Locus 5499

Sequence ID	X_DroMel_CAF1
Location	14,267,028 – 14,267,294
Length	266
Max. P	0.983174

overview

Window 0

Location	14,267,028 – 14,267,139
Length	111
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	91.99
Mean single sequence MFE	-25.15
Consensus MFE	-20.83
Energy contribution	-21.45
Covariance contribution	0.62
Combinations/Pair	1.03
Mean z-score	-3.19
Structure conservation index	0.83
SVM decision value	1.74
SVM RNA-class probability	0.974990
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14267028 111 + 22224390
UUCCCCUAAGCAAUAAAUCCUUUA-ACUAUUUUGAUAGUU-UGAAAUCAACAGCUUACAAAGUUCUGAUUUCCAGUACAAAGUGCUCAAGAAGCCAAUAGGGGAAAACGCCAC
((((((((.((............(-(((((....))))))-.(((((((..((((.....)))).))))))).(((((...)))))......))...))))))))........ ( -24.90)
>DroSec_CAF1 7690 112 + 1
UUCCCCUAAGCAAUAAAUCCUUUAAAUUAUUUUGAUAGUU-UGAAAUCAACAGCUUAAAAAGUUCUGAUUUCCACUACAAAGUGCUUAAAAAGCCAACAGGGGAAAACGCCAC
(((((((.....................((((((.((((.-.(((((((..((((.....)))).))))))).))))))))))(((.....)))....)))))))........ ( -25.80)
>DroSim_CAF1 11681 112 + 1
UUCCCCUAAGCAAUAAAUCCUUUAAACUAUUUUGAUAGUU-UGAAAUCAACAGCUUACAAAGUUCUGAUUUCCACUACAAAGUGCUUAAAAAGCCAACAGGGGAAAACGCCAC
(((((((.....................((((((.((((.-.(((((((..((((.....)))).))))))).))))))))))(((.....)))....)))))))........ ( -25.80)
>DroYak_CAF1 10863 112 + 1
UUCGCCUAAGUAAUAAGCCCUUUA-AGUAUUUUGAUAGUUUUGAAAUCAACAGCUUGCAAAGUUCUGAUUUCCAUUACAAAGUGCUUAAGAAGCCAACAGGGAAAAACAUCAC
(((.(((..((.....((..((((-(((((((((.((((...(((((((..((((.....)))).))))))).)))))))))))))))))..))..))))))))......... ( -24.10)
>consensus
UUCCCCUAAGCAAUAAAUCCUUUA_ACUAUUUUGAUAGUU_UGAAAUCAACAGCUUACAAAGUUCUGAUUUCCACUACAAAGUGCUUAAAAAGCCAACAGGGGAAAACGCCAC
(((((((.....................((((((.((((...(((((((..((((.....)))).))))))).))))))))))(((.....)))....)))))))........ (-20.83 = -21.45 +   0.62)

alignment

secondary structure

dotplot

Window 1

Location	14,267,099 – 14,267,214
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.39
Mean single sequence MFE	-34.06
Consensus MFE	-33.14
Energy contribution	-32.42
Covariance contribution	-0.72
Combinations/Pair	1.20
Mean z-score	-1.52
Structure conservation index	0.97
SVM decision value	1.94
SVM RNA-class probability	0.983174
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14267099 115 - 22224390
GAGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGUCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUGCGAUAGGUGGCGUUUUCCCCUAUUGGCUUCUUGAGCACUUUGUACU
....-----...(((((((((((..((((((..((((((....((.....)).))))))..)))))).......(((((((.((......)))))))))..)))))))))))........ ( -32.10)
>DroSec_CAF1 7762 115 - 1
GGGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUCCGAUAGGUGGCGUUUUCCCCUGUUGGCUUUUUAAGCACUUUGUAGU
....-----...(((((((((((..((((((..((((((....((.....)).))))))..))))))......((((((((.((......)))))))))).)))))))))))........ ( -34.50)
>DroSim_CAF1 11753 115 - 1
GGGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUCCGAUAGGUGGCGUUUUCCCCUGUUGGCUUUUUAAGCACUUUGUAGU
....-----...(((((((((((..((((((..((((((....((.....)).))))))..))))))......((((((((.((......)))))))))).)))))))))))........ ( -34.50)
>DroEre_CAF1 10662 115 - 1
GAGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUCCGAUAGGUGGCGUUCUCCCCUGUUGGCUUCUUAAACACUUUGUAAU
....-----...(((((((((((..((((((..((((((....((.....)).))))))..))))))......((((((((.((......)))))))))).)))))))))))........ ( -37.00)
>DroYak_CAF1 10935 120 - 1
UGGAGAGAGGAUGUGUUUAAGGAUGAUUGAUUGCAAGGCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUGCGAUAGGUGAUGUUUUUCCCUGUUGGCUUCUUAAGCACUUUGUAAU
............(((((((((((..((((((..(((((((((......)))))..))))..)))))).......(((((((.((......)))))))))..)))))))))))........ ( -32.20)
>consensus
GGGA_____GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCUUAACUCAAUGGGCGGCUUGACAUCGAUAAAUUUCCGAUAGGUGGCGUUUUCCCCUGUUGGCUUCUUAAGCACUUUGUAAU
............(((((((((((..((((((..((((((....((.....)).))))))..))))))......((((((((.((......)))))))))).)))))))))))........ (-33.14 = -32.42 +  -0.72)

alignment

secondary structure

dotplot

Window 2

Location	14,267,179 – 14,267,294
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.96
Mean single sequence MFE	-39.02
Consensus MFE	-33.92
Energy contribution	-34.04
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	1.17
SVM RNA-class probability	0.926281
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14267179 115 - 22224390
AUGCCGGAAAAGUCCCGGGGCCCGGAGAUUUUGUUUGAGCCUGAUUGGCAAGAUGGCUGGCAGUCGAUUGGACCUGAAUCGAGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGUCU
....((((((((((((((...)))).)))))).)))).(((.....))).....((((.(((((((((((..(((..(((....-----))).......))).))))))))))).)))). ( -40.30)
>DroSec_CAF1 7842 115 - 1
AUGCCGGAAAAGUCCCGGGGCCCGGAGAUUUUGCUUGAGCCUGAUUGGCAAGAUGGUUGGCAGUCGAUUGGACCUGAAUCGGGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCU
.((((((.((((((((((...)))).))))))((....))....))))))....((((.(((((((((((..(((..(((....-----))).......))).))))))))))).)))). ( -41.50)
>DroSim_CAF1 11833 115 - 1
AUGCCGGAAAAGUCCCGGGGCCCAGAGAUUUUGCUUGAGCCUGAUUGGCAAGAUGGUUGGCAGUCGAUUGGACCUGAAUCGGGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCU
.(((((((....)))..((((...(((......)))..))))....))))....((((.(((((((((((..(((..(((....-----))).......))).))))))))))).)))). ( -39.20)
>DroEre_CAF1 10742 115 - 1
AUGCCGGAAAAGUCCCGGGGCCCGGAGAUUUUGCUUGAGCCUGAUUGGCAAGAUGCCUGGCAGUCGAUUGGACCUGAAUCGAGA-----GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCU
...((((.......))))(((.(((..((((((((...........)))))))).))..(((((((((((..(((..(((....-----))).......))).)))))))))))).))). ( -38.00)
>DroYak_CAF1 11015 120 - 1
AUGCCGGAAAAGUCCCGGGGCCCGGAGAUUUUGCUUGAGCCUGAUUGGCAAGAUGGUUGGCAGUCGAUUGGACCUGAAUCUGGAGAGAGGAUGUGUUUAAGGAUGAUUGAUUGCAAGGCU
..(((((.((((((((((...)))).)))))).))...(((.....)))..........(((((((((((..(((..((((.......)))).......))).)))))))))))..))). ( -36.10)
>consensus
AUGCCGGAAAAGUCCCGGGGCCCGGAGAUUUUGCUUGAGCCUGAUUGGCAAGAUGGUUGGCAGUCGAUUGGACCUGAAUCGGGA_____GAUGUGUUUAAGGAUGAUUGAUUGCGAGCCU
.((((((.((((((((((...)))).))))))((....))....))))))....((((.(((((((((((..(((..(((.........))).......))).))))))))))).)))). (-33.92 = -34.04 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:25 2006