Locus 748

Sequence ID	X_DroMel_CAF1
Location	2,046,744 – 2,046,838
Length	94
Max. P	0.986973

overview

Window 2

Location	2,046,744 – 2,046,838
Length	94
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	74.92
Mean single sequence MFE	-30.92
Consensus MFE	-21.68
Energy contribution	-23.04
Covariance contribution	1.36
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.70
SVM decision value	1.46
SVM RNA-class probability	0.955656
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2046744 94 + 22224390
UUAAAUAGCAGGCGCUGGCAGAGCAAACGACCCG----UACGGACAGCAUGAGUCCCAGGGCUUUUGGGUCGUCCUGUCCACACCCCCCACCCCCCCG
.......(((((.(((.....)))..((((((((----(....)).....(((((....)))))..)))))))))))).................... ( -24.90)
>DroSec_CAF1 13418 89 + 1
UUAAAUAGCAGGCGCUGGCAGGGCAAACGACCCG----CCCGGACAGCAUGAGUCCCCGGGCUUUUGGGUCGUCCUGC----ACA-CCCCACCCCCCA
..........((.(.(((((((....((((((((----(((((...((....))..))))))....))))))))))))----.))-.)))........ ( -35.30)
>DroSim_CAF1 11104 89 + 1
UUAAAUAGCAGGCGCUGGCAGAGCAAACGACCCG----CCCGGACAGCAUGAGUCCCCGGGCUUUUGGGUCGUCCUGC----AGC-CCCACCCCCCCA
..........((.((((.(((.(...((((((((----(((((...((....))..))))))....))))))))))))----)))-.))......... ( -35.20)
>DroEre_CAF1 13436 72 + 1
UUAAAUAGAAGGCGCUGGCAGAGCAAACGACCCG----CCCGGACACUAA--AUGUCCGGGCUUUUGGGUCCUCCC--------C-A-----------
..........((.(((.....)))....((((((----((((((((....--.)))))))))....)))))....)--------)-.----------- ( -29.50)
>DroYak_CAF1 13593 80 + 1
UUAAAUAGAAGGCGCUGGCAGAGCAAACGACCCGCCCGCCCGGAUAGUAA--AUGUCCGGGCUUUUGGCUCCUCCUGC----UUC-C-----------
.....(((.(((.((((((.(..(....)..).))).(((((((((....--.)))))))))....))).))).))).----...-.----------- ( -29.70)
>consensus
UUAAAUAGCAGGCGCUGGCAGAGCAAACGACCCG____CCCGGACAGCAUGAGUCCCCGGGCUUUUGGGUCGUCCUGC____ACC_CCC__CCCCCC_
.......(((((.(((.....)))..((((((((....(((((.............)))))....))))))))))))).................... (-21.68 = -23.04 +   1.36)

alignment

secondary structure

dotplot

Window 3

Location	2,046,744 – 2,046,838
Length	94
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	74.92
Mean single sequence MFE	-38.38
Consensus MFE	-20.70
Energy contribution	-21.90
Covariance contribution	1.20
Combinations/Pair	1.09
Mean z-score	-2.33
Structure conservation index	0.54
SVM decision value	2.06
SVM RNA-class probability	0.986973
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2046744 94 - 22224390
CGGGGGGGUGGGGGGUGUGGACAGGACGACCCAAAAGCCCUGGGACUCAUGCUGUCCGUA----CGGGUCGUUUGCUCUGCCAGCGCCUGCUAUUUAA
.....((((((.((((((((.(((((((((((....((....((((.......)))))).----.))))))))....)))))).))))).)))))).. ( -36.20)
>DroSec_CAF1 13418 89 - 1
UGGGGGGUGGGG-UGU----GCAGGACGACCCAAAAGCCCGGGGACUCAUGCUGUCCGGG----CGGGUCGUUUGCCCUGCCAGCGCCUGCUAUUUAA
(((.(((((.((-((.----((((.(((((((....(((((((.((....).).))))))----)))))))))))).).)))..))))).)))..... ( -43.80)
>DroSim_CAF1 11104 89 - 1
UGGGGGGGUGGG-GCU----GCAGGACGACCCAAAAGCCCGGGGACUCAUGCUGUCCGGG----CGGGUCGUUUGCUCUGCCAGCGCCUGCUAUUUAA
..((.(((((.(-((.----((((.(((((((....(((((((.((....).).))))))----))))))))))))...)))..))))).))...... ( -45.80)
>DroEre_CAF1 13436 72 - 1
-----------U-G--------GGGAGGACCCAAAAGCCCGGACAU--UUAGUGUCCGGG----CGGGUCGUUUGCUCUGCCAGCGCCUUCUAUUUAA
-----------.-.--------((((((((((....((((((((((--...)))))))))----))))))....(((.....)))..)))))...... ( -33.20)
>DroYak_CAF1 13593 80 - 1
-----------G-GAA----GCAGGAGGAGCCAAAAGCCCGGACAU--UUACUAUCCGGGCGGGCGGGUCGUUUGCUCUGCCAGCGCCUUCUAUUUAA
-----------.-(((----..((((((.((.....(((((((...--......))))))).(((((((.....)).))))).)).)))))).))).. ( -32.90)
>consensus
_GGGGGG__GGG_GGU____GCAGGACGACCCAAAAGCCCGGGGACUCAUGCUGUCCGGG____CGGGUCGUUUGCUCUGCCAGCGCCUGCUAUUUAA
....................(((((..(((((.....((((((.(.......).)))))).....)))))(((.((...)).))).)))))....... (-20.70 = -21.90 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:51 2006