Locus 2128

Sequence ID 2R_DroMel_CAF1
Location 7,960,616 – 7,960,724
Length 108
Max. P 0.758294
window3529 window3530

overview

Window 9

Location 7,960,616 – 7,960,724
Length 108
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 75.64
Mean single sequence MFE -25.90
Consensus MFE -14.19
Energy contribution -14.55
Covariance contribution 0.36
Combinations/Pair 1.30
Mean z-score -1.78
Structure conservation index 0.55
SVM decision value 0.34
SVM RNA-class probability 0.695699
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7960616 108 + 20766785
CAUGCUCCCUGUUGCUUU-UUCACAUUUUUUUUUUCC-UUUCAGCUC--AGUU---AGUAAAUUGAGCAUCAACGUGCGCUCCGGCUGACUUAGCUGUCCCUGGAGUUCCUU---UUG
...((........))...-..............((((-...(((((.--((((---(((.....(.((((....)))).)....))))))).))))).....))))......---... ( -24.60)
>DroSec_CAF1 12574 105 + 1
CAUGCUCCCUGUUGCUUU-UUAGCAUUUU---UUUCC-UUUCAGCUC--AGUU---AGUAAAUUGAGCAUCAACGUGCGCUCCGGCUGACUUAGCUGUCCCCGGAGUUCCUU---UUG
...((.(.....((((..-..))))....---.....-.....((((--((((---....))))))))......).))(((((((..(((......))).))))))).....---... ( -29.60)
>DroSim_CAF1 12270 105 + 1
CAUGCUCGCUGUUGCUUU-UUCACAUUUU---UUUCC-UUUCAGCUC--AGUU---AGUAAAUUGAGCAUCAACGUGCGCUCCGGCUGACUUAGCUGUCCCCGGAGUUCCUU---UUG
...((.(((....))...-..........---.....-.....((((--((((---....))))))))......).))(((((((..(((......))).))))))).....---... ( -28.70)
>DroEre_CAF1 12628 101 + 1
CGUGCUCCCUGUUGCUUU-UUCA--UU-----UUUUC-UUUCAGCUC--AGUU---AGUAAAUUGAGCAUCAACGUGCGCUCCGGCUGACUUAGCUGUCCCCGGAGUUCUUU---UUG
(((((........))...-....--..-----.....-.....((((--((((---....))))))))....))).(.(((((((..(((......))).))))))).)...---... ( -26.90)
>DroMoj_CAF1 18760 111 + 1
CUUUCUUGCUCUUGCUCUGCUUCCAU------UACUUUCUGC-ACUUCUUCUUUGGCGUAAAUUGAGCAUCAAGAUGAAAGCUGGAAGGAAAAGUUAUGCCAUAAGUAGCUUAAGUUC
((((((.(((((((...(((((...(------(((.....((-.(.........)))))))...))))).))))).....)).))))))..(((((((.......)))))))...... ( -19.70)
>consensus
CAUGCUCCCUGUUGCUUU_UUCACAUUUU___UUUCC_UUUCAGCUC__AGUU___AGUAAAUUGAGCAUCAACGUGCGCUCCGGCUGACUUAGCUGUCCCCGGAGUUCCUU___UUG
...((.(..((.(((((...............................................))))).))..).))(((((((..(((......))).)))))))........... (-14.19 = -14.55 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,960,616 – 7,960,724
Length 108
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 75.64
Mean single sequence MFE -26.30
Consensus MFE -13.63
Energy contribution -15.15
Covariance contribution 1.52
Combinations/Pair 1.21
Mean z-score -1.87
Structure conservation index 0.52
SVM decision value 0.49
SVM RNA-class probability 0.758294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7960616 108 - 20766785
CAA---AAGGAACUCCAGGGACAGCUAAGUCAGCCGGAGCGCACGUUGAUGCUCAAUUUACU---AACU--GAGCUGAAA-GGAAAAAAAAAAUGUGAA-AAAGCAACAGGGAGCAUG
...---......((((..(..(((((.(((.((...((((((.....).)))))......))---.)))--.)))))...-............(((...-...))).)..)))).... ( -22.90)
>DroSec_CAF1 12574 105 - 1
CAA---AAGGAACUCCGGGGACAGCUAAGUCAGCCGGAGCGCACGUUGAUGCUCAAUUUACU---AACU--GAGCUGAAA-GGAAA---AAAAUGCUAA-AAAGCAACAGGGAGCAUG
(((---...(..((((((.(((......)))..))))))..)...)))((((((........---..((--(..((....-))...---....((((..-..)))).))).)))))). ( -30.30)
>DroSim_CAF1 12270 105 - 1
CAA---AAGGAACUCCGGGGACAGCUAAGUCAGCCGGAGCGCACGUUGAUGCUCAAUUUACU---AACU--GAGCUGAAA-GGAAA---AAAAUGUGAA-AAAGCAACAGCGAGCAUG
...---......((((((.(((......)))..)))))).((.(((((.((((...(((((.---....--...((....-))...---.....)))))-..)))).))))).))... ( -33.19)
>DroEre_CAF1 12628 101 - 1
CAA---AAAGAACUCCGGGGACAGCUAAGUCAGCCGGAGCGCACGUUGAUGCUCAAUUUACU---AACU--GAGCUGAAA-GAAAA-----AA--UGAA-AAAGCAACAGGGAGCACG
(((---...(..((((((.(((......)))..))))))..)...))).(((((........---..((--(.(((....-.....-----..--....-..)))..))).))))).. ( -24.43)
>DroMoj_CAF1 18760 111 - 1
GAACUUAAGCUACUUAUGGCAUAACUUUUCCUUCCAGCUUUCAUCUUGAUGCUCAAUUUACGCCAAAGAAGAAGU-GCAGAAAGUA------AUGGAAGCAGAGCAAGAGCAAGAAAG
...(((..((((....))))....(((((.(((...(((((((((((..(((.(..(((........)))...).-)))..)))..------)))))))).))).))))).))).... ( -20.70)
>consensus
CAA___AAGGAACUCCGGGGACAGCUAAGUCAGCCGGAGCGCACGUUGAUGCUCAAUUUACU___AACU__GAGCUGAAA_GGAAA___AAAAUGUGAA_AAAGCAACAGGGAGCAUG
............((((((.(((......)))..)))))).((.(.(((.((((...(((((.................................)))))...)))).))).).))... (-13.63 = -15.15 +   1.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:06 2006