------------ACUU-UGUGCUCC---UGCAGCUGCUCGCCUCCUGCCUGGCGCUGGCUCUGGCCAAGCCACAGCAUCCGCCAGCUGCCC
-----------------------------....-........---.(((((((...((....(((.((((..((((....)))).))))..)))...))))))))).. ( -27.70)
>DroSec_CAF1 10500 96 - 1
UUUACGAAUAAUAUA----------UAUAUUUG-UAAUCUUUUCAC-UAGCUUUUCGCUACCUUCGUGGCCCUGGCGGUGGCCAAGCCCCAGCACCAACCUGCUGCCC
.(((((((((.....----------..))))))-))).........-.........(((((....)))))...(((((.(((...)))))((((......))))))). ( -23.50)
>DroSim_CAF1 14281 94 - 1
UUUACGAAU--UCAA----------UAUAUUUG-UUAUCUUUUCAC-UAGCUUUUCGCUACCUUCGUGGCCCUGGCGGUGGCCAAGCCCCAGCACCAACCUGCUGCCC
...(((((.--..((----------((....))-))..........-((((.....))))..)))))(((..((((....)))).))).(((((......)))))... ( -20.90)
>DroWil_CAF1 14709 94 - 1
CA--U-----------GGAUAACAAACCCUUGCGUCCCCUUUUCAG-CUCCUGUUCGUCUCCUGCCUGGCAUUGACUUUGGCCAAGCCACAGCAUCAGCAAGCUGCCC
..--.-----------((((..(((....))).))))......(((-((.(((...(((........)))..((.((.((((...)))).)))).)))..)))))... ( -18.10)
>DroYak_CAF1 3452 107 - 1
UUUAUGAAUUCAAUACAAUUAAACACUUAUUCC-UAAUCUCCUUACACAGCUUUUCGCUACUUUCGUGGCUCUGGCGGUGGCCAAGCCCCAGCACCAACCUGCUGCCC
.................................-.............((((.....(((((....))))).((((.(((......))))))).........))))... ( -19.80)
>consensus
UUUACGAAU___AUA__________UAUAUUUC_UAAUCUUUUCAC_CAGCUUUUCGCUACCUUCGUGGCCCUGGCGGUGGCCAAGCCACAGCACCAACCUGCUGCCC
.................................................(((....(((((....)))))..((((....)))))))..((((........))))... (-12.26 = -13.07 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:49 2006