Locus 3425

Sequence ID	3R_DroMel_CAF1
Location	9,302,693 – 9,302,797
Length	104
Max. P	0.726816

overview

Window 4

Location	9,302,693 – 9,302,797
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.83
Mean single sequence MFE	-28.63
Consensus MFE	-18.95
Energy contribution	-18.90
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-1.58
Structure conservation index	0.66
SVM decision value	0.41
SVM RNA-class probability	0.726816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9302693 104 + 27905053
----G------AGCUGGG--GGAGCA----AUGAAGGAGUCCUGGACACCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGGCCGGUAAUCAAAGCAUGAAAUUA
----.------.(((..(--(..((.----.((((((.(((...))).)).(((((((....))))))).)))).((((((...((....)).)))))).))..))..)))......... ( -29.60)
>DroPse_CAF1 71481 100 + 1
----G------AGCAGG---ACAGCG-------AUGGCAUUGGCGUUGGCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGACCGGUAAUCAAAGCAUGAAAUUA
----.------.(((.(---...((.-------...))..((((.((((..(((((((....)))))))..)))).)))).....).))).(((((....(....)....)))))..... ( -29.60)
>DroEre_CAF1 74662 101 + 1
----U------AUCUGGG--GGAGCA-------AAGGAGUCCUGGACAUCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGGCCGGUAAUCAAAGCAUGAAAUUA
----.------.((..((--(...(.-------...)..)))..)).(((.(((((((....)))))))......((((((...((....)).))))))))).................. ( -23.30)
>DroWil_CAF1 74325 103 + 1
----U------AAAUGGGCAAUGGCA-------AAGGCAAUGGCACUGGCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGACCGGUAAUCAAAGCAUGAAAUUA
----.------..((.((..(((((.-------...((((((((..(((..(((((((....)))))))..)))..)))))......))))))))..)).)).................. ( -26.00)
>DroAna_CAF1 72772 112 + 1
ACCAG------CGCCAGG--ACAUCAGAUCAGGAGUGAGCUCGGUGCGGCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGACCGGUAAUCAAAGCAUGAAAUUA
(((.(------((((..(--((....).))..(((....))))))))((..(((((((....)))))))..))..((((((...((....)).))))))))).................. ( -31.80)
>DroPer_CAF1 74572 106 + 1
----GAGCAGGAGCAGG---ACAGCG-------AUGGCGAUGGCGUUGGCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGACCGGUAAUCAAAGCAUGAAAUUA
----..((.((..((.(---((.((.-------(((...(((((.((((..(((((((....)))))))..)))).)))))....)))))))).)).)).)).................. ( -31.50)
>consensus
____G______AGCUGGG__ACAGCA_______AAGGAGUUCGCGACGGCGACGACACAAAAGUGUCGUAUUCAAGGUCAUAAAACGUGCGUCAUGACCGGUAAUCAAAGCAUGAAAUUA
.......................((..........................(((((((....)))))))......((((((...((....)).))))))..........))......... (-18.95 = -18.90 +  -0.05)

alignment

secondary structure

dotplot

Window 5

Location	9,302,693 – 9,302,797
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.83
Mean single sequence MFE	-24.27
Consensus MFE	-17.63
Energy contribution	-17.97
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.03
Structure conservation index	0.73
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9302693 104 - 27905053
UAAUUUCAUGCUUUGAUUACCGGCCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGGUGUCCAGGACUCCUUCAU----UGCUCC--CCCAGCU------C----
.........((..(((.......((..(((((.((.((((......)))).(((((((....))))))))))))))..))......))).----.))...--.......------.---- ( -23.62)
>DroPse_CAF1 71481 100 - 1
UAAUUUCAUGCUUUGAUUACCGGUCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGCCAACGCCAAUGCCAU-------CGCUGU---CCUGCU------C----
.........((.(((......((((((((........))))))))(((...(((((((....)))))))...)))...))).))...-------.((...---...)).------.---- ( -24.20)
>DroEre_CAF1 74662 101 - 1
UAAUUUCAUGCUUUGAUUACCGGCCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGAUGUCCAGGACUCCUU-------UGCUCC--CCCAGAU------A----
.....(((((((.........)).))))).(((.(((((..(((.((((...((((((....)))))))))).))).))))).....-------)))...--.......------.---- ( -19.80)
>DroWil_CAF1 74325 103 - 1
UAAUUUCAUGCUUUGAUUACCGGUCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGCCAGUGCCAUUGCCUU-------UGCCAUUGCCCAUUU------A----
.........((..........((((((((........))))))))......(((((((....))))))).))(((((.((.......-------)).))))).......------.---- ( -24.10)
>DroAna_CAF1 72772 112 - 1
UAAUUUCAUGCUUUGAUUACCGGUCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGCCGCACCGAGCUCACUCCUGAUCUGAUGU--CCUGGCG------CUGGU
.....(((.....)))..(((((((((((........))))))))......(((((((....)))))))(((((((.(.((.(((....))).))).)))--...))))------..))) ( -29.20)
>DroPer_CAF1 74572 106 - 1
UAAUUUCAUGCUUUGAUUACCGGUCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGCCAACGCCAUCGCCAU-------CGCUGU---CCUGCUCCUGCUC----
.........((.(((......((((((((........))))))))......(((((((....)))))))...))).))....((...-------.((...---...))....))..---- ( -24.70)
>consensus
UAAUUUCAUGCUUUGAUUACCGGUCAUGACGCACGUUUUAUGACCUUGAAUACGACACUUUUGUGUCGUCGCCAACCCCAACGCCUU_______UGCUGU__CCCAGCU______C____
.....(((.....))).....((((((((........))))))))......(((((((....)))))))................................................... (-17.63 = -17.97 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:39 2006