Locus 1479

Sequence ID 3R_DroMel_CAF1
Location 4,282,234 – 4,282,329
Length 95
Max. P 0.996224
window2457 window2458

overview

Window 7

Location 4,282,234 – 4,282,329
Length 95
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 76.91
Mean single sequence MFE -17.22
Consensus MFE -9.24
Energy contribution -9.64
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.54
SVM decision value 2.67
SVM RNA-class probability 0.996224
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4282234 95 + 27905053
AAUGCGUAUGCUUAAUAUUGCAUAACGCCGUAUGCAUUCCAA-AUGCACAUUAACUGCACACAAAUACGGAUCCACACAUACCAAUACAACAUA--CC-------------
...((((((((........)))).)))).(((((........-.((((.......)))).........((...........)).......))))--).------------- ( -15.40)
>DroPse_CAF1 92471 101 + 1
AAUGCGUAUGCUUAAUAUUGCAUAACCCCGUAUGCAUUCCAA-AAGCACAUUAACUGCACACAGAUGCAGAUGUUCCCCCUCUCUCA---CACACCCA--CAGACAC----
...((((.(((((.....((((((......))))))......-)))))......(((((......))))))))).............---........--.......---- ( -17.00)
>DroSec_CAF1 83754 90 + 1
AAUGCGUAUGCUUAAUAUUGCAUAACGC-GUAAGCAU-CCAA-AUGCACAUUAACUGCACACAAAUACGGACCCACACAUAC-AAUA---CAUA--C---CA---------
.((((((((((........)))).))))-))..((((-....-))))...................................-....---....--.---..--------- ( -14.90)
>DroSim_CAF1 83706 94 + 1
AAUGCGUAUGCUUAAUAUUGCAUAACGCCGUAUGCAUUCCAA-AUGCACAUUAACUGCACACAAAUACGGACCCACGCAUACCAAUA---CAUA--CC--CA---------
.((((((((((........))))....((((((((((.....-))))........((....)).))))))....)))))).......---....--..--..--------- ( -19.50)
>DroWil_CAF1 93065 105 + 1
AAUGCGUAUGCUUAAUAUUGCAUAACCCCGCAUGCAUGCCAAAAAGCACAUUAACUGCACACGAACUGGCACACAAACAUAC-ACCG---CAUA--CAUACAUGCAUAUGU
.((((((((((........)))))....)))))...(((((....(((.......)))........))))).....(((((.-...(---(((.--.....)))).))))) ( -19.30)
>consensus
AAUGCGUAUGCUUAAUAUUGCAUAACGCCGUAUGCAUUCCAA_AUGCACAUUAACUGCACACAAAUACGGACCCACACAUAC_AAUA___CAUA__CA__CA_________
..(((.(((((........))))).........((((......)))).........))).................................................... ( -9.24 =  -9.64 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,282,234 – 4,282,329
Length 95
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 76.91
Mean single sequence MFE -29.30
Consensus MFE -15.52
Energy contribution -17.76
Covariance contribution 2.24
Combinations/Pair 1.16
Mean z-score -2.65
Structure conservation index 0.53
SVM decision value 2.50
SVM RNA-class probability 0.994664
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4282234 95 - 27905053
-------------GG--UAUGUUGUAUUGGUAUGUGUGGAUCCGUAUUUGUGUGCAGUUAAUGUGCAU-UUGGAAUGCAUACGGCGUUAUGCAAUAUUAAGCAUACGCAUU
-------------..--............((((((((...((((.....(((..((.....))..)))-.)))))))))))).((((.((((........))))))))... ( -26.60)
>DroPse_CAF1 92471 101 - 1
----GUGUCUG--UGGGUGUG---UGAGAGAGGGGGAACAUCUGCAUCUGUGUGCAGUUAAUGUGCUU-UUGGAAUGCAUACGGGGUUAUGCAAUAUUAAGCAUACGCAUU
----......(--((.(((((---(...(((..(....).)))(((((((((((((..(((.......-)))...)))))))))....))))........)))))).))). ( -26.70)
>DroSec_CAF1 83754 90 - 1
---------UG---G--UAUG---UAUU-GUAUGUGUGGGUCCGUAUUUGUGUGCAGUUAAUGUGCAU-UUGG-AUGCUUAC-GCGUUAUGCAAUAUUAAGCAUACGCAUU
---------..---(--((((---((((-(((((((((((((((.....(((..((.....))..)))-.)))-..))))))-))))...))))).....))))))..... ( -26.70)
>DroSim_CAF1 83706 94 - 1
---------UG--GG--UAUG---UAUUGGUAUGCGUGGGUCCGUAUUUGUGUGCAGUUAAUGUGCAU-UUGGAAUGCAUACGGCGUUAUGCAAUAUUAAGCAUACGCAUU
---------((--.(--((((---(.(((((((((((((..((((((..(((..((.....))..)))-.........))))))..)))))).))))))))))))).)).. ( -30.30)
>DroWil_CAF1 93065 105 - 1
ACAUAUGCAUGUAUG--UAUG---CGGU-GUAUGUUUGUGUGCCAGUUCGUGUGCAGUUAAUGUGCUUUUUGGCAUGCAUGCGGGGUUAUGCAAUAUUAAGCAUACGCAUU
.....((((((....--))))---))((-(((((((((((((((((.....(..((.....))..)...))))))))).((((......)))).....))))))))))... ( -36.20)
>consensus
_________UG__GG__UAUG___UAUU_GUAUGUGUGGGUCCGUAUUUGUGUGCAGUUAAUGUGCAU_UUGGAAUGCAUACGGCGUUAUGCAAUAUUAAGCAUACGCAUU
.............................((((((((...((((.....(((..((.....))..)))..)))))))))))).((((.((((........))))))))... (-15.52 = -17.76 +   2.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:35 2006