Locus 3242

Sequence ID	3L_DroMel_CAF1
Location	9,486,813 – 9,487,038
Length	225
Max. P	0.923250

overview

Window 4

Location	9,486,813 – 9,486,933
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.63
Mean single sequence MFE	-28.98
Consensus MFE	-16.77
Energy contribution	-18.58
Covariance contribution	1.81
Combinations/Pair	1.19
Mean z-score	-1.88
Structure conservation index	0.58
SVM decision value	0.14
SVM RNA-class probability	0.603631
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9486813 120 - 23771897
AGUAACACCAUAACACCAUAUUUUAUGCCCACAGGAGAAGGAUAUUUAUGUGAAGAAAAUGACUUUCAACGAUAAGACGCUGAAGGAUCUGUUAUCCUUUUUACCUGUUGGUGAAUACAA
.(((.(((((......((((...))))...((((((((((((((.((((.........))))((((((.((......)).))))))......)))))))))..))))))))))..))).. ( -26.90)
>DroSec_CAF1 4042 112 - 1
AGUAACA--------CCAUAUUCUAUGCCCACAGGAGAAGGAUAUCUAUGUGAAGAAAAUGACUUUCAACGAUAAGACGCUGAAGGACCUGCUAUCCUUUUUACCUGAUGGUGAAUACAA
.(((.((--------((((............((((((((((((((((......)))......((((((.((......)).))))))......)))))))))..))))))))))..))).. ( -27.10)
>DroSim_CAF1 3797 112 - 1
AGUAACA--------CCAUAUUCUAUGCCCACAGGAGAAGGAUAUCUAUGUGAAGAAAAUGACUUUCAACGAUAAGACGCUGAAGGACCUGUUAUCCUUUUUACCUGAUGGCGAAUACAA
.......--------...(((((...(((..((((((((((((((((......)))......((((((.((......)).))))))......)))))))))..))))..))))))))... ( -27.30)
>DroEre_CAF1 3610 111 - 1
AGUAUCG--------CC-UUUUGUAUGCCCACAGGAGAAGGAUAUCUAUGUGAAAAGAAUGACUUUCAACGAUAAGACGGUGAAGGACCUGCUUUCCUUCCUACCUGAUGGCGAAUACAA
.((((((--------((-...((......))((((.((((((..(((........)))....((((((.((......)).))))))........))))))...))))..)))).)))).. ( -28.60)
>DroYak_CAF1 5815 111 - 1
AGUAUCG--------CC-UUUUCUAUGCCAACAGGAGAAGGAUAUCUAUGUGAAGAAAAUGACUUUCAACGAUAAGACGGUGAAGGACCUGCUCUCCUUCUUACCUGAUGGCGAGUACAA
.......--------..-.......(((((.(((((((((((..(((......)))......((((((.((......)).))))))........)))))))..)))).)))))....... ( -29.60)
>DroPer_CAF1 9425 104 - 1
AUAAUCC--------CCAUCUU--UUUCCAACAGGAAAAGGAUAUCUUUCUGAAACAGAUGACGCUCAGUGAGAAGGCCGUCCGGGACCUGCCA------CUGCCCAAUGGGGAAUACAA
....(((--------(((((((--(((((....)))))))))).((..((((...)))).)).(..(((((.(.(((((.....)).))).)))------)))..)...)))))...... ( -34.40)
>consensus
AGUAACA________CCAUAUUCUAUGCCCACAGGAGAAGGAUAUCUAUGUGAAGAAAAUGACUUUCAACGAUAAGACGCUGAAGGACCUGCUAUCCUUUUUACCUGAUGGCGAAUACAA
.........................((((..(((((((((((((((.....)).........((((((.((......)).))))))......)))))))))..))))..))))....... (-16.77 = -18.58 +   1.81)

alignment

secondary structure

dotplot

Window 5

Location	9,486,933 – 9,487,038
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.06
Mean single sequence MFE	-18.97
Consensus MFE	-8.75
Energy contribution	-10.42
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.46
SVM decision value	1.15
SVM RNA-class probability	0.923250
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9486933 105 - 23771897
AUAUUCUAUAUGUUUCACGAUUCCCUAAUGGCAGCCACCAAUGCCAACCACUCGUGUCCAUAUACAGUAAGUACAAACAUGUA--U--CUCAAUUGUUAUUUCACGUCA-----------
.((((.((((((...(((((........(((((........))))).....)))))..)))))).)))).(((((....))))--)--.....................----------- ( -18.92)
>DroSec_CAF1 4154 105 - 1
AUAUUCUAUAUGUUUCACGAUUCCCUAAUGGCAGCCACCAAUGCCAACCACUCGUGUCCAUAUACCGUAUGUACAAAGAUGUA--U--CUCAAUUGUUAUUUCAAUUCU-----------
((((..((((((...(((((........(((((........))))).....)))))..))))))..))))(((((....))))--)--...(((((......)))))..----------- ( -19.12)
>DroSim_CAF1 3909 105 - 1
AUAUUCUAUAUGUUUCACGAUUCCCUAAUGGCAGCCACCAAUGCCAACCACUCGUGUCCAUAUACCGUAUGUACAUAGAUGUA--U--CUCAAUUGUUAUUUCAAGUCA-----------
((((..((((((...(((((........(((((........))))).....)))))..))))))..))))(((((....))))--)--.....................----------- ( -18.12)
>DroEre_CAF1 3721 107 - 1
AUUUUCUAUAUGUUUCACGAUUCCUUAAUGGCAGCCACCAAUGCCAAUCACACGUGUCCAUAUACCGUAGGUACAUAUAUGUACAUAUCUCCAUUGCUUUUU--GGUUA-----------
......((((((...((((.........(((((........)))))......))))..))))))......(((((....)))))......(((........)--))...----------- ( -19.16)
>DroYak_CAF1 5926 116 - 1
AUUUUCUAUAUGUUUCACGAUUCCUUAAUGGCAGCCACCAAUGCCAAUCACUCGUGUCCAUAUACCGUAUGUACAUAAAUAUA--UCUUUACACCAAAUAAC--AAUUAACAAUAACAAU
......((((((...(((((........(((((........))))).....)))))..))))))..((((((......)))))--)................--................ ( -16.42)
>DroPer_CAF1 9529 100 - 1
CUGUUCUACAUAUUCCACGACUCUCUGAUGAGCGCCACAAAUGCCAAUCACACCUGUCCCUAUCAGGUAAGUCGUGGCUAUCC--U--UUCUCUCACUC-----AGUGU-----------
..............((((((((...((((..(((.......)))..)))).(((((.......))))).))))))))......--.--...........-----.....----------- ( -22.10)
>consensus
AUAUUCUAUAUGUUUCACGAUUCCCUAAUGGCAGCCACCAAUGCCAACCACUCGUGUCCAUAUACCGUAUGUACAUACAUGUA__U__CUCAAUUGUUAUUU__AGUCA___________
......((((((...(((((........(((((........))))).....)))))..))))))........................................................ ( -8.75 = -10.42 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:52 2006