Locus 7040

Sequence ID 3R_DroMel_CAF1
Location 18,576,402 – 18,576,615
Length 213
Max. P 0.991045
window11401 window11402 window11403

overview

Window 1

Location 18,576,402 – 18,576,502
Length 100
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 78.62
Mean single sequence MFE -23.14
Consensus MFE -17.94
Energy contribution -18.63
Covariance contribution 0.69
Combinations/Pair 1.16
Mean z-score -2.24
Structure conservation index 0.78
SVM decision value 1.99
SVM RNA-class probability 0.985045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18576402 100 - 27905053
AGUUCAAUCACUGCUUUGCUGCCUGGGCUGCCAGGUAACAAAAAGUUAUUAAAAACACAACU--ACUUCUCCUCUUAAGUUAUUUGCAGCUAAAUGGCAGAA
..................(((((..((((((.(((((((...(((.................--.........)))..)))))))))))))....))))).. ( -22.57)
>DroSec_CAF1 1446 90 - 1
AGUUCAAUCACUGCUUUGCUGCCAGGGUUGCCACGAAAUGA-AAGUUAUUAAAAACAUUAU-----------UAUUACGUUAUAUGCAGCUAAAUGGCAGAA
..................((((((.((((((.(((.(((((-(((((......))).)).)-----------)))).))).....))))))...)))))).. ( -20.70)
>DroSim_CAF1 1453 90 - 1
AGUUCAAUCACUGCUUUGCUGCCAGGGCUGCCAGGUAAUGA-AAGUUAUUAAAAACAAUAU-----------UCUUACGUUAUUUGUAGCUAAAUGGCAGAA
..................((((((.((((((.((((((((.-(((.((((......)))).-----------.))).))))))))))))))...)))))).. ( -27.40)
>DroEre_CAF1 1465 97 - 1
AGUUGAAUCACUGCUUUGCUGCCAGGGCUGCCAGGUACUGA-AAGUAAUA----CCACUAAUUAAUUUCUUCACUUAAGUUAUUUGCAGCUAAAUUGCAGUA
.........(((((...(((((...((((...((((...((-((.((((.----......)))).))))...)))).))))....)))))......))))). ( -21.90)
>consensus
AGUUCAAUCACUGCUUUGCUGCCAGGGCUGCCAGGUAAUGA_AAGUUAUUAAAAACACUAU___________UCUUAAGUUAUUUGCAGCUAAAUGGCAGAA
..................((((((.((((((.(((((((.......................................)))))))))))))...)))))).. (-17.94 = -18.63 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 18,576,502 – 18,576,615
Length 113
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 74.13
Mean single sequence MFE -34.47
Consensus MFE -18.67
Energy contribution -20.57
Covariance contribution 1.89
Combinations/Pair 1.30
Mean z-score -2.49
Structure conservation index 0.54
SVM decision value 2.25
SVM RNA-class probability 0.991045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18576502 113 + 27905053
GUUACUUUCUUAGGCAGACCAUGUCACUGCAUUUGCAGGCAAAGCCCUGCAGUAGUAACCAUUAUUU--UGUAUGACCAUCCAUGUGAUGGUCACCCUAUGCGAGUAACUGUUCG
(((((((.(.((((..(((((.((.(((((...((((((......))))))))))).)).......(--..((((......))))..))))))..)))).).)))))))...... ( -36.60)
>DroVir_CAF1 2331 110 + 1
GCUACGCAAUUAGGCGGACCGUU-GGCUGUAUUG-AAGGUAGUCGUGCAUCAAAAACAUCGAAAGUCUGUGA---ACAAGUCGUACUCUGGUCACACUUAUUUGGUAACAGCUAC
....(((......)))......(-((((((((..-((...(((.(((.((((.......(((.....((...---.))..))).....))))))))))..))..)).))))))). ( -25.00)
>DroSec_CAF1 1536 113 + 1
GUUACUUUAUUAGGCAUACCAUGUCACUGUAUUGCCAGGCAAAGCCCUGCAGUAGUAACCAUCAUUU--UGCAUGACCAACCAUGUGAUGGCCACCCUAAGCGAGUAACUGUUCG
(((((((..(((((...............((((((..(((...)))..))))))((..(((((....--.(((((......))))))))))..)))))))..)))))))...... ( -31.10)
>DroSim_CAF1 1543 113 + 1
GUUACUUUUGUAGGCAGACCAUGCCACUGCAUUUGCAGGCAAAGCCCUGCAGUAGUAACCAUCAUUU--UGCAUGACCAACCAUGUGAUGGUCACCCUAAGCGAGUAACUGUUCA
(((((((...((((..((((((...(((((...((((((......)))))))))))...........--.(((((......))))).))))))..))))...)))))))...... ( -38.20)
>DroEre_CAF1 1562 113 + 1
GUUACUCUCUUAGGAAGACCAUGCCACUGCAUUCUCAAGCAAAGGCCUACUGAAGUAACCAUCAUUC--GGCAUGCCCAACCAUGGGAUGGUCACCCUAAGCGAGUAACUGUUCG
(((((((.((((((..((((((.(((.(((........)))..(((...(((((..........)))--))...)))......))).))))))..)))))).)))))))...... ( -43.00)
>DroYak_CAF1 1449 113 + 1
GUUACUUUCUUAGGAAGACCAUGCCACUUCAUUCGCAAGCAAAGCCCUACGGUAGUAACCAUCAUUU--CGCAUGACCAGUCAUGUGAUGGUCACCCUAAGCGCGUAACUGUUCG
(((((...((((((..((((((((..........))).............(((....)))......(--(((((((....)))))))))))))..))))))...)))))...... ( -32.90)
>consensus
GUUACUUUCUUAGGCAGACCAUGCCACUGCAUUCGCAGGCAAAGCCCUACAGUAGUAACCAUCAUUU__UGCAUGACCAACCAUGUGAUGGUCACCCUAAGCGAGUAACUGUUCG
(((((((.((((((..((((((.....(((........))).............................(((((......))))).))))))..)))))).)))))))...... (-18.67 = -20.57 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,576,502 – 18,576,615
Length 113
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.13
Mean single sequence MFE -37.40
Consensus MFE -19.63
Energy contribution -21.80
Covariance contribution 2.17
Combinations/Pair 1.30
Mean z-score -2.49
Structure conservation index 0.52
SVM decision value 2.18
SVM RNA-class probability 0.989820
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18576502 113 - 27905053
CGAACAGUUACUCGCAUAGGGUGACCAUCACAUGGAUGGUCAUACA--AAAUAAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGACAUGGUCUGCCUAAGAAAGUAAC
......((((((..(.(((((((((((((.....)))))))))...--........((((((.(((((((......))))))...).))))))........)))).)..)))))) ( -39.20)
>DroVir_CAF1 2331 110 - 1
GUAGCUGUUACCAAAUAAGUGUGACCAGAGUACGACUUGU---UCACAGACUUUCGAUGUUUUUGAUGCACGACUACCUU-CAAUACAGCC-AACGGUCCGCCUAAUUGCGUAGC
......((((((((.((.(((.((((.(((.....)))((---(((.((((.......)))).))).))...........-..........-...))))))).)).))).))))) ( -20.50)
>DroSec_CAF1 1536 113 - 1
CGAACAGUUACUCGCUUAGGGUGGCCAUCACAUGGUUGGUCAUGCA--AAAUGAUGGUUACUACUGCAGGGCUUUGCCUGGCAAUACAGUGACAUGGUAUGCCUAAUAAAGUAAC
......((((((.((....((((((((((((((((....)))))..--...)))))))))))...)).((((..((((((.((......)).)).)))).)))).....)))))) ( -35.50)
>DroSim_CAF1 1543 113 - 1
UGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCA--AAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGGCAUGGUCUGCCUACAAAAGUAAC
......((((((....(((((((((((((((((((....)))))..--...)))))))))))...(((((.((.(((((((....)))..)))).))))))))))....)))))) ( -39.30)
>DroEre_CAF1 1562 113 - 1
CGAACAGUUACUCGCUUAGGGUGACCAUCCCAUGGUUGGGCAUGCC--GAAUGAUGGUUACUUCAGUAGGCCUUUGCUUGAGAAUGCAGUGGCAUGGUCUUCCUAAGAGAGUAAC
......(((((((.(((((((.((((((.((((.(((.((....))--.))).))))((((....))))(((.((((........)))).))))))))).))))))).))))))) ( -49.20)
>DroYak_CAF1 1449 113 - 1
CGAACAGUUACGCGCUUAGGGUGACCAUCACAUGACUGGUCAUGCG--AAAUGAUGGUUACUACCGUAGGGCUUUGCUUGCGAAUGAAGUGGCAUGGUCUUCCUAAGAAAGUAAC
......(((((...(((((((((((((((((((((....)))))..--...))))))))))......((((((.((((.((.......)))))).))))))))))))...))))) ( -40.70)
>consensus
CGAACAGUUACUCGCUUAGGGUGACCAUCACAUGGUUGGUCAUGCA__AAAUGAUGGUUACUACUGCAGGGCUUUGCCUGCAAAUGCAGUGGCAUGGUCUGCCUAAGAAAGUAAC
......((((((..((((((..((((((..(((((....)))))............((((((....((((......)))).......))))))))))))..))))))..)))))) (-19.63 = -21.80 +   2.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:06 2006