Locus 7354

Sequence ID	X_DroMel_CAF1
Location	18,349,271 – 18,349,479
Length	208
Max. P	0.996466

overview

Window 3

Location	18,349,271 – 18,349,370
Length	99
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	81.84
Mean single sequence MFE	-39.04
Consensus MFE	-29.52
Energy contribution	-29.84
Covariance contribution	0.32
Combinations/Pair	1.25
Mean z-score	-1.70
Structure conservation index	0.76
SVM decision value	0.41
SVM RNA-class probability	0.725594
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18349271 99 - 22224390
AAAAAUUCGCACGCGGU-----GGUCAAUGUGACCGUUCG---UCGCGUGGUGGGAAAACGUGCGCUAGUGCGAACUCAAACCGUGGUUGAUAACUGGGCUGGCGGA
.....(((((.((((((-----((((.....))))(((((---.(((.(((((.(......).)))))))))))))....))))))(((.(....).)))..))))) ( -34.20)
>DroSec_CAF1 2196 102 - 1
AAAAAUUCGCACGCGGU-----GGUCAGUGUGGCCGUUCGUCGUCGCGUGGUGGGAAAACGUGCGCCAGUGCGGACUCAAACCAUGGUUGGUAAAUGGGCUGGCGGA
.....(((((((((...-----.....))))(.(((((..(((.(.((((((..((...((..(....)..))...))..))))))).)))..))))).)..))))) ( -35.50)
>DroSim_CAF1 962 102 - 1
AAAAAUUCGCACGCGGU-----GGUCAGUGUGGCCGUUCGUCGUCGCGUGGUGGGAAAACGUGCGCCAGUGCGGGCUCAAACCAUGGUUGGUAACUGGGCUGGCGGG
.....((((((((((((-----((((.....))))).......)))))).)))))........(((((((.(((.....(((....))).....))).))))))).. ( -37.21)
>DroEre_CAF1 1956 103 - 1
-AAAAUUCACACGCGGUGUGACCGUUAGUGCGACCGUUCG---CCGCGUUGUGCGAAAAUGUGCGCCAGCGCGGACUCAAACCGUGGUUAGGAACUGGGCUGGCGUA
-......(((((((((((.(((.(((.....))).)))))---))))).))))........(((((((((.(((..((.(((....))).))..))).))))))))) ( -43.60)
>DroYak_CAF1 1777 98 - 1
-AAAAUUCACACGCGGU-----UGCCAGUGUGACCGUGUG---UCGGUUUGUGGGAAAAAGUACGCCAGCGCGGACUCGAAUUAUGGUUUGGAACUGGGCUGGCGUA
-.((((..(((((((((-----..(....)..))))))))---)..))))...........(((((((((.(((..((((((....))))))..))).))))))))) ( -44.70)
>consensus
AAAAAUUCGCACGCGGU_____GGUCAGUGUGACCGUUCG___UCGCGUGGUGGGAAAACGUGCGCCAGUGCGGACUCAAACCAUGGUUGGUAACUGGGCUGGCGGA
.....(((((((((((......((((.....))))........)))))).)))))........(((((((.(((.....(((....))).....))).))))))).. (-29.52 = -29.84 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	18,349,370 – 18,349,479
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	97.88
Mean single sequence MFE	-36.08
Consensus MFE	-35.18
Energy contribution	-34.86
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.98
SVM decision value	2.70
SVM RNA-class probability	0.996466
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18349370 109 - 22224390
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUCUCGAAUCGACACGGCGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUGGCCAAAAA
............(((.((((((((((((...((((((((((...)))...))))))).)))))........((((.....))))........)))).))).)))..... ( -36.00)
>DroSec_CAF1 2298 108 - 1
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUCUCGAAUCGACACGGCGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUGGCCAAAA-
............(((.((((((((((((...((((((((((...)))...))))))).)))))........((((.....))))........)))).))).)))....- ( -36.00)
>DroSim_CAF1 1064 108 - 1
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUCUCGAAUCGACACGGCGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUGGCCAAAA-
............(((.((((((((((((...((((((((((...)))...))))))).)))))........((((.....))))........)))).))).)))....- ( -36.00)
>DroEre_CAF1 2059 108 - 1
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUUUCAAAUCGACACGACGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUGGCCAAAA-
............(((.((((((((((((...(((((((((.....))...))))))).)))))........((((.....))))........)))).))).)))....- ( -34.20)
>DroYak_CAF1 1875 108 - 1
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUCUCUAAUCGACACGGCGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUCGCCAAAA-
............((((((((((((((((...(((((((............))))))).)))))........((((.....))))........)))).)))))))....- ( -38.20)
>consensus
UCCACUGCAAAAGGCGGGCGCGCGGCGUUUCAAUCGUCUCGAAUCGACACGGCGAUUUAUGCUGUCUUUUCCAGCUUUCAGCUGCUUUUUCUGCGCUGCUGGCCAAAA_
............(((.((((((((((((...(((((((((.....))...))))))).)))))........((((.....))))........)))).))).)))..... (-35.18 = -34.86 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:52 2006