Locus 1139

Sequence ID	2R_DroMel_CAF1
Location	4,540,570 – 4,540,673
Length	103
Max. P	0.923428

overview

Window 4

Location	4,540,570 – 4,540,673
Length	103
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	75.95
Mean single sequence MFE	-21.95
Consensus MFE	-12.92
Energy contribution	-12.87
Covariance contribution	-0.06
Combinations/Pair	1.06
Mean z-score	-1.57
Structure conservation index	0.59
SVM decision value	0.39
SVM RNA-class probability	0.716924
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4540570 103 + 20766785
U-ACUCGUAUUUAUA-UACAAAUGUAUGUACAAGUAGCAUGCUCCAGAGAGCAGGCC-----GAGCAAUACGAGUUUCUCCGCUUAUGCAAUAAGCCAGCCAGCCCUAUA
.-(((((((((((((-(((....)))))))......((.(((((....))))).)).-----....)))))))))......((((((...)))))).............. ( -26.80)
>DroSec_CAF1 14176 99 + 1
U-ACUCGUAUAUACAGUACA----UAUAUAC-AGUAGCAUGCUCCAGAGAGCAGGCC-----GAGCAAUACGAGUUUCGCCGCUUAUGCAAUAAGCCAGCCAGCCCUAUA
(-(((.(((((((.......----)))))))-))))((.(((((....)))))(((.-----((((.......)))).)))((((((...))))))..)).......... ( -25.20)
>DroSim_CAF1 14190 100 + 1
U-ACUCGUAUAUACAGUACA----UAUAUAC-AGUAGCAUGCUCCAGAGAGCAGGCC----CAAGCAAUACGAGUUUCUCCGCUUAUGCAAUAAGCCAGCCAGCCCUAUA
.-((((((((.(((.(((..----....)))-.)))((.(((((....))))).)).----......))))))))......((((((...)))))).............. ( -23.00)
>DroYak_CAF1 14057 97 + 1
U-UCGAGUAUAU---GUACG----UAUAUAC-AGUAGCAUGCUCCAGAGAGCAGGCCGAGCAGAGCAAUACGAGUUUCUCCGCUUAUGCAAUAAGCC----AGCCCUAUA
.-....((((((---(....----)))))))-.((((..(((((....)))))(((.((((.(((.(((....))).))).))))..((.....)).----.))))))). ( -23.80)
>DroMoj_CAF1 17547 88 + 1
CAACGCAGCAAUUCA------------AUAU--AUAACAUGCUCUAAAGAGCAUGCA-----GAGCAAUACGAGUUUCUCCGCUUAUGCAAUAAGCAA---AGCCCUAAA
....(.((.(((((.------------....--....(((((((....)))))))..-----.(....)..))))).)).)((((.(((.....))))---)))...... ( -18.40)
>DroAna_CAF1 15284 82 + 1
--------AUAU---G--------UAUUUCAAGACAACAUGCUCCAAAGAGCAGGCC-----AAGCCAUACGAGUUUCUCCGCUUAUGCAAUAAGCC----AGCCCUAAA
--------...(---(--------(((............(((((....)))))(((.-----..)))))))).........((((((...)))))).----......... ( -14.50)
>consensus
U_ACUCGUAUAUACAGUACA____UAUAUAC_AGUAGCAUGCUCCAGAGAGCAGGCC_____GAGCAAUACGAGUUUCUCCGCUUAUGCAAUAAGCCA___AGCCCUAUA
.......................................(((((....)))))(((......((((.......))))....((((((...))))))......)))..... (-12.92 = -12.87 +  -0.06)

alignment

secondary structure

dotplot

Window 5

Location	4,540,570 – 4,540,673
Length	103
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	75.95
Mean single sequence MFE	-28.35
Consensus MFE	-17.65
Energy contribution	-17.48
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.82
Structure conservation index	0.62
SVM decision value	1.15
SVM RNA-class probability	0.923428
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4540570 103 - 20766785
UAUAGGGCUGGCUGGCUUAUUGCAUAAGCGGAGAAACUCGUAUUGCUC-----GGCCUGCUCUCUGGAGCAUGCUACUUGUACAUACAUUUGUA-UAUAAAUACGAGU-A
..........(((.((.....))...)))......(((((((((....-----(((.(((((....))))).)))...((((((......))))-))..)))))))))-. ( -31.90)
>DroSec_CAF1 14176 99 - 1
UAUAGGGCUGGCUGGCUUAUUGCAUAAGCGGCGAAACUCGUAUUGCUC-----GGCCUGCUCUCUGGAGCAUGCUACU-GUAUAUA----UGUACUGUAUAUACGAGU-A
((..((..(.((((.(((((...))))))))).)..))..)).(((((-----(((.(((((....))))).)))...-(((((((----(.....))))))))))))-) ( -33.00)
>DroSim_CAF1 14190 100 - 1
UAUAGGGCUGGCUGGCUUAUUGCAUAAGCGGAGAAACUCGUAUUGCUUG----GGCCUGCUCUCUGGAGCAUGCUACU-GUAUAUA----UGUACUGUAUAUACGAGU-A
.....((.((((.((((((..(((...((((......))))..))).))----))))(((((....))))).))))))-(((((((----(.....))))))))....-. ( -30.60)
>DroYak_CAF1 14057 97 - 1
UAUAGGGCU----GGCUUAUUGCAUAAGCGGAGAAACUCGUAUUGCUCUGCUCGGCCUGCUCUCUGGAGCAUGCUACU-GUAUAUA----CGUAC---AUAUACUCGA-A
....(((((----(((.....))...(((((((............)))))))))))))((((....))))........-((((((.----.....---))))))....-. ( -28.00)
>DroMoj_CAF1 17547 88 - 1
UUUAGGGCU---UUGCUUAUUGCAUAAGCGGAGAAACUCGUAUUGCUC-----UGCAUGCUCUUUAGAGCAUGUUAU--AUAU------------UGAAUUGCUGCGUUG
...(((((.---.(((....(((....)))(((...))))))..))))-----)((((((((....))))))))...--....------------............... ( -23.10)
>DroAna_CAF1 15284 82 - 1
UUUAGGGCU----GGCUUAUUGCAUAAGCGGAGAAACUCGUAUGGCUU-----GGCCUGCUCUUUGGAGCAUGUUGUCUUGAAAUA--------C---AUAU--------
((((((((.----((((....((....((((......))))...))..-----))))(((((....)))))....))))))))...--------.---....-------- ( -23.50)
>consensus
UAUAGGGCU___UGGCUUAUUGCAUAAGCGGAGAAACUCGUAUUGCUC_____GGCCUGCUCUCUGGAGCAUGCUACU_GUAUAUA____UGUACUGUAUAUACGAGU_A
.....(((.....((((....(((...((((......))))..))).......))))(((((....))))).)))................................... (-17.65 = -17.48 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:27 2006