Locus 325

Sequence ID	3R_DroMel_CAF1
Location	1,249,534 – 1,249,627
Length	93
Max. P	0.889316

overview

Window 6

Location	1,249,534 – 1,249,627
Length	93
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-22.72
Consensus MFE	-7.28
Energy contribution	-9.52
Covariance contribution	2.24
Combinations/Pair	1.06
Mean z-score	-2.37
Structure conservation index	0.32
SVM decision value	0.96
SVM RNA-class probability	0.889316
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1249534 93 + 27905053
-----CAUAAAGUGACAAUAUUGCUCAUACGCAACGUUGCCACAGUCUCA-GUUA-UCCCCAUUAG-ACACCCAUAAGCAUAAUGGUACCGCUGGACCCAC
-----......(((.(((..((((......))))..))).))).(((.((-((..-...((((((.-.(........)..))))))....))))))).... ( -23.30)
>DroSec_CAF1 24734 93 + 1
-----CAUAAAGUGACAAUAUUGCUCAUACGCAACGUUGCCCCAGUCUCA-GUUA-UCCCCAUUAG-ACACCCAUAAGGAUGAUGGUCCCGCUGGACCCAC
-----......(((.(((..((((......))))..))).....(((.((-((..-...((((((.-.(........)..))))))....))))))).))) ( -21.50)
>DroEre_CAF1 24077 93 + 1
-----CAUAAAGUGGCAAUAUUGCUUAUACGCAACGUUGCCACAGUCUCA-GUUA-UGCCCAUUAG-ACACCCAUAAGUAAGAUAGCCCCACUGGACCCAC
-----......(((((((..((((......))))..))))))).(((.((-((..-.((..(((..-((........))..))).))...))))))).... ( -26.70)
>DroYak_CAF1 28194 93 + 1
-----CAUAAAGUUACAAUAUUGCUUAUACGCAACGUUGCCACAGUCUUA-GUUA-UCCCCAUUGG-ACAAUCAUAAGUAAGAUGGCCCGACCGGACCUAC
-----......((..(((..((((......))))..)))..)).((((((-.(((-(((.....))-)......))).))))))((.((....)).))... ( -18.00)
>DroAna_CAF1 23457 97 + 1
ACAGUCGCAAUGUCGCAAUAUUGCUCAUACGCCCUGUGGCCAUACACUCAAGUUACUCUCCAUUAGGGCGCUCAUAAGUAU----UUCCCAUUGGACCCAC
...(((.(((((..(.((((((.......((((((((((......((....))......))).)))))))......)))))----).).)))))))).... ( -24.12)
>consensus
_____CAUAAAGUGACAAUAUUGCUCAUACGCAACGUUGCCACAGUCUCA_GUUA_UCCCCAUUAG_ACACCCAUAAGUAUGAUGGUCCCACUGGACCCAC
...........(((.((((.((((......)))).)))).))).........................................(((((....)))))... ( -7.28 =  -9.52 +   2.24)

alignment

secondary structure

dotplot

Window 7

Location	1,249,534 – 1,249,627
Length	93
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	79.21
Mean single sequence MFE	-29.94
Consensus MFE	-15.84
Energy contribution	-17.28
Covariance contribution	1.44
Combinations/Pair	1.18
Mean z-score	-2.00
Structure conservation index	0.53
SVM decision value	0.39
SVM RNA-class probability	0.718622
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1249534 93 - 27905053
GUGGGUCCAGCGGUACCAUUAUGCUUAUGGGUGU-CUAAUGGGGA-UAAC-UGAGACUGUGGCAACGUUGCGUAUGAGCAAUAUUGUCACUUUAUG-----
...(((((((..((.((((((.((........))-.))))))..)-)..)-)).))))(((((((..((((......))))..)))))))......----- ( -31.90)
>DroSec_CAF1 24734 93 - 1
GUGGGUCCAGCGGGACCAUCAUCCUUAUGGGUGU-CUAAUGGGGA-UAAC-UGAGACUGGGGCAACGUUGCGUAUGAGCAAUAUUGUCACUUUAUG-----
.(.(((((((..(..(((((((((....))))).-...))))...-)..)-)).)))).)(((((..((((......))))..)))))........----- ( -28.60)
>DroEre_CAF1 24077 93 - 1
GUGGGUCCAGUGGGGCUAUCUUACUUAUGGGUGU-CUAAUGGGCA-UAAC-UGAGACUGUGGCAACGUUGCGUAUAAGCAAUAUUGCCACUUUAUG-----
...((((((((..(.((((..((((....)))).-...)))).).-..))-)).))))(((((((..((((......))))..)))))))......----- ( -33.60)
>DroYak_CAF1 28194 93 - 1
GUAGGUCCGGUCGGGCCAUCUUACUUAUGAUUGU-CCAAUGGGGA-UAAC-UAAGACUGUGGCAACGUUGCGUAUAAGCAAUAUUGUAACUUUAUG-----
...(((((....)))))......((((.(.((((-((.....)))-))))-))))...((.((((..((((......))))..)))).))......----- ( -26.60)
>DroAna_CAF1 23457 97 - 1
GUGGGUCCAAUGGGAA----AUACUUAUGAGCGCCCUAAUGGAGAGUAACUUGAGUGUAUGGCCACAGGGCGUAUGAGCAAUAUUGCGACAUUGCGACUGU
...(((((((((...(----((((((((..(((((((..(((...(((((....)).)))..))).))))))))))))...))))....))))).)))).. ( -29.00)
>consensus
GUGGGUCCAGUGGGACCAUCAUACUUAUGGGUGU_CUAAUGGGGA_UAAC_UGAGACUGUGGCAACGUUGCGUAUGAGCAAUAUUGUCACUUUAUG_____
...(((((....)))))......(((((..........)))))...............(((((((.(((((......))))).)))))))........... (-15.84 = -17.28 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:28 2006