Locus 8140

Sequence ID 3R_DroMel_CAF1
Location 21,862,066 – 21,862,159
Length 93
Max. P 0.658363
window13093 window13094

overview

Window 3

Location 21,862,066 – 21,862,159
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.11
Mean single sequence MFE -22.08
Consensus MFE -16.76
Energy contribution -16.79
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.76
SVM decision value 0.12
SVM RNA-class probability 0.591649
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21862066 93 + 27905053
AACACCAA-C-----GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAAUGUCAGUGGAAAGGAAAACAGAGAAG---C--------AG----------
..(((..(-(-----(..((((.......(((((((((((.............)))))))))))))))..)))..)))..................---.--------..---------- ( -22.53)
>DroVir_CAF1 49494 102 + 1
AACACCAA-C-----GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAACCUCAAUGUAAAAGAAAACAGAGAAGAGCUAAAAGC--AG----------
........-(-----((((((((....))))(((((((((.............)))))))))).))))...(((..(((........))))))....((.....))--..---------- ( -21.52)
>DroPse_CAF1 47479 102 + 1
AACACCAA-C-----GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAAUGUCAGGCUAAAAGAAAACAGAGGAG------------AGCACACACAAG
........-(-----((((((((....))))(((((((((.............)))))))))).))))..(((...(((.................------------)))..))).... ( -20.05)
>DroGri_CAF1 43372 102 + 1
AACACCAA-C-----GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAACGUCAAUGUAAAAGAAAACAGAGAAGAGCUAAGAGC--AG----------
.(((...(-(-----(..((((.......(((((((((((.............)))))))))))))))..)))...)))..................((.....))--..---------- ( -22.33)
>DroWil_CAF1 50797 110 + 1
AACACCAAACGAGCGGAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAAUGUCAGUGUAAAAGAAAACACAAGAGAACCCAGAGACAAA----------
.........((((((..((((((....))))))(((((((.............))))))).)).))))..((((.((((........))))..(......)...))))..---------- ( -26.02)
>DroPer_CAF1 47751 102 + 1
AACACCAA-C-----GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAAUGUCAGGCUAAAAGAAAACAGAGGAG------------AGCACACACAAG
........-(-----((((((((....))))(((((((((.............)))))))))).))))..(((...(((.................------------)))..))).... ( -20.05)
>consensus
AACACCAA_C_____GAGCGAGAAAAAUCUUGUGGGAAACUUGAGGGCAAAGUGUUUCCCACGAUUCGAAUGUCAGUGUAAAAGAAAACAGAGAAG____________AG__________
...........................(((((((((((((.............)))))))))(((......))).......))))................................... (-16.76 = -16.79 +   0.03)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,862,066 – 21,862,159
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.11
Mean single sequence MFE -22.87
Consensus MFE -15.54
Energy contribution -16.15
Covariance contribution 0.61
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.68
SVM decision value 0.26
SVM RNA-class probability 0.658363
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21862066 93 - 27905053
----------CU--------G---CUUCUCUGUUUUCCUUUCCACUGACAUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC-----G-UUGGUGUU
----------..--------.---..................(((..((...(((...(((((((((.............)))))))))..((....)))))...-----)-)..))).. ( -22.82)
>DroVir_CAF1 49494 102 - 1
----------CU--GCUUUUAGCUCUUCUCUGUUUUCUUUUACAUUGAGGUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC-----G-UUGGUGUU
----------..--((.....))..................((((..(.(..(((...(((((((((.............)))))))))..((....)))))..)-----.-)..)))). ( -23.72)
>DroPse_CAF1 47479 102 - 1
CUUGUGUGUGCU------------CUCCUCUGUUUUCUUUUAGCCUGACAUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC-----G-UUGGUGUU
............------------.................((((..((...(((...(((((((((.............)))))))))..((....)))))...-----)-)..).))) ( -19.92)
>DroGri_CAF1 43372 102 - 1
----------CU--GCUCUUAGCUCUUCUCUGUUUUCUUUUACAUUGACGUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC-----G-UUGGUGUU
----------..--((.....))..................((((..(((..(((...(((((((((.............)))))))))..((....)))))..)-----)-)..)))). ( -27.32)
>DroWil_CAF1 50797 110 - 1
----------UUUGUCUCUGGGUUCUCUUGUGUUUUCUUUUACACUGACAUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUCCGCUCGUUUGGUGUU
----------...((((...(((((((..((((........)))).)).....)))))(((((((((.............))))))))).)))).......((.(((......))).)). ( -23.52)
>DroPer_CAF1 47751 102 - 1
CUUGUGUGUGCU------------CUCCUCUGUUUUCUUUUAGCCUGACAUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC-----G-UUGGUGUU
............------------.................((((..((...(((...(((((((((.............)))))))))..((....)))))...-----)-)..).))) ( -19.92)
>consensus
__________CU____________CUCCUCUGUUUUCUUUUACACUGACAUUCGAAUCGUGGGAAACACUUUGCCCUCAAGUUUCCCACAAGAUUUUUCUCGCUC_____G_UUGGUGUU
.........................................((((..(..........(((((((((.............))))))))).(((....)))............)..)))). (-15.54 = -16.15 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:30 2006