Locus 3476

Sequence ID	3R_DroMel_CAF1
Location	9,395,156 – 9,395,270
Length	114
Max. P	0.835717

overview

Window 1

Location	9,395,156 – 9,395,270
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	91.93
Mean single sequence MFE	-24.88
Consensus MFE	-21.60
Energy contribution	-21.52
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.87
SVM decision value	0.73
SVM RNA-class probability	0.835717
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9395156 114 + 27905053
UUCCUUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGUUUGCCUUUGUAUAAAUUU--UUUCUGCCUCAUUUGAUGCAGAGAAUGAAAAGUUUCCAU----GCACCCC
....((((((((((..((..(((((.(((((((...))))))).)))))..))...............--..(((((.((....)).))))))))))))))).......----....... ( -25.40)
>DroVir_CAF1 76266 116 + 1
UUCCGUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGGUUGCCUUUGUAUACAUUUUUUUUCCGCCUCAUUUGAUGCAGAGAAUGAAAAGUUUUCAU----GCACCGC
.....((((((((.(((..((((((.(((((((...))))))).)))))).........................((.((....)).)).)))))))))))........----....... ( -25.70)
>DroPse_CAF1 27196 114 + 1
UUCCUUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGUUUGCCUUUGUAUAAAUUU--UUUCUGCCUCAUUUGGUGCAGAGAAUGAAAAGUUUCCAC----ACACCGC
....((((((((((..((..(((((.(((((((...))))))).)))))..))...............--..(((((.((....)).))))))))))))))).......----....... ( -24.50)
>DroGri_CAF1 77037 115 + 1
UUCCGUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGGUUGCCUUUGUAUACAUUUU-UUUCCGCCUCAUUUGAUGCAGAGAAUGAAAAGUUUUCUU----GCAUCGC
....((...((.....((.((((((.(((((((...))))))).)))))).))....))...)).....-..............((((((((((((.....)))))).)----))))).. ( -27.30)
>DroWil_CAF1 21959 118 + 1
UUCCGUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGUUUGCCUUUGUAUAAAUUU--UUUCUGCCUCAUUUGAUGCAGAGAAUGAAAAGUUUCCCUAGCUGCACCUU
.....(((((((((..((..(((((.(((((((...))))))).)))))..))...............--..(((((.((....)).))))))))))))))................... ( -25.10)
>DroMoj_CAF1 85485 115 + 1
UUCCGCUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGGUUGCCUUUGUAUACAUUUU-UUUCCGGCUCAUUUGAUCCACAGAAUGAAAAGUUUUCAU----GCACCGC
....((((((((((..((.((((((.(((((((...))))))).)))))).))................-.....((.((....)).))...)))))))).((......----))...)) ( -21.30)
>consensus
UUCCGUUUUCAUUUCUCGUCCGUUACGUUUGAGUGAUUCAAACUUGACGGUUGCCUUUGUAUAAAUUU__UUUCCGCCUCAUUUGAUGCAGAGAAUGAAAAGUUUCCAU____GCACCGC
.....((((((((.(((...(((((.(((((((...))))))).)))))..........................((.((....)).)).)))))))))))................... (-21.60 = -21.52 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	9,395,156 – 9,395,270
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	91.93
Mean single sequence MFE	-23.79
Consensus MFE	-21.26
Energy contribution	-20.93
Covariance contribution	-0.33
Combinations/Pair	1.12
Mean z-score	-1.36
Structure conservation index	0.89
SVM decision value	0.41
SVM RNA-class probability	0.723271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9395156 114 - 27905053
GGGGUGC----AUGGAAACUUUUCAUUCUCUGCAUCAAAUGAGGCAGAAA--AAAUUUAUACAAAGGCAAACGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAAAGGAA
.......----..(....)((((((((((((((.((....)).)))))..--...................((((..((((((.....))))))......)))).).))))))))..... ( -23.80)
>DroVir_CAF1 76266 116 - 1
GCGGUGC----AUGAAAACUUUUCAUUCUCUGCAUCAAAUGAGGCGGAAAAAAAAUGUAUACAAAGGCAACCGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAACGGAA
.((((((----(((((.....)))....(((((.((....)).)))))......))))))..........((((...((((((.....))))))...))))..............))... ( -23.90)
>DroPse_CAF1 27196 114 - 1
GCGGUGU----GUGGAAACUUUUCAUUCUCUGCACCAAAUGAGGCAGAAA--AAAUUUAUACAAAGGCAAACGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAAAGGAA
((..(((----(((....).........(((((..(....)..)))))..--......)))))...))...((((..((((((.....))))))......))))................ ( -24.20)
>DroGri_CAF1 77037 115 - 1
GCGAUGC----AAGAAAACUUUUCAUUCUCUGCAUCAAAUGAGGCGGAAA-AAAAUGUAUACAAAGGCAACCGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAACGGAA
.......----........((((((((((((((.((....)).)))....-...................((((...((((((.....))))))...))))..))).))))))))..... ( -23.30)
>DroWil_CAF1 21959 118 - 1
AAGGUGCAGCUAGGGAAACUUUUCAUUCUCUGCAUCAAAUGAGGCAGAAA--AAAUUUAUACAAAGGCAAACGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAACGGAA
....(((.(..(((....)))..)....(((((.((....)).)))))..--..............)))..((((..((((((.....))))))......))))................ ( -24.20)
>DroMoj_CAF1 85485 115 - 1
GCGGUGC----AUGAAAACUUUUCAUUCUGUGGAUCAAAUGAGCCGGAAA-AAAAUGUAUACAAAGGCAACCGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAGCGGAA
(((((..----......)))(((((((((((...........(((.....-..............)))..((((...((((((.....))))))...)))))).)).))))))))).... ( -23.31)
>consensus
GCGGUGC____AUGAAAACUUUUCAUUCUCUGCAUCAAAUGAGGCAGAAA__AAAUGUAUACAAAGGCAAACGUCAAGUUUGAAUCACUCAAACGUAACGGACGAGAAAUGAAAACGGAA
...................((((((((((((((.((....)).))))).......................((((..((((((.....))))))......)))).).))))))))..... (-21.26 = -20.93 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:09 2006