Locus 165

Sequence ID 4_DroMel_CAF1
Location 1,071,386 – 1,071,530
Length 144
Max. P 0.998192
window265 window266

overview

Window 5

Location 1,071,386 – 1,071,505
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.59
Mean single sequence MFE -26.41
Consensus MFE -12.93
Energy contribution -13.80
Covariance contribution 0.87
Combinations/Pair 1.17
Mean z-score -2.98
Structure conservation index 0.49
SVM decision value 3.03
SVM RNA-class probability 0.998192
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1071386 119 + 1281640
UAAUUCAAGUGAGUUCUCUUAAAGCACGUUGCUUA-AACUAGAAAACUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAAGUUUUUUCAUGUGAUCAUGAAAUCAUACGAAAAAACACCA
...(((....(((((.(((..((((.....)))).-....))).)))))((((.(((............))).)))))))((((((((.((((((......)))))).)))))))).... ( -31.40)
>DroSec_CAF1 4472 107 + 1
UAAUUCAAGUGAUUUCUCUUAAAGAAAC---ACUA-GACUAGAAAUCUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC----AAAACAU-----AAAACACAA
....((.((((.(((((.....))))))---))).-))....(((((((((((.(((............))).)))))))))))(((.((((...----...))))-----..))).... ( -27.70)
>DroSim_CAF1 3867 107 + 1
UAAUUCAAGUGAUUUCUCUUAAAGAAAC---ACUA-GACUAGAAAACUCGACCACCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC----AAAACAU-----AAAACACAA
....((.((((.(((((.....))))))---))).-))........(((((((((((............)))))))))))((((....((((...----...))))-----.)))).... ( -29.30)
>DroEre_CAF1 6000 97 + 1
UAAUUC-------------------ACGCUGCUUACAAAUGUAAAACUCCACCUUCAUUUCAAAGAUUUCGAUGGUGGCGUUCUGUCCAUGUGGC----AAUACAUACGAAAAAACACAA
......-------------------..((..(((((....))))(((.(((((.((..............)).))))).)))........)..))----..................... ( -17.24)
>consensus
UAAUUCAAGUGAUUUCUCUUAAAGAAAC___ACUA_AACUAGAAAACUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC____AAAACAU_____AAAACACAA
..........................................(((((((((((.(((............))).))))))))))).....((((......................)))). (-12.93 = -13.80 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,071,425 – 1,071,530
Length 105
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 75.61
Mean single sequence MFE -23.53
Consensus MFE -13.09
Energy contribution -13.78
Covariance contribution 0.69
Combinations/Pair 1.17
Mean z-score -2.06
Structure conservation index 0.56
SVM decision value 0.76
SVM RNA-class probability 0.843408
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1071425 105 + 1281640
AGAAAACUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAAGUUUUUUCAUGUGAUCAUGAAAUCAUACGAAAAAACACCAUACUU-----------CGCAAGAAACA--ACAUGUGCG
.......((((((.(((............))).)))))).((((((((.((((((......)))))).)))))))).......((-----------(....)))...--......... ( -27.10)
>DroSec_CAF1 4508 96 + 1
AGAAAUCUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC----AAAACAU-----AAAACACAAUACUU-----------CGGAAGAAACA--ACAUGCGCG
..(((((((((((.(((............))).)))))))))))((.((((((..----....)..-----............((-----------(....)))...--))))).)). ( -25.30)
>DroSim_CAF1 3903 96 + 1
AGAAAACUCGACCACCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC----AAAACAU-----AAAACACAAUACUU-----------CGCAAGAAACA--ACAUGCGCG
......(((((((((((............)))))))))))((.((((.((((...----...))))-----............((-----------(....)))..)--))).))... ( -26.80)
>DroEre_CAF1 6021 113 + 1
GUAAAACUCCACCUUCAUUUCAAAGAUUUCGAUGGUGGCGUUCUGUCCAUGUGGC----AAUACAUACGAAAAAACACAAUACUUCUAAUUAUGAUUACAAGAAACAUA-AAUGUGCA
....(((.(((((.((..............)).))))).)))..(..((((((..----................)))....(((.((((....)))).))).......-.)))..). ( -14.91)
>consensus
AGAAAACUCGACCUCCAUUUUGAAGAUUUUGGUGGUUGAGGUUUGUUCAUGUGAC____AAAACAU_____AAAACACAAUACUU___________CGCAAGAAACA__ACAUGCGCG
..(((((((((((.(((............))).)))))))))))((.((((((......................)))..................(....).........))).)). (-13.09 = -13.78 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:52 2006