Locus 3220

Sequence ID X_DroMel_CAF1
Location 8,527,641 – 8,527,754
Length 113
Max. P 0.988144
window5283 window5284

overview

Window 3

Location 8,527,641 – 8,527,754
Length 113
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -26.60
Consensus MFE -21.04
Energy contribution -21.08
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -2.65
Structure conservation index 0.79
SVM decision value 2.11
SVM RNA-class probability 0.988144
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8527641 113 + 22224390
AACAGCUGAUU--GAGGCUAAACUUGAAAUACCCUAUAAUUACAGGGUACAUAGAGUCGGGUACAUAAUGUCGCGUGACAAGCGACACUAAGAACGAAAAAAGAGAAGAAUAGGG
.....((((((--(((......)))....((((((........)))))).....))))))((.(.((.((((((.......)))))).)).).)).................... ( -23.50)
>DroSec_CAF1 2549 109 + 1
AACAGCUGAUU--AAGGCUAAACUUGAAAUACCCUGUAAUUACAGGGUACAUGGAGUG----AAUGAAUGUUGCGUGACAAGCGACACUAAGAACGAAAAUAGAAAAGAAUAGAG
...((((....--..))))..((((.(..((((((((....))))))))..).)))).----......((((((.......))))))............................ ( -25.90)
>DroSim_CAF1 2549 109 + 1
AACAGCUGAUU--GAGGCUAAACUUGAAAUACCCUGUAAUUACAGGGUACAUGGAGUG----AAUGAAUGUUGCGUGACAAGCGACACUAAGAACGAAAAUAGAAAAGAAUAGGG
...((((....--..))))..((((.(..((((((((....))))))))..).)))).----......((((((.......))))))............................ ( -25.90)
>DroEre_CAF1 2492 107 + 1
AACAGCUGAUGCAGUGGUUAAACUUGAAAUACCCUGUAAUUACAGGGUACAUCGAGU--------GAAUGUUGCGUGACAAGCGCCAGUAGGAACGAAAAUAAAAAGCAAUAGAG
....(((.(((((..(.....((((((..((((((((....))))))))..))))))--------...)..))))).....(..((....))..)..........)))....... ( -29.40)
>DroYak_CAF1 2497 107 + 1
AACAGCUGAUGCGGUGGCUAAACUUGAAAUACCCUGUAAUUACAGGGUACAUUGAAU--------GAAUGUUGCGUGACAAGCGUCAGUAGGAACGAAAAUAGAAAACAAUAGAA
..(.((((((((.((.((...........((((((((....))))))))((((....--------.))))....)).))..)))))))).)........................ ( -28.30)
>consensus
AACAGCUGAUU__GAGGCUAAACUUGAAAUACCCUGUAAUUACAGGGUACAUGGAGU_____A__GAAUGUUGCGUGACAAGCGACACUAAGAACGAAAAUAGAAAAGAAUAGAG
...((((........))))...((((...((((((((....))))))))...................((((((.......)))))).))))....................... (-21.04 = -21.08 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,527,641 – 8,527,754
Length 113
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 86.11
Mean single sequence MFE -22.23
Consensus MFE -15.28
Energy contribution -14.96
Covariance contribution -0.32
Combinations/Pair 1.11
Mean z-score -2.32
Structure conservation index 0.69
SVM decision value 0.73
SVM RNA-class probability 0.834390
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8527641 113 - 22224390
CCCUAUUCUUCUCUUUUUUCGUUCUUAGUGUCGCUUGUCACGCGACAUUAUGUACCCGACUCUAUGUACCCUGUAAUUAUAGGGUAUUUCAAGUUUAGCCUC--AAUCAGCUGUU
....................((...(((((((((.......)))))))))...))..((((....(((((((((....)))))))))....))))((((...--.....)))).. ( -28.20)
>DroSec_CAF1 2549 109 - 1
CUCUAUUCUUUUCUAUUUUCGUUCUUAGUGUCGCUUGUCACGCAACAUUCAUU----CACUCCAUGUACCCUGUAAUUACAGGGUAUUUCAAGUUUAGCCUU--AAUCAGCUGUU
..........................(((((.((.......)).)))))....----.(((....(((((((((....)))))))))....))).((((...--.....)))).. ( -20.10)
>DroSim_CAF1 2549 109 - 1
CCCUAUUCUUUUCUAUUUUCGUUCUUAGUGUCGCUUGUCACGCAACAUUCAUU----CACUCCAUGUACCCUGUAAUUACAGGGUAUUUCAAGUUUAGCCUC--AAUCAGCUGUU
..........................(((((.((.......)).)))))....----.(((....(((((((((....)))))))))....))).((((...--.....)))).. ( -20.10)
>DroEre_CAF1 2492 107 - 1
CUCUAUUGCUUUUUAUUUUCGUUCCUACUGGCGCUUGUCACGCAACAUUC--------ACUCGAUGUACCCUGUAAUUACAGGGUAUUUCAAGUUUAACCACUGCAUCAGCUGUU
.......(((..........((.((....)).)).......(((......--------(((.((.(((((((((....))))))))).)).)))........)))...))).... ( -23.54)
>DroYak_CAF1 2497 107 - 1
UUCUAUUGUUUUCUAUUUUCGUUCCUACUGACGCUUGUCACGCAACAUUC--------AUUCAAUGUACCCUGUAAUUACAGGGUAUUUCAAGUUUAGCCACCGCAUCAGCUGUU
...........................((((.(((((.......(((((.--------....)))))(((((((....)))))))....)))))...((....)).))))..... ( -19.20)
>consensus
CUCUAUUCUUUUCUAUUUUCGUUCUUAGUGUCGCUUGUCACGCAACAUUC__U_____ACUCCAUGUACCCUGUAAUUACAGGGUAUUUCAAGUUUAGCCUC__AAUCAGCUGUU
................................((((((......)))...........(((....(((((((((....)))))))))....)))..............))).... (-15.28 = -14.96 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:07 2006