Locus 2371

Sequence ID 2L_DroMel_CAF1
Location 6,423,248 – 6,423,346
Length 98
Max. P 0.923688
window3821 window3822

overview

Window 1

Location 6,423,248 – 6,423,346
Length 98
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.74
Mean single sequence MFE -33.22
Consensus MFE -21.88
Energy contribution -22.97
Covariance contribution 1.09
Combinations/Pair 1.17
Mean z-score -1.52
Structure conservation index 0.66
SVM decision value 0.61
SVM RNA-class probability 0.798889
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6423248 98 + 22407834
AAUCUUUCCGAGUCG------------AGAUGAAACCGCUGCGCCCUGUGGCGCUGUCGAACAGCAACUGACAGCUGAAUUCCCAGCAC-GAAGCUUUUAU-GGAAAGAUCG
.(((((((((.(((.------------((.((....(((.(((((....))))).).)).....)).))))).((((......))))..-..........)-)))))))).. ( -31.40)
>DroPse_CAF1 19094 106 + 1
UAUGUUU-UGCGUCGUUUUUUCGAAAUAGGAACAACCGUUGCACCUCGUGGCGCUGCC-----GCAACUGACAGCCGAGCGGCAAGCAUUGAAUCUUUUAUUGGAAAAAUCU
.......-......((((((((((...((((......((..(.....)..))((((((-----((.............))))).)))......))))...)))))))))).. ( -26.12)
>DroSim_CAF1 9762 98 + 1
AAUCUUUCCGAGUCG------------AGGGGAAACCGCUGCGCCUUGUGGCGCUGUCGAACAGCAACUGACAGCUGAGUUCCCAGCAC-GGAGCUUUUAU-GGAAAGAUCG
.(((((((((..(((------------(.((....))...(((((....)))))..)))).((((........))))((((((......-))))))....)-)))))))).. ( -40.00)
>DroEre_CAF1 10542 98 + 1
AAUCUUUCCGAGUCG------------UGGGGAAACCGCUGCGCCUUGUGGCGCUGUCGAACAGCAACUGACAGCUGAGUUCCCAGCAC-GAAGCUUUUAU-GGAAAGAUCG
.((((((((((((((------------(((((((..(((((((((....)))((((.....))))....).)))).)..)))))..)))-)..))))....-)))))))).. ( -38.60)
>DroYak_CAF1 10100 98 + 1
AAUCUUUCCGAGUCG------------AGGGGAAACCGCUGCGCCUUGUGGCGCUGUCGAACAGCAACUGACAGCUGAGCUCCCGGCAC-GAAGCUUUUAU-GGAAAGAUCG
.(((((((((.....------------..((....))((((((((....)))))..(((..((((........)))).((.....)).)-))))).....)-)))))))).. ( -37.10)
>DroPer_CAF1 19466 106 + 1
UAUGUUU-UGCGUCGUUUUUUCGAAAUAGGAACAACCGUUGCACCUCGUGGCGCUGCC-----GCAACUGACAGCCGAGCGGCAAGCAUUGAAUCUUUUAUUGGAAAAAUCU
.......-......((((((((((...((((......((..(.....)..))((((((-----((.............))))).)))......))))...)))))))))).. ( -26.12)
>consensus
AAUCUUUCCGAGUCG____________AGGGGAAACCGCUGCGCCUUGUGGCGCUGUCGAACAGCAACUGACAGCUGAGCUCCCAGCAC_GAAGCUUUUAU_GGAAAGAUCG
.((((((((..(((..............((.....))((.(((((....))))).))............))).((((......))))...............)))))))).. (-21.88 = -22.97 +   1.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,423,248 – 6,423,346
Length 98
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.74
Mean single sequence MFE -33.62
Consensus MFE -21.48
Energy contribution -23.03
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value 1.16
SVM RNA-class probability 0.923688
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6423248 98 - 22407834
CGAUCUUUCC-AUAAAAGCUUC-GUGCUGGGAAUUCAGCUGUCAGUUGCUGUUCGACAGCGCCACAGGGCGCAGCGGUUUCAUCU------------CGACUCGGAAAGAUU
.(((((((((-......(((.(-((.(((((......((((((...........)))))).)).))).))).)))((((......------------.)))).))))))))) ( -35.10)
>DroPse_CAF1 19094 106 - 1
AGAUUUUUCCAAUAAAAGAUUCAAUGCUUGCCGCUCGGCUGUCAGUUGC-----GGCAGCGCCACGAGGUGCAACGGUUGUUCCUAUUUCGAAAAAACGACGCA-AAACAUA
.(((((((......)))))))...(((.((((((...((.....)).))-----))))(((((....)))))....((((((.............)))))))))-....... ( -25.92)
>DroSim_CAF1 9762 98 - 1
CGAUCUUUCC-AUAAAAGCUCC-GUGCUGGGAACUCAGCUGUCAGUUGCUGUUCGACAGCGCCACAAGGCGCAGCGGUUUCCCCU------------CGACUCGGAAAGAUU
.(((((((((-.....(((...-..)))(((((..(.(((((.....((((.....))))(((....)))))))))..)))))..------------......))))))))) ( -38.80)
>DroEre_CAF1 10542 98 - 1
CGAUCUUUCC-AUAAAAGCUUC-GUGCUGGGAACUCAGCUGUCAGUUGCUGUUCGACAGCGCCACAAGGCGCAGCGGUUUCCCCA------------CGACUCGGAAAGAUU
.(((((((((-.....((..((-(((..(((((((..(((((.....((((.....))))(((....))))))))))))))).))------------))))).))))))))) ( -38.80)
>DroYak_CAF1 10100 98 - 1
CGAUCUUUCC-AUAAAAGCUUC-GUGCCGGGAGCUCAGCUGUCAGUUGCUGUUCGACAGCGCCACAAGGCGCAGCGGUUUCCCCU------------CGACUCGGAAAGAUU
.(((((((((-......((...-..)).(((((..(.(((((.....((((.....))))(((....)))))))))..)))))..------------......))))))))) ( -37.20)
>DroPer_CAF1 19466 106 - 1
AGAUUUUUCCAAUAAAAGAUUCAAUGCUUGCCGCUCGGCUGUCAGUUGC-----GGCAGCGCCACGAGGUGCAACGGUUGUUCCUAUUUCGAAAAAACGACGCA-AAACAUA
.(((((((......)))))))...(((.((((((...((.....)).))-----))))(((((....)))))....((((((.............)))))))))-....... ( -25.92)
>consensus
CGAUCUUUCC_AUAAAAGCUUC_GUGCUGGGAACUCAGCUGUCAGUUGCUGUUCGACAGCGCCACAAGGCGCAGCGGUUUCCCCU____________CGACUCGGAAAGAUU
.(((((((((...............(((((....))))).(((.((((.....)))).(((((....)))))..........................)))..))))))))) (-21.48 = -23.03 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:27 2006