Locus 9312

Sequence ID	3R_DroMel_CAF1
Location	24,779,653 – 24,779,790
Length	137
Max. P	0.695782

overview

Window 6

Location	24,779,653 – 24,779,766
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.22
Mean single sequence MFE	-33.28
Consensus MFE	-30.82
Energy contribution	-30.90
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.10
Structure conservation index	0.93
SVM decision value	0.09
SVM RNA-class probability	0.577751
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779653 113 + 27905053
UUGGGCCAGACACCCUGUAAAAGUUAAUGUAACGGCGCAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUUCUCCCCGGAG---ACU----
.((((((((.....)))................((((((......)))..((..(((.((.....)).)))(((.....)))))..)))..)))))...((((....)))---)..---- ( -34.50)
>DroSec_CAF1 10735 116 + 1
UUGGGGCAGACACCCUGUAAAAGUUAAUGUAACGGCGCAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUUCUCCCCAGAGACGACU----
(((((((((.....))))....(..(((((...((((((......)))..((.((((.((.....)).))))))....(((.....)))..))).)))))..))))))........---- ( -33.00)
>DroSim_CAF1 6112 116 + 1
UUGGGGCAGACACCCUGUAAAAGUUAAUGUAACGGCGCAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUUCUCCCCAGAGACGACU----
(((((((((.....))))....(..(((((...((((((......)))..((.((((.((.....)).))))))....(((.....)))..))).)))))..))))))........---- ( -33.00)
>DroEre_CAF1 19730 113 + 1
UUGGGGCAGACACCCUGUAAAAGUUAAUGUAACGGCGCAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUGCUCCCCAGAGACU-------
((((((.((.((...(((....((((...))))((((((......)))..((.((((.((.....)).))))))....(((.....)))..))).))))))))))))).....------- ( -32.60)
>DroYak_CAF1 11321 120 + 1
UUGGGGCAGACACCCUGUAAAAGUUAAUGUAACGGCGUAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUUCUCCCCAGAGACGGUAUUUU
(((((((((.....))))....(..(((((...(((((............((.((((.((.....)).))))))....(((.....)))))))).)))))..))))))............ ( -33.30)
>consensus
UUGGGGCAGACACCCUGUAAAAGUUAAUGUAACGGCGCAUUUAAUUGCACGCACGGAAUGAAUUCCACUCCGGCACUCGGCCGCAUGCCACGCCCACAUUCUCCCCAGAGACGACU____
(((((((((.....)))).......(((((...((((((......)))..((.((((.((.....)).))))))....(((.....)))..))).)))))...)))))............ (-30.82 = -30.90 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	24,779,653 – 24,779,766
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.22
Mean single sequence MFE	-41.48
Consensus MFE	-38.82
Energy contribution	-39.06
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.15
Structure conservation index	0.94
SVM decision value	0.34
SVM RNA-class probability	0.695782
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779653 113 - 27905053
----AGU---CUCCGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUGCGCCGUUACAUUAACUUUUACAGGGUGUCUGGCCCAA
----..(---(((....))))...(((((..(((((.(....(((((((((((((.....))))))).))(((((......)))))..........)))).....).)))))..))))). ( -41.40)
>DroSec_CAF1 10735 116 - 1
----AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUGCGCCGUUACAUUAACUUUUACAGGGUGUCUGCCCCAA
----.........((((((((.(((((((((.(((((((((.....)))((((((.....))))))..))))))........)))))((((...))))...)))).....))).))))). ( -41.60)
>DroSim_CAF1 6112 116 - 1
----AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUGCGCCGUUACAUUAACUUUUACAGGGUGUCUGCCCCAA
----.........((((((((.(((((((((.(((((((((.....)))((((((.....))))))..))))))........)))))((((...))))...)))).....))).))))). ( -41.60)
>DroEre_CAF1 19730 113 - 1
-------AGUCUCUGGGGAGCAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUGCGCCGUUACAUUAACUUUUACAGGGUGUCUGCCCCAA
-------......((((((((((.(.(((((.(((((((((.....)))((((((.....))))))..))))))........)))))((((...)))).......).))).)).))))). ( -40.60)
>DroYak_CAF1 11321 120 - 1
AAAAUACCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUACGCCGUUACAUUAACUUUUACAGGGUGUCUGCCCCAA
.............((((((((.(((((((((((((((((((.....)))((((((.....))))))..)))))).......))))))((((...))))...)))).....))).))))). ( -42.21)
>consensus
____AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAAAUGCGCCGUUACAUUAACUUUUACAGGGUGUCUGCCCCAA
..............((((..(((((((((((.(((((((((.....)))((((((.....))))))..))))))........)))))..))))))........(((.....))))))).. (-38.82 = -39.06 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	24,779,693 – 24,779,790
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.83
Mean single sequence MFE	-36.94
Consensus MFE	-30.16
Energy contribution	-30.56
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.82
SVM decision value	0.15
SVM RNA-class probability	0.609028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779693 97 - 27905053
GUCCGUU-U-GUUGGCAG-----GCGAAAAA-------------AGU---CUCCGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
(((((((-(-(....)))-----))......-------------..(---(((....))))....))))...(((((((((.....)))((((((.....))))))..))))))...... ( -36.90)
>DroSec_CAF1 10775 106 - 1
GUCCGUU-UAGCUGGCAGUCGUGGCGAAAAA-------------AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
.......-..(((.(((.((..(((((....-------------..)))))((....)))).))).)))...(((((((((.....)))((((((.....))))))..))))))...... ( -36.10)
>DroSim_CAF1 6152 101 - 1
GUCCGUU-UUGUUGGCAG-----GCGAAAAA-------------AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
(((((((-((.(..(.((-----((((....-------------..)))))))..).))))...)))))...(((((((((.....)))((((((.....))))))..))))))...... ( -39.50)
>DroEre_CAF1 19770 97 - 1
GUCCGUU--UGUUGGCAG-----GCGAAAAA----------------AGUCUCUGGGGAGCAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
(((((((--(.(..(.((-----((......----------------.)))))..).))))....))))...(((((((((.....)))((((((.....))))))..))))))...... ( -36.50)
>DroYak_CAF1 11361 115 - 1
GUCCGUUUUUGUUGGCAG-----GCACAAAACCAAAAAAAAAAAUACCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
((((((((((.(..(.((-----((.......................)))))..).))))))..))))...(((((((((.....)))((((((.....))))))..))))))...... ( -35.70)
>consensus
GUCCGUU_UUGUUGGCAG_____GCGAAAAA_____________AGUCGUCUCUGGGGAGAAUGUGGGCGUGGCAUGCGGCCGAGUGCCGGAGUGGAAUUCAUUCCGUGCGUGCAAUUAA
(((((.........((.......))........................((((....))))...)))))...(((((((((.....)))((((((.....))))))..))))))...... (-30.16 = -30.56 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:20 2006