Locus 1173

Sequence ID 2R_DroMel_CAF1
Location 4,651,305 – 4,651,445
Length 140
Max. P 0.830156
window2056 window2057

overview

Window 6

Location 4,651,305 – 4,651,409
Length 104
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 84.01
Mean single sequence MFE -27.43
Consensus MFE -15.44
Energy contribution -18.12
Covariance contribution 2.69
Combinations/Pair 1.13
Mean z-score -2.69
Structure conservation index 0.56
SVM decision value 0.50
SVM RNA-class probability 0.761439
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4651305 104 + 20766785
AUCAGCGAUCUGCUUAGCCAGUGAACUGUUCUGAACUGCUAAUUGAUAAUAUGUAUGCGGCAACACCU---ACAUAUGUACAUACGUAUGUGUAUACUUACAUA---U-------UU
.....((((..((((((.(((....)))..))))...))..)))).......(((((((....)....---((((((((....)))))))))))))).......---.-------.. ( -23.00)
>DroSec_CAF1 5703 104 + 1
AUCAGCGAUCUGCUUAGCCAGUGAACUGUUCUGAACUGCUAAUUGAUAAUAUGUAUGCGGCAACACCU---ACAUACAUACAUAUGUAUGUAUGUGUAUACUUA---U-------UU
.....((((..((((((.(((....)))..))))...))..))))..((((.(((((((....)....---((((((((((....)))))))))))))))).))---)-------). ( -29.00)
>DroSim_CAF1 5988 104 + 1
AUCAGCGAUCUGCUUAGCCAGUGAACUGUUCUGAACUGCUAAUUGAUAAUAUGUAUGCGGCAACACCU---ACAUACAUACAUAUGUAUGUGUGUGUAUACUUA---U-------UU
.....((((..((((((.(((....)))..))))...))..))))..((((.(((((((....)....---((((((((((....)))))))))))))))).))---)-------). ( -29.00)
>DroEre_CAF1 5881 109 + 1
AUCAGCGAUCUGCUUAGUCAGUGAACUGUUCUGAACUGCUAAUUGAUAAUAUGUAUGGGGCAACACCUUGUACAUAUGUACAUAUG--------CAUAUACUUUUGAUUCGCACACU
....((((((...((((.(((....)))..))))..(((....((...(((((((..(((.....)))..)))))))...))...)--------)).........)).))))..... ( -28.70)
>consensus
AUCAGCGAUCUGCUUAGCCAGUGAACUGUUCUGAACUGCUAAUUGAUAAUAUGUAUGCGGCAACACCU___ACAUACAUACAUAUGUAUGUGUGUAUAUACUUA___U_______UU
((((((.....))((((.((((............)))))))).)))).....(((((((....).......((((((((((....))))))))))))))))................ (-15.44 = -18.12 +   2.69)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 4,651,345 – 4,651,445
Length 100
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 81.06
Mean single sequence MFE -25.05
Consensus MFE -13.61
Energy contribution -13.55
Covariance contribution -0.06
Combinations/Pair 1.17
Mean z-score -2.54
Structure conservation index 0.54
SVM decision value 0.71
SVM RNA-class probability 0.830156
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4651345 100 - 20766785
UAAGUGGCAAAUGCGACGCAGUUUCAACUCGAAUCUAA-------A---UAUGUAAGUAUACACAUACGUAUGUACAUAUGU---AGGUGUUGCCGCAUACAUAUUAUCAAUU
...(((((((......((.(((....))))).(((((.-------(---((((((..(((((......)))))))))))).)---)))).)))))))................ ( -25.10)
>DroSec_CAF1 5743 100 - 1
UAAGUGGCAAAUGCGACGCAGUUUCAACUCGAAUCUAA-------A---UAAGUAUACACAUACAUACAUAUGUAUGUAUGU---AGGUGUUGCCGCAUACAUAUUAUCAAUU
...(((((((((((.....((.(((.....))).))..-------.---...)))).(((.(((((((((....))))))))---).))))))))))................ ( -26.70)
>DroSim_CAF1 6028 100 - 1
UAAGUGGCAAAUGCGACGCAGUUUCAACUCGAAUCUAA-------A---UAAGUAUACACACACAUACAUAUGUAUGUAUGU---AGGUGUUGCCGCAUACAUAUUAUCAAUU
...(((((((((((.....((.(((.....))).))..-------.---...)))).(((..((((((((....))))))))---..))))))))))................ ( -25.50)
>DroEre_CAF1 5921 105 - 1
UAAGUAGAAAGUGCGACGCAGUUUUAGCUCGAAUCGAGUGUGCGAAUCAAAAGUAUAUG--------CAUAUGUACAUAUGUACAAGGUGUUGCCCCAUACAUAUUAUCAAUU
...(((....(.(((((((.......(((((...)))))(((((.(((....).)).))--------))).(((((....)))))..))))))))...)))............ ( -22.90)
>consensus
UAAGUGGCAAAUGCGACGCAGUUUCAACUCGAAUCUAA_______A___UAAGUAUACACACACAUACAUAUGUACAUAUGU___AGGUGUUGCCGCAUACAUAUUAUCAAUU
...(((((....(((((((((.(((.....))).))..............................((((((....)))))).....))))))).)).)))............ (-13.61 = -13.55 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:17 2006