Locus 3863

Sequence ID 3R_DroMel_CAF1
Location 10,516,299 – 10,516,413
Length 114
Max. P 0.797353
window6186 window6187

overview

Window 6

Location 10,516,299 – 10,516,413
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.27
Mean single sequence MFE -25.56
Consensus MFE -12.84
Energy contribution -12.87
Covariance contribution 0.03
Combinations/Pair 1.38
Mean z-score -1.74
Structure conservation index 0.50
SVM decision value 0.28
SVM RNA-class probability 0.665828
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10516299 114 + 27905053
U-UGGUUCAUUUCAGUUGUGUCUCCUCUAUUUUUUU-UUAUAUUUUGUUUACAAGCUGGUCUAA-UAGUUGCUGCAUCGCUCUUUGAGGUUUACUUU---GAGCGAUUAGCAUAGUGGCC
.-.(((.(((((((((((((.......(((......-..))).......))).)))))).....-....(((((.(((((((...(((.....))).---)))))))))))).))))))) ( -25.84)
>DroSec_CAF1 166458 104 + 1
U-UGGUUC-----AGUUGU---UCCACUAUUU--UU-UUAUAUUUUGUUUACAAGCGGUUCUAA-UAGUUGCUGCAACGCUUUUUGAGGUUUACCUU---AAGCGAUUAGCAUAGUGGUC
.-......-----......---.(((((((..--..-.................(((((.....-.....)))))..((((...(((((....))))---)))))......))))))).. ( -23.00)
>DroSim_CAF1 62760 104 + 1
U-UGGUUC-----AGUUGU---UCCACUAUUU--UU-UUAUAUUUUGUUUACAAGCGGUUCUAA-UAGUUGCUGCAACGCUUUUUGAGGUUUACCUU---AAGCGAUUAGCAUAGUGGCC
.-......-----......---.(((((((..--..-.................(((((.....-.....)))))..((((...(((((....))))---)))))......))))))).. ( -22.80)
>DroEre_CAF1 63318 105 + 1
U-UGGUUC-----AGUUGU---UCGUCUAUUU--UUUGUAUAUUUUGCUUACAAGAGGGUCUAA-UAGUGGCUGCAUUGCUUGUUGAGGUUUACCUC---AAGCGAUUAGCACUGUGGCA
.-......-----......---..(((..(((--((((((.........))))))))).....(-(((((.(((.((((((...(((((....))))---))))))))))))))))))). ( -28.20)
>DroYak_CAF1 63404 105 + 1
U-UGGUUU-----AGUUGU---UCCUCUAUUU--UUUGUAUGCUUUGUUUACAAGAGGCUCUAA-UAGUGGCUGCAUCGCUUUUUGAGGUUUACCUC---AGGCGAUUAGCAUAGUCGCC
.-....((-----((....---.(((((....--..((((.((...)).)))))))))..))))-..((((((((((((((...(((((....))))---)))))))..))..)))))). ( -28.00)
>DroPer_CAF1 62118 95 + 1
UUUGGUUU-----A--------------AUUU--GU-UGCUGCUUUGUUUACCCACGACAGAAGGCAG-UGCUUGAUCGCA--CAGAGGUUUACCUUUCCGACCAUUUAGCAUAUGGUCA
...((...-----.--------------....--..-((((..((((((.......)))))).))))(-(((......)))--)(((((....)))))))((((((.......)))))). ( -25.50)
>consensus
U_UGGUUC_____AGUUGU___UCCUCUAUUU__UU_UUAUAUUUUGUUUACAAGCGGCUCUAA_UAGUUGCUGCAUCGCUUUUUGAGGUUUACCUU___AAGCGAUUAGCAUAGUGGCC
......................................................................((((...(((((...((((....))))...)))))..))))......... (-12.84 = -12.87 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 10,516,299 – 10,516,413
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.27
Mean single sequence MFE -20.75
Consensus MFE -7.55
Energy contribution -8.22
Covariance contribution 0.67
Combinations/Pair 1.18
Mean z-score -2.24
Structure conservation index 0.36
SVM decision value 0.61
SVM RNA-class probability 0.797353
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10516299 114 - 27905053
GGCCACUAUGCUAAUCGCUC---AAAGUAAACCUCAAAGAGCGAUGCAGCAACUA-UUAGACCAGCUUGUAAACAAAAUAUAA-AAAAAAAUAGAGGAGACACAACUGAAAUGAACCA-A
((......((((.(((((((---...............)))))))..))))....-......(((.((((........(((..-......)))..(....)))))))).......)).-. ( -20.46)
>DroSec_CAF1 166458 104 - 1
GACCACUAUGCUAAUCGCUU---AAGGUAAACCUCAAAAAGCGUUGCAGCAACUA-UUAGAACCGCUUGUAAACAAAAUAUAA-AA--AAAUAGUGGA---ACAACU-----GAACCA-A
..((((((((((...(((((---.(((....)))....)))))....))).....-..........(((....))).......-..--..))))))).---......-----......-. ( -19.60)
>DroSim_CAF1 62760 104 - 1
GGCCACUAUGCUAAUCGCUU---AAGGUAAACCUCAAAAAGCGUUGCAGCAACUA-UUAGAACCGCUUGUAAACAAAAUAUAA-AA--AAAUAGUGGA---ACAACU-----GAACCA-A
..((((((((((...(((((---.(((....)))....)))))....))).....-..........(((....))).......-..--..))))))).---......-----......-. ( -19.30)
>DroEre_CAF1 63318 105 - 1
UGCCACAGUGCUAAUCGCUU---GAGGUAAACCUCAACAAGCAAUGCAGCCACUA-UUAGACCCUCUUGUAAGCAAAAUAUACAAA--AAAUAGACGA---ACAACU-----GAACCA-A
.....(((((((.((.((((---((((....)))))...))).))..)))..(((-((.(.....)(((((.........))))).--.)))))....---...)))-----).....-. ( -17.20)
>DroYak_CAF1 63404 105 - 1
GGCGACUAUGCUAAUCGCCU---GAGGUAAACCUCAAAAAGCGAUGCAGCCACUA-UUAGAGCCUCUUGUAAACAAAGCAUACAAA--AAAUAGAGGA---ACAACU-----AAACCA-A
(((.....(((..(((((.(---((((....)))))....)))))))))))....-((((..(((((((((.........))))..--....))))).---....))-----))....-. ( -23.90)
>DroPer_CAF1 62118 95 - 1
UGACCAUAUGCUAAAUGGUCGGAAAGGUAAACCUCUG--UGCGAUCAAGCA-CUGCCUUCUGUCGUGGGUAAACAAAGCAGCA-AC--AAAU--------------U-----AAACCAAA
.((((((.......))))))((.((((((.......(--(((......)))-)))))))((((..((......))..))))..-..--....--------------.-----...))... ( -24.01)
>consensus
GGCCACUAUGCUAAUCGCUU___AAGGUAAACCUCAAAAAGCGAUGCAGCAACUA_UUAGAACCGCUUGUAAACAAAAUAUAA_AA__AAAUAGAGGA___ACAACU_____GAACCA_A
.........(((...(((((....(((....)))....)))))....)))...................................................................... ( -7.55 =  -8.22 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:54 2006