Locus 6768

Sequence ID	3R_DroMel_CAF1
Location	17,852,625 – 17,852,736
Length	111
Max. P	0.845178

overview

Window 8

Location	17,852,625 – 17,852,736
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-44.33
Consensus MFE	-24.97
Energy contribution	-24.25
Covariance contribution	-0.72
Combinations/Pair	1.33
Mean z-score	-1.92
Structure conservation index	0.56
SVM decision value	0.62
SVM RNA-class probability	0.801548
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17852625 111 + 27905053
UUUGCAUC---UCCAUGCUUCUGAUGCAUGGGGCAUUCUGGUGGCGGGGCACCACUGCCGCUCAUGUACUUGGCGUGGUCCACCGGCACACUCUUCGUGGCCUCCAUUUGCACU
..((((.(---(((((((.......)))))))).....(((.(((((((.(((((.((((..........))))))))))).))....(((.....)))))).)))..)))).. ( -44.20)
>DroPse_CAF1 769 114 + 1
UUGUUAUCGCCCCCCUGCUUCUGGUGCAUGGGGCACUCCGGCGGCGGUGAGCCACCUGCGGCCAUGUGCUUGGCAUGAUCAGCCGGCACACCUUUCGGCGCUUCCAUCUGUACG
.((..(.(((((((((((.......))).))))......(((.((((((...)))).)).))).((((((.(((.......)))))))))......)))).)..))........ ( -43.10)
>DroEre_CAF1 770 111 + 1
UUUGAAUC---UCCAUGCUUCUGAUGCAUGGGGCAUUCUGGUGGCGGGGAACCACCAGCGCCCAUGUACUUGGCGUGGUCCACCGGCACACUCUUAGUGGCCUCCAUUUGCACA
...(((((---(((((((.......)))))))).)))).(((((.((....))((((.((((.........)))))))))))))(((.(((.....))))))............ ( -45.50)
>DroWil_CAF1 705 108 + 1
UGUUCGUC------UUGUUUCUUAUGCAUGGGACAUUCGGGUGGUGGUGAUCCACCGCCAGCCAUGUGCUUGGCAUGAUCAGCUGGCGUACUCUUGGUGGCCUCCAUCUGUACG
.....(((------..(((..((((((..((.((((..((.((((((((...)))))))).)))))).))..))))))..))).)))((((....(((((...))))).)))). ( -41.40)
>DroYak_CAF1 793 111 + 1
CUCGCAUC---UCCAUGCUUCUGGUGCAUGGGGCAUUCUGGUGGCGGGGAACCACCACCGCUCAUGUACUUGGCGUGGUCUACCGGCACACUCUUCGUGGCCUCCAUUUGCACU
...(((..---.(((((((...((((((((((......((((((.((....)).)))))))))))))))).)))))))......(((.(((.....))))))......)))... ( -48.80)
>DroPer_CAF1 1720 114 + 1
UUGUUAUCGCCCCCCUGCUUCUGGUGCAUGGGGCACUCCGGCGGCGGUGAGCCACCUGCGGCCAUGUGCUUGGCAUGAUCGGCCGGCACACCUUUCGGCGCUUCCAUCUGUACG
.((..(.(((((((((((.......))).))))......(((.((((((...)))).)).))).((((((.(((.......)))))))))......)))).)..))........ ( -43.00)
>consensus
UUUGCAUC___UCCAUGCUUCUGAUGCAUGGGGCAUUCUGGUGGCGGGGAACCACCACCGCCCAUGUACUUGGCAUGAUCAACCGGCACACUCUUCGUGGCCUCCAUCUGCACG
........................((((((((((...(((((((.((....)).))......(((((.....)))))....)))))..(((.....)))))).)))..)))).. (-24.97 = -24.25 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	17,852,625 – 17,852,736
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.96
Mean single sequence MFE	-43.37
Consensus MFE	-23.84
Energy contribution	-23.98
Covariance contribution	0.14
Combinations/Pair	1.23
Mean z-score	-2.05
Structure conservation index	0.55
SVM decision value	0.77
SVM RNA-class probability	0.845178
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17852625 111 - 27905053
AGUGCAAAUGGAGGCCACGAAGAGUGUGCCGGUGGACCACGCCAAGUACAUGAGCGGCAGUGGUGCCCCGCCACCAGAAUGCCCCAUGCAUCAGAAGCAUGGA---GAUGCAAA
..((((..(((.((((((.....))).)))(((((((((((((............))).)))))...))))).))).......((((((.......)))))).---..)))).. ( -43.80)
>DroPse_CAF1 769 114 - 1
CGUACAGAUGGAAGCGCCGAAAGGUGUGCCGGCUGAUCAUGCCAAGCACAUGGCCGCAGGUGGCUCACCGCCGCCGGAGUGCCCCAUGCACCAGAAGCAGGGGGGCGAUAACAA
.((.(((.(((..(((((....))))).))).)))....((((..((((.((((.((.((((...)))))).))))..))))(((.(((.......))).)))))))...)).. ( -48.80)
>DroEre_CAF1 770 111 - 1
UGUGCAAAUGGAGGCCACUAAGAGUGUGCCGGUGGACCACGCCAAGUACAUGGGCGCUGGUGGUUCCCCGCCACCAGAAUGCCCCAUGCAUCAGAAGCAUGGA---GAUUCAAA
(((((.......((((((.....))).)))((((.....))))..))))).((((.((((((((.....))))))))...))))(((((.......)))))..---........ ( -46.90)
>DroWil_CAF1 705 108 - 1
CGUACAGAUGGAGGCCACCAAGAGUACGCCAGCUGAUCAUGCCAAGCACAUGGCUGGCGGUGGAUCACCACCACCCGAAUGUCCCAUGCAUAAGAAACAA------GACGAACA
.......((((.(((............((((((((....(((...)))..))))))))(((((....)))))........))))))).............------........ ( -28.70)
>DroYak_CAF1 793 111 - 1
AGUGCAAAUGGAGGCCACGAAGAGUGUGCCGGUAGACCACGCCAAGUACAUGAGCGGUGGUGGUUCCCCGCCACCAGAAUGCCCCAUGCACCAGAAGCAUGGA---GAUGCGAG
.((((...(((.((((((.....))).)))((....))...))).))))....((((((((((....))))))))........((((((.......)))))).---...))... ( -43.80)
>DroPer_CAF1 1720 114 - 1
CGUACAGAUGGAAGCGCCGAAAGGUGUGCCGGCCGAUCAUGCCAAGCACAUGGCCGCAGGUGGCUCACCGCCGCCGGAGUGCCCCAUGCACCAGAAGCAGGGGGGCGAUAACAA
.............(((((....))))).(((((((..((((.......))))..))..(((((....))))))))))..((((((.(((.......)))..))))))....... ( -48.20)
>consensus
CGUACAAAUGGAGGCCACGAAGAGUGUGCCGGCGGACCACGCCAAGCACAUGGCCGCAGGUGGUUCACCGCCACCAGAAUGCCCCAUGCACCAGAAGCAUGGA___GAUGAAAA
.......((((.(((........((((((.(((.......)))..)))))).......((((((.....)))))).....)))))))........................... (-23.84 = -23.98 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:27 2006