Locus 5727

Sequence ID	3L_DroMel_CAF1
Location	15,604,092 – 15,604,313
Length	221
Max. P	0.999711

overview

Window 0

Location	15,604,092 – 15,604,193
Length	101
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.35
Mean single sequence MFE	-22.68
Consensus MFE	-16.71
Energy contribution	-16.77
Covariance contribution	0.06
Combinations/Pair	1.21
Mean z-score	-1.40
Structure conservation index	0.74
SVM decision value	-0.03
SVM RNA-class probability	0.518129
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15604092 101 - 23771897
GAUAGAGGUAGGGG-----------UGUUGUAUACUAUAGUACUUGCCUGGUGACAAUCCCA----AAAAAAAAG----AAAUGAUUACAGAAAACGCUUACAUAACUCUAUGAGGAAUA
.(((((((((((.(-----------(.((((((((....)))......((....))......----.........----.......)))))...)).)))))....))))))........ ( -18.30)
>DroSec_CAF1 27200 112 - 1
AAUAGAGGUAGGGGCGUAAAAAGAUUGUUGUAUAGCAUAGUACUUGCCUGGUGACAAUCCCA----AAAAAAUAG----AAAUGAUUACAGAAAACGCUUGCAUAACUCUAUGAGGAAUA
.((((((.((.((((((.....((((((..(...(((.......)))...)..))))))...----......((.----...))..........))))))...)).))))))........ ( -23.60)
>DroSim_CAF1 27114 111 - 1
GAUAGAGGUAGGGGCGUAAAAAGAUUGUUGUAUAGCAUAGUACUUGCCUGGUGACAAUCCCA----AAAAAAUAG----AAAUGAUUACAGAA-AUGCUUGCAUAACUCUAUGAGGAAUA
.((((((.((.((((((.....((((((..(...(((.......)))...)..))))))...----......((.----...)).........-))))))...)).))))))........ ( -21.90)
>DroYak_CAF1 29226 120 - 1
AAUGGAGGCAGGGGCGUAAAAAGAUUGUUGUAUGGCAUAGUACUUGCCUGGUGACAAUCCCAAUACAAAAAAAAGAAAAAAAUGAUUACAGAAACCGCUUGCAUAACUCUAUGAGGAAUU
.(((((((((((((.(((....((((((..(..((((.......))))..)..))))))....)))................((....))....)).)))))....))))))........ ( -26.90)
>consensus
AAUAGAGGUAGGGGCGUAAAAAGAUUGUUGUAUAGCAUAGUACUUGCCUGGUGACAAUCCCA____AAAAAAAAG____AAAUGAUUACAGAAAACGCUUGCAUAACUCUAUGAGGAAUA
.(((((((((((.(........((((((..(...(((.......)))...)..)))))).......................((....)).....).)))))....))))))........ (-16.71 = -16.77 +   0.06)

alignment

secondary structure

dotplot

Window 1

Location	15,604,193 – 15,604,313
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-41.01
Consensus MFE	-35.88
Energy contribution	-36.24
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-3.46
Structure conservation index	0.87
SVM decision value	3.93
SVM RNA-class probability	0.999711
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15604193 120 + 23771897
UGAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUCGACACACACACAGUAGCCGGCUUGAAAGGUCGAUUUUGGCCCGGUUCUGUUCAUAAAAAGUCUGAAAAACGA
........((((.((((......((.((((((((.((((((.....(((((.....((.(((.....)))))....)))))..)))))))))))))).))........))))...)))). ( -40.04)
>DroSec_CAF1 27312 120 + 1
UGAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUGGACUCACACACAGUAGCCGGCUUGAAAGGUCGAUUUUGGCCCGGUUCUGUUCAUAAAAUGUCUGAAAAACGA
........((((.((((......((.((((((((.((((((.((((((..........)))).))(((((.....)))))...)))))))))))))).))........))))...)))). ( -43.44)
>DroSim_CAF1 27225 120 + 1
UGAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUCGACUCACACACAGUAGCCGGCUUGAAAGGUCGAUAUUGGCCCGGUUCUGUUCAUAAAAUGUCUGAAAAACGA
........((((.((((......((.((((((((.((((((((...((((((....((.(((.....)))))...)))))))))))))))))))))).))........))))...)))). ( -42.84)
>DroEre_CAF1 27211 120 + 1
UAAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUCGACUCACUCACAGUAGCCGGCUUGAAAGGUCGAUUUUGGCCCGGUUGUGUUCGUAAAAUGUCUGAAAAAUGA
........((((.((((....((((.((.(((((.((((((.....((((((...(((.(((.....))))))..))))))..))))))))))).)).))))......))))...)))). ( -41.00)
>DroYak_CAF1 29346 120 + 1
CGAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUCGACUCACACACAGUAGCCGCAUUGAAAGGUCGAUUUUGGCCCGGUUCUGUUCAUAAAAUGUCUGAAAAAUGA
........((((.((((......((.((((((((.((((((.....((((((......((((......))))...))))))..)))))))))))))).))........))))...)))). ( -37.74)
>consensus
UGAACUUCCGUUGCAGAACAAACGACCAGAACCGUGGCCAAUGCACUCGACUCACACACAGUAGCCGGCUUGAAAGGUCGAUUUUGGCCCGGUUCUGUUCAUAAAAUGUCUGAAAAACGA
........((((.((((......((.((((((((.((((((.(((((............))).))(((((.....)))))...)))))))))))))).))........))))...)))). (-35.88 = -36.24 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	15,604,193 – 15,604,313
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-41.82
Consensus MFE	-38.18
Energy contribution	-39.02
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.54
Structure conservation index	0.91
SVM decision value	3.88
SVM RNA-class probability	0.999679
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15604193 120 - 23771897
UCGUUUUUCAGACUUUUUAUGAACAGAACCGGGCCAAAAUCGACCUUUCAAGCCGGCUACUGUGUGUGUGUCGAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUCA
(((((...((((......((((.((((((((((((((..(((((....((.(((((...))).)).)).))))).....)))))).)))))))).))))....)))).)))))....... ( -41.30)
>DroSec_CAF1 27312 120 - 1
UCGUUUUUCAGACAUUUUAUGAACAGAACCGGGCCAAAAUCGACCUUUCAAGCCGGCUACUGUGUGUGAGUCCAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUCA
(((((...((((((....((((.((((((((((((((....((....))......((.((((..(....)..)))))).)))))).)))))))).)))).)).)))).)))))....... ( -40.20)
>DroSim_CAF1 27225 120 - 1
UCGUUUUUCAGACAUUUUAUGAACAGAACCGGGCCAAUAUCGACCUUUCAAGCCGGCUACUGUGUGUGAGUCGAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUCA
(((((...((((((....((((.(((((((((((((((.(((((...(((.(((((...))).)).))))))))....))))))).)))))))).)))).)).)))).)))))....... ( -45.50)
>DroEre_CAF1 27211 120 - 1
UCAUUUUUCAGACAUUUUACGAACACAACCGGGCCAAAAUCGACCUUUCAAGCCGGCUACUGUGAGUGAGUCGAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUUA
........((((((....((((.((.(((((((((((..(((((...(((..((((...))).)..)))))))).....)))))).))))).)).)))).)).)))).(((....))).. ( -38.50)
>DroYak_CAF1 29346 120 - 1
UCAUUUUUCAGACAUUUUAUGAACAGAACCGGGCCAAAAUCGACCUUUCAAUGCGGCUACUGUGUGUGAGUCGAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUCG
........((((((....((((.((((((((((((((..(((((...(((((((((...)))))).)))))))).....)))))).)))))))).)))).)).)))).(((....))).. ( -43.60)
>consensus
UCGUUUUUCAGACAUUUUAUGAACAGAACCGGGCCAAAAUCGACCUUUCAAGCCGGCUACUGUGUGUGAGUCGAGUGCAUUGGCCACGGUUCUGGUCGUUUGUUCUGCAACGGAAGUUCA
........((((((....((((.((((((((((((((..(((((...(((..((((...))).)..)))))))).....)))))).)))))))).)))).)).)))).(((....))).. (-38.18 = -39.02 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:56 2006