Locus 1904

Sequence ID	3L_DroMel_CAF1
Location	5,330,261 – 5,330,366
Length	105
Max. P	0.787843

overview

Window 3

Location	5,330,261 – 5,330,366
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.45
Mean single sequence MFE	-34.27
Consensus MFE	-27.85
Energy contribution	-27.85
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.14
Structure conservation index	0.81
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5330261 105 + 23771897
UUUGC----------GUUGUGUCA-AGCGAUUGGCAUCUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAGGAG----
.....----------...((((((-(....)))))))(((((((((..(((((((((.........)))))..))))..........(((((.......))))))))))))))...---- ( -36.80)
>DroVir_CAF1 104692 115 + 1
UUAUCUUAGAUGCAGGUAUAGACA-GACGGUGCUCAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAAGUG----
..(((((...(((..(((.((.((-((((.((((..((((......))))..))))(....).)))))))).)))..))).)))))....(((((.(((...))).))))).....---- ( -33.80)
>DroGri_CAF1 85745 105 + 1
UUGUA----------GCUUAGACA-CUCGGCGCUCAAUUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAUGUG----
(((.(----------((...(...-..)...)))))).((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))....---- ( -30.60)
>DroWil_CAF1 82350 110 + 1
CAGAG----------ACUUUGUCGCUGCGGCUUUCAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAGGAUUCUG
(((((----------.....((((...))))......(((((((((..(((((((((.........)))))..))))..........(((((.......))))))))))))))..))))) ( -36.50)
>DroMoj_CAF1 14839 105 + 1
UUAUC----------AAAUAAGCA-AACGUUUUGCAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAAAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAUGUG----
.....----------......(((-(.....)))).((((((((((..(((((((((.........)))))..))))..........(((((.......))))))))))))).)).---- ( -31.50)
>DroAna_CAF1 76597 105 + 1
UUCGA----------ACUCUGCCA-GUCGAUGUUCAUCUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAGGUU----
...((----------((((.....-...)).))))(((((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))))).---- ( -36.40)
>consensus
UUAUC__________ACUUAGACA_AACGGUGUUCAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAGGUG____
......................................((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))........ (-27.85 = -27.85 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	5,330,261 – 5,330,366
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.45
Mean single sequence MFE	-32.47
Consensus MFE	-29.09
Energy contribution	-29.20
Covariance contribution	0.11
Combinations/Pair	1.09
Mean z-score	-1.54
Structure conservation index	0.90
SVM decision value	0.58
SVM RNA-class probability	0.787843
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5330261 105 - 23771897
----CUCCUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGAUGCCAAUCGCU-UGACACAAC----------GCAAA
----...((((((((((((((.......))))).....(((((.......))))).(((.....))).......))))))))).........(((-((...))).----------))... ( -32.50)
>DroVir_CAF1 104692 115 - 1
----CACUUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUGAGCACCGUC-UGUCUAUACCUGCAUCUAAGAUAA
----..(((((.....(((((.......))))).......((((.(((.(((((((((....)).(((.((...((....))..)))))...)))-)).)).))).)))).))))).... ( -32.10)
>DroGri_CAF1 85745 105 - 1
----CACAUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAAUUGAGCGCCGAG-UGUCUAAGC----------UACAA
----....(((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))).((((((...(..-...)...))----------).))) ( -31.10)
>DroWil_CAF1 82350 110 - 1
CAGAAUCCUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUGAAAGCCGCAGCGACAAAGU----------CUCUG
((((...((((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))))(((...((....))..)))...----------.)))) ( -34.50)
>DroMoj_CAF1 14839 105 - 1
----CACAUGGUUCCAUCCGGGAUCGAACCGGAGACCUUUUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUGCAAAACGUU-UGCUUAUUU----------GAUAA
----....(((((((((((((.......))))).....(((((.......))))).(((.....))).......))))))))...((((.....)-)))......----------..... ( -28.30)
>DroAna_CAF1 76597 105 - 1
----AACCUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGAUGAACAUCGAC-UGGCAGAGU----------UCGAA
----...((((((((((((((.......))))).....(((((.......))))).(((.....))).......))))))))).(((((.((...-.....))))----------))).. ( -36.30)
>consensus
____CACCUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUGAAAACCGAC_UGACAAAGC__________GACAA
.......((((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))))..................................... (-29.09 = -29.20 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:31 2006