Locus 5238

Sequence ID X_DroMel_CAF1
Location 13,668,362 – 13,668,471
Length 109
Max. P 0.737680
window8486 window8487

overview

Window 6

Location 13,668,362 – 13,668,471
Length 109
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.89
Mean single sequence MFE -28.10
Consensus MFE -12.62
Energy contribution -11.90
Covariance contribution -0.72
Combinations/Pair 1.21
Mean z-score -2.61
Structure conservation index 0.45
SVM decision value 0.44
SVM RNA-class probability 0.737680
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13668362 109 + 22224390
UCUGCAAUUAAAUGAGU----UGGCAACGCCGGCA--AGUACAGUUCACACAAAACACCCGCUAAUACGAACUUGUAUUAUACAU---UAUUCACUC-GCAAGUGAAUUAAUUGCCAUA
...(((((((((((.((----((((...)))))).--((((((((((.....................)))).))))))...)))---)(((((((.-...)))))))))))))).... ( -26.60)
>DroSec_CAF1 3498 105 + 1
UCUGCAAUUAAAUGAGG----UGGCAACGCCGGCA--CGUACAGUUUACACAAAACA----CUAAUGCCAACUUGUAUUAUACAU---UAUUCACUC-GCAAGUGAAUUAAUUGCCAUA
...(((((((((((.((----((....))))((((--......((((.....)))).----....)))).............)))---)(((((((.-...)))))))))))))).... ( -27.50)
>DroSim_CAF1 4145 105 + 1
UCUGCAAUUAAAUGAGG----UGGCAACGCCGGCA--CGUACAGUUUACACAAAACA----CUAAUGCCAACUUGUAUUAUACAU---UAUUCACUC-GCAAGUGAAUUAAUUGCCAUA
...(((((((((((.((----((....))))((((--......((((.....)))).----....)))).............)))---)(((((((.-...)))))))))))))).... ( -27.50)
>DroEre_CAF1 3569 109 + 1
UCUGCAAUUAAUUGAGG----UGGCAACGCUUGCG--CGUACAGUUUACACAAAACACACGCUAAUGCCAACUUGUAUUAUACAU---UACUCACUC-GCAAGUGAAUUAAUUGCCAAA
...((((((((((....----.(....)(((((((--(((...((((.....))))..))))((((((......)))))).....---.........-)))))).)))))))))).... ( -27.10)
>DroYak_CAF1 3484 112 + 1
UCUGCAAUUAAAUGAGG----UGGCAACGCCGGCG--CGUACAGUUUACACAAAACACACGCUAAUACCAACUUGUAUUAUACAUUAUUACUCACUC-GCAAGUGAAUUAAUUGCUAUG
...(((((((((((.((----((....))))...(--(((...((((.....))))..))))((((((......))))))..)))).....(((((.-...)))))..))))))).... ( -28.00)
>DroAna_CAF1 6637 109 + 1
UGAGC-------UGAGCUGCCUGGCAACUCUGGCGGAGGUACAGUCGACACAAAACACAGGCAACUCUCGACAUGUAUGAUACAG---GACCCGCUCCGGGAGCAGAUCGGUGGCUAGA
...((-------(((.(((((((....(((.....)))((((((((((..........((....)).))))).)))))....)))---..((((...)))).)))).)))))....... ( -31.90)
>consensus
UCUGCAAUUAAAUGAGG____UGGCAACGCCGGCA__CGUACAGUUUACACAAAACACACGCUAAUGCCAACUUGUAUUAUACAU___UACUCACUC_GCAAGUGAAUUAAUUGCCAUA
.....................((((((...........((((((((.......................))).))))).............(((((.....))))).....)))))).. (-12.62 = -11.90 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,668,362 – 13,668,471
Length 109
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.89
Mean single sequence MFE -29.82
Consensus MFE -18.13
Energy contribution -17.75
Covariance contribution -0.38
Combinations/Pair 1.22
Mean z-score -1.52
Structure conservation index 0.61
SVM decision value -0.00
SVM RNA-class probability 0.531583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13668362 109 - 22224390
UAUGGCAAUUAAUUCACUUGC-GAGUGAAUA---AUGUAUAAUACAAGUUCGUAUUAGCGGGUGUUUUGUGUGAACUGUACU--UGCCGGCGUUGCCA----ACUCAUUUAAUUGCAGA
....((((((((((((((...-.))))))((---((((.((((((......))))))(((((((....((....))..))))--)))..))))))...----......))))))))... ( -26.60)
>DroSec_CAF1 3498 105 - 1
UAUGGCAAUUAAUUCACUUGC-GAGUGAAUA---AUGUAUAAUACAAGUUGGCAUUAG----UGUUUUGUGUAAACUGUACG--UGCCGGCGUUGCCA----CCUCAUUUAAUUGCAGA
..(((((((..(((((((...-.))))))).---.............((((((((...----.((((.....)))).....)--))))))))))))))----................. ( -27.80)
>DroSim_CAF1 4145 105 - 1
UAUGGCAAUUAAUUCACUUGC-GAGUGAAUA---AUGUAUAAUACAAGUUGGCAUUAG----UGUUUUGUGUAAACUGUACG--UGCCGGCGUUGCCA----CCUCAUUUAAUUGCAGA
..(((((((..(((((((...-.))))))).---.............((((((((...----.((((.....)))).....)--))))))))))))))----................. ( -27.80)
>DroEre_CAF1 3569 109 - 1
UUUGGCAAUUAAUUCACUUGC-GAGUGAGUA---AUGUAUAAUACAAGUUGGCAUUAGCGUGUGUUUUGUGUAAACUGUACG--CGCAAGCGUUGCCA----CCUCAAUUAAUUGCAGA
....((((((((((((((...-.))))))).---............((.(((((...((((((((...((....))...)))--)))..))..)))))----.))....)))))))... ( -31.40)
>DroYak_CAF1 3484 112 - 1
CAUAGCAAUUAAUUCACUUGC-GAGUGAGUAAUAAUGUAUAAUACAAGUUGGUAUUAGCGUGUGUUUUGUGUAAACUGUACG--CGCCGGCGUUGCCA----CCUCAUUUAAUUGCAGA
....((((((((((((((...-.)))))))................((.(((((...((((((((...((....))...)))--)))..))..)))))----.))....)))))))... ( -29.60)
>DroAna_CAF1 6637 109 - 1
UCUAGCCACCGAUCUGCUCCCGGAGCGGGUC---CUGUAUCAUACAUGUCGAGAGUUGCCUGUGUUUUGUGUCGACUGUACCUCCGCCAGAGUUGCCAGGCAGCUCA-------GCUCA
...(((....(((((((((...)))))))))---..................((((((((((.((((((.((.((.......)).))))))...)))))))))))).-------))).. ( -35.70)
>consensus
UAUGGCAAUUAAUUCACUUGC_GAGUGAAUA___AUGUAUAAUACAAGUUGGCAUUAGCGUGUGUUUUGUGUAAACUGUACG__CGCCGGCGUUGCCA____CCUCAUUUAAUUGCAGA
..(((((((..((((((((...))))))))......((((((((((((.................)))))))....)))))..........)))))))..................... (-18.13 = -17.75 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:59 2006