Locus 7976

Sequence ID	3R_DroMel_CAF1
Location	21,379,302 – 21,379,408
Length	106
Max. P	0.952136

overview

Window 0

Location	21,379,302 – 21,379,408
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.40
Mean single sequence MFE	-24.57
Consensus MFE	-17.53
Energy contribution	-17.51
Covariance contribution	-0.02
Combinations/Pair	1.23
Mean z-score	-2.38
Structure conservation index	0.71
SVM decision value	1.42
SVM RNA-class probability	0.952136
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21379302 106 + 27905053
--------------AAAUCAAAGACUACUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAAUAACAAACGGCAGAUAUGGUAUGGUAUACUAUAUUCCAUA
--------------.................(((((..((((((((.((........)).))))))))((....))............))))).((((((((((....)))))..))))) ( -26.50)
>DroSec_CAF1 73757 106 + 1
--------------AAAUCAAAGACUACUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAAUAACAAACGGCAGAUAUGGUAUGGUAUAUUAUAUUCCAUA
--------------.................(((((..((((((((.((........)).))))))))((....))............))))).(((((.(((........))).))))) ( -24.30)
>DroSim_CAF1 70194 106 + 1
--------------AAAUCAAAGACUACUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAAUAACAAACGGCAGAUAUGGUAUGGUAUACUAUAUUCCAUA
--------------.................(((((..((((((((.((........)).))))))))((....))............))))).((((((((((....)))))..))))) ( -26.50)
>DroEre_CAF1 73357 101 + 1
--------------AAAUCAAAGACUGCUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAACAACAAACAACAGAUAUGGCAUGGUAU-----AUCUCGCA
--------------.......(((.((((...(((((.((((((((.((........)).))))))))((....))....................))))).)))).-----.))).... ( -22.90)
>DroYak_CAF1 72997 95 + 1
--------------AAAUCAAAGAGUACUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAAUAACAAACAACAGAUAUGGUAUAGUA-----------GUA
--------------.........(.((((...(((((.((((((((.((........)).))))))))((....))....................))))).))))-----------.). ( -21.50)
>DroPer_CAF1 112545 115 + 1
GACCAGCGUGCAAAAAAUCAAAGACUACUUACGGCCAUGGCUAAUAUUCCACUAAA-GUUUAUUAGCCACAACUGCA--AUAA--AAGCACAUAUUUUGCACUGGGAACCAUAGCCGUUG
...((((((((((((......................(((((((((..(.......-)..)))))))))....(((.--....--..)))....))))))))..((........)))))) ( -25.70)
>consensus
______________AAAUCAAAGACUACUUAUUGCCACGGCUAAUAUGCCGCCAAAUGUUUAUUAGCCGCAGCUGCACAAUAACAAACGACAGAUAUGGUAUGGUAUACUAUAUUCCAUA
.........................((((...((((((((((((((..(........)..)))))))))...(((...............)))...))))).)))).............. (-17.53 = -17.51 +  -0.02)

alignment

secondary structure

dotplot

Window 1

Location	21,379,302 – 21,379,408
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.40
Mean single sequence MFE	-27.52
Consensus MFE	-19.90
Energy contribution	-18.87
Covariance contribution	-1.03
Combinations/Pair	1.28
Mean z-score	-1.58
Structure conservation index	0.72
SVM decision value	0.72
SVM RNA-class probability	0.832911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21379302 106 - 27905053
UAUGGAAUAUAGUAUACCAUACCAUAUCUGCCGUUUGUUAUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGUAGUCUUUGAUUU--------------
(((((.(((...))).))))).((...((((....(((......)))((..(((((((((..(........)..)))))))))..)).....))))....))....-------------- ( -26.30)
>DroSec_CAF1 73757 106 - 1
UAUGGAAUAUAAUAUACCAUACCAUAUCUGCCGUUUGUUAUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGUAGUCUUUGAUUU--------------
(((((.(((...))).))))).((...((((....(((......)))((..(((((((((..(........)..)))))))))..)).....))))....))....-------------- ( -26.30)
>DroSim_CAF1 70194 106 - 1
UAUGGAAUAUAGUAUACCAUACCAUAUCUGCCGUUUGUUAUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGUAGUCUUUGAUUU--------------
(((((.(((...))).))))).((...((((....(((......)))((..(((((((((..(........)..)))))))))..)).....))))....))....-------------- ( -26.30)
>DroEre_CAF1 73357 101 - 1
UGCGAGAU-----AUACCAUGCCAUAUCUGUUGUUUGUUGUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGCAGUCUUUGAUUU--------------
....((((-----((........)))))).(((((((((((..((..(((((.(((((.......))))).)).....)))))..)))))))))))..........-------------- ( -27.70)
>DroYak_CAF1 72997 95 - 1
UAC-----------UACUAUACCAUAUCUGUUGUUUGUUAUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGUACUCUUUGAUUU--------------
...-----------((((.................(((......)))((..(((((((((..(........)..)))))))))..))....))))...........-------------- ( -21.50)
>DroPer_CAF1 112545 115 - 1
CAACGGCUAUGGUUCCCAGUGCAAAAUAUGUGCUU--UUAU--UGCAGUUGUGGCUAAUAAAC-UUUAGUGGAAUAUUAGCCAUGGCCGUAAGUAGUCUUUGAUUUUUUGCACGCUGGUC
...((((..(((...)))((((((((.....(((.--...(--(((.((..(((((((((..(-(.....))..)))))))))..)).))))..)))........))))))))))))... ( -37.02)
>consensus
UAUGGAAUAUAGUAUACCAUACCAUAUCUGCCGUUUGUUAUUGUGCAGCUGCGGCUAAUAAACAUUUGGCGGCAUAUUAGCCGUGGCAAUAAGUAGUCUUUGAUUU______________
...................(((......(((.............)))((..(((((((((..(........)..)))))))))..)).....)))......................... (-19.90 = -18.87 +  -1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:23 2006