Locus 6615

Sequence ID 3R_DroMel_CAF1
Location 17,411,115 – 17,411,305
Length 190
Max. P 0.800931
window10768 window10769

overview

Window 8

Location 17,411,115 – 17,411,205
Length 90
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 75.69
Mean single sequence MFE -23.22
Consensus MFE -14.48
Energy contribution -14.70
Covariance contribution 0.22
Combinations/Pair 1.21
Mean z-score -1.33
Structure conservation index 0.62
SVM decision value 0.20
SVM RNA-class probability 0.630985
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17411115 90 - 27905053
CCAAAAGAA--------------UAUGCCAUUU-UCGUUCGC-UUUACGACCUGAGUUCAUUUGAAGUUAGCGGCCAUUAUUCCGGGACAAUUGUUUGUCGUAAAA----------
((....(((--------------((.(((....-((((....-...)))).((((.(((....))).)))).)))...))))).))(((((....)))))......---------- ( -20.30)
>DroPse_CAF1 17135 113 - 1
--A-AAGAGUCCUAACCCACCCACAGGGCACUUUUUACUCAUUUUUAUGGCAUGAAUUCAUUUGAAAUUAACGGCCAUUAUUUCAGGGCAAUUGUUUGUCGUAAAAGAGGAAAAAA
--.-.....((((..(((.......)))...(((((((........(((((.(((.(((....))).)))...)))))........(((((....))))))))))))))))..... ( -23.20)
>DroSec_CAF1 15202 89 - 1
CCG-AAGAA--------------UAGGCCACUU-UUGUUCGC-UUUACGACCUGAGUUCAUUUGAAGUUAGCGGCCAUUAUUCCGGGACAAUUGUUUGUCGUAAAA----------
(((-..(((--------------((((((....-....(((.-....))).((((.(((....))).)))).))))..))))))))(((((....)))))......---------- ( -24.30)
>DroSim_CAF1 12497 89 - 1
CCG-AAGAA--------------UAGGCCACUU-UUGUUCGC-UUUACGACCUGAGUUCAUUUGAAGUUAGCGGCCAUUAUUCCGGGACAAUUGUUUGUCGUAAAA----------
(((-..(((--------------((((((....-....(((.-....))).((((.(((....))).)))).))))..))))))))(((((....)))))......---------- ( -24.30)
>DroEre_CAF1 13946 100 - 1
CCG-AAGAGUCC--ACCAAUAGACAGGCCACUU-UUACUCGC-UUUACGACC-UAGUUCAUUUGAAGUAAGUGGCCGUUAUUUCGAGACAAUUGUUUGUCGUAAAA----------
.((-(((.(((.--.......))).(((((((.-....(((.-....)))..-((.(((....))).)))))))))....))))).(((((....)))))......---------- ( -26.20)
>DroYak_CAF1 12203 88 - 1
CCG-AAGAG---------------AGGCCUAUU-UUACUCGC-UUUACGACGUUAGUUCCUUUGAAGUUAGCGGCCAUUAUUUCGAGACAAUUGUUUGUCGUAGAA----------
.((-(((.(---------------(((((....-....(((.-....))).((((((((....))).))))))))).)).))))).(((((....)))))......---------- ( -21.00)
>consensus
CCG_AAGAA______________UAGGCCACUU_UUACUCGC_UUUACGACCUGAGUUCAUUUGAAGUUAGCGGCCAUUAUUCCGGGACAAUUGUUUGUCGUAAAA__________
.........................((((.........(((......))).((((.(((....))).)))).))))..........(((((....)))))................ (-14.48 = -14.70 +   0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,411,205 – 17,411,305
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 70.33
Mean single sequence MFE -29.30
Consensus MFE -18.22
Energy contribution -16.75
Covariance contribution -1.47
Combinations/Pair 1.61
Mean z-score -1.33
Structure conservation index 0.62
SVM decision value 0.62
SVM RNA-class probability 0.800931
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17411205 100 + 27905053
-------------GGUAUAUGGAGUUGUACCAGGCGGUAUCUGUUUUCCGAG--GCUUUUAAUCGGAAAGUUUUUUAUAUCGGCUUUAC-----AGGAGUUGAAAAACGAAGGGUGGAAA
-------------((((((......)))))).(.((((((...((((((((.--........))))))))......)))))).)(((((-----....(((....))).....))))).. ( -25.20)
>DroPse_CAF1 17248 96 + 1
---------------------GCGCCGUGCCAGGCGCUGUUCCCGAUUCGAAGUGGU-UUUAUAGGAGCUGCG-GUAGCGCGGCAUUACUUGAAAGAAGUCGUUAAAUAAAUGGUGGGG-
---------------------(((((......)))))....((((.(((.(((((((-.........((((((-....)))))))))))))))).....(((((.....))))))))).- ( -29.70)
>DroSec_CAF1 15291 98 + 1
-------------GCUAUAUAGAGUUGUACCAGGCGGUGUCUGCUUUCCGAG--GGU-UUAAUCGGAAAGUUU-UUAGAUCGACUUUAC-----AGGAGUCGGAAAACGGAGGGUGGAAA
-------------...........((.((((...(.(((((((((((((((.--...-....)))))))))..-..))))((((((...-----..))))))....)).)..)))).)). ( -28.00)
>DroSim_CAF1 12586 99 + 1
-------------GCUAUAUAGAGUUGUACCAGGCGGUGUCUGCUUUCCGAG--GGUUUUAAUCGGAAAGUUU-UUAGACCGACUUUAC-----AGGAGUCGGAAAACGGAGGGUGGAAA
-------------...........((.((((...(.((.((((((((((((.--........)))))))))..-..)))(((((((...-----..)))))))...)).)..)))).)). ( -29.70)
>DroEre_CAF1 14046 112 + 1
GACUCCAGCAAACGCUAUAUGGAGUUGUACCAGGCUGUGCCAGUUUUCCGAG--GGUUUUCAUCAGAAAGUUU-UUAAACCGGCUUUAC-----AGGAGCUGGAAAACGAAGGGUGGAAA
(((((((((....))....))))))).((((.(((...))).((((((((((--..(((((....)))))..)-)).....(((((...-----..))))))))))))....)))).... ( -34.00)
>DroYak_CAF1 12291 107 + 1
GAUUCC-----ACGCUAUAUGGAGUUGUACCAGGCGAUGCCAGUUUUCCGAA--GGUUUUCAUCAGAAUGUUU-UUAGAUCUGCUUUAC-----AGGAGCUGGAAAACGUAGGGUGAAAA
.....(-----((.((((.(((.(((((.....))))).)))((((((((.(--(((((.(((....)))...-..))))))((((...-----..)))))))))))))))).))).... ( -29.20)
>consensus
_____________GCUAUAUGGAGUUGUACCAGGCGGUGUCUGCUUUCCGAG__GGUUUUAAUCGGAAAGUUU_UUAGAUCGGCUUUAC_____AGGAGUCGGAAAACGAAGGGUGGAAA
........................((.((((...........(((((((((...........)))))))))........((((((((........)))))))).........)))).)). (-18.22 = -16.75 +  -1.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:56 2006