Locus 2514

Sequence ID	X_DroMel_CAF1
Location	6,684,102 – 6,684,222
Length	120
Max. P	0.998207

overview

Window 7

Location	6,684,102 – 6,684,222
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.30
Mean single sequence MFE	-36.13
Consensus MFE	-35.74
Energy contribution	-35.30
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-4.33
Structure conservation index	0.99
SVM decision value	3.03
SVM RNA-class probability	0.998207
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6684102 120 + 22224390
GUAAACGAUGUAGCGGUUGCAUUCAAUCCAAUCUACAUAAUACGUACAUACAUAUUGCUUUGAGUUUUCCAUAGCCGCUGCAUCGUUUACAACCAGUCUGCAAUGUCUGCCGACACCGAA
(((((((((((((((((((.((((((..((((.....................))))..))))))......))))))))))))))))))).....(((.(((.....))).)))...... ( -39.80)
>DroSec_CAF1 13843 115 + 1
GUAAACGAUGCACCGGUUGCAUUCAAUCCAACCUACAU---ACGUACAUA--UAUUGCUUUGAGUUUUCCAUAGCCGCUGCAUCGUUUACAACCAGUCAGCAAUGUCUGCCGACACCGAA
((((((((((((.((((((.((((((..(((..(((..---..)))....--..)))..))))))......)))))).)))))))))))).....(((.(((.....))).)))...... ( -35.10)
>DroEre_CAF1 13606 111 + 1
GUAAACGGUGCAGCGGUUGCAUUCAAUCCAACCUUCAU-------ACAUA--UAUUGCUUUCAGUUUUCCUUAGCCGCUGCAUCGUUUACAACCAGUUUGCAAUGUCUGCCGAUACCGAA
(((((((((((((((((((((.................-------.....--...)))....((.....)).)))))))))))))))))).....(((.(((.....))).)))...... ( -32.41)
>DroYak_CAF1 13577 111 + 1
GUAAACGGUGCAGCGGUUGCAUUCAAUCCAACCUACAU-------ACAUA--UAUUGCUUUGAGUUUUCCUUAGCCGCUGCAUCGUUUACAACCAGUUUGCAAUGUCUGCCGAUUCCGAA
(((((((((((((((((((.((((((..(((..((...-------...))--..)))..))))))......)))))))))))))))))))....((((.(((.....))).))))..... ( -37.20)
>consensus
GUAAACGAUGCAGCGGUUGCAUUCAAUCCAACCUACAU_______ACAUA__UAUUGCUUUGAGUUUUCCAUAGCCGCUGCAUCGUUUACAACCAGUCUGCAAUGUCUGCCGACACCGAA
(((((((((((((((((((.((((((..(((.......................)))..))))))......))))))))))))))))))).....(((.(((.....))).)))...... (-35.74 = -35.30 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	6,684,102 – 6,684,222
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.30
Mean single sequence MFE	-34.95
Consensus MFE	-28.75
Energy contribution	-31.50
Covariance contribution	2.75
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.82
SVM decision value	1.22
SVM RNA-class probability	0.932179
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6684102 120 - 22224390
UUCGGUGUCGGCAGACAUUGCAGACUGGUUGUAAACGAUGCAGCGGCUAUGGAAAACUCAAAGCAAUAUGUAUGUACGUAUUAUGUAGAUUGGAUUGAAUGCAACCGCUACAUCGUUUAC
..(((((((....)))))))..........((((((((((.(((((((.(((.....))).)))(((((((....))))))).((((............))))..)))).)))))))))) ( -34.30)
>DroSec_CAF1 13843 115 - 1
UUCGGUGUCGGCAGACAUUGCUGACUGGUUGUAAACGAUGCAGCGGCUAUGGAAAACUCAAAGCAAUA--UAUGUACGU---AUGUAGGUUGGAUUGAAUGCAACCGGUGCAUCGUUUAC
......((((((((...)))))))).....((((((((((((.(.(((.(((.....))).))).(((--(((....))---)))).(((((.((...)).)))))).)))))))))))) ( -40.80)
>DroEre_CAF1 13606 111 - 1
UUCGGUAUCGGCAGACAUUGCAAACUGGUUGUAAACGAUGCAGCGGCUAAGGAAAACUGAAAGCAAUA--UAUGU-------AUGAAGGUUGGAUUGAAUGCAACCGCUGCACCGUUUAC
.(((((....((((...))))..)))))..(((((((.((((((.(((.((.....))...)))....--.....-------.....(((((.((...)).))))))))))).))))))) ( -33.50)
>DroYak_CAF1 13577 111 - 1
UUCGGAAUCGGCAGACAUUGCAAACUGGUUGUAAACGAUGCAGCGGCUAAGGAAAACUCAAAGCAAUA--UAUGU-------AUGUAGGUUGGAUUGAAUGCAACCGCUGCACCGUUUAC
.((((.....((((...))))...))))..(((((((.((((((.(((...((....))..)))....--.....-------.....(((((.((...)).))))))))))).))))))) ( -31.20)
>consensus
UUCGGUAUCGGCAGACAUUGCAAACUGGUUGUAAACGAUGCAGCGGCUAAGGAAAACUCAAAGCAAUA__UAUGU_______AUGUAGGUUGGAUUGAAUGCAACCGCUGCACCGUUUAC
..(((((((....)))))))..........((((((((((((((.(((.(((.....))).))).......................(((((.((...)).))))))))))))))))))) (-28.75 = -31.50 +   2.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:38 2006