Locus 1435

Sequence ID	X_DroMel_CAF1
Location	4,322,913 – 4,323,068
Length	155
Max. P	0.951642

overview

Window 9

Location	4,322,913 – 4,323,004
Length	91
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	94.13
Mean single sequence MFE	-32.50
Consensus MFE	-27.93
Energy contribution	-28.24
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.55
Structure conservation index	0.86
SVM decision value	1.41
SVM RNA-class probability	0.951642
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4322913 91 + 22224390
UCGAUGUUGCUGUUGCUGUUGCUGUUGCCAAUGCUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCAGCAAUGUCGCCGUAUUUUU
.((((((((((((((((((((((..(((((....))))).....))).)))))))))(((((....))))))))))))))).......... ( -37.60)
>DroSec_CAF1 109174 85 + 1
UCAAUGUUGCUGU------UGCUGUUGCCAAUGCUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGUCGUAUUUUU
......(((((((------(((((((((((....))))..........))))))))))))))(((((((.((((...)))).)).))))). ( -29.10)
>DroSim_CAF1 102511 85 + 1
UCAAUGUUGCUGU------UGCUGUUGCCAAUGCUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUU
.....((((((((------((((..(((((....))))).....))).)))))))))(((((....)))))(((......)))........ ( -30.20)
>DroEre_CAF1 116162 85 + 1
UCGAUGUUGCUGU------UGCUGUUGCCAUUGCUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUU
.((((((((((((------(((((((..(.((((......)))).)..)))))))))(((((....))))))))))))))).......... ( -33.10)
>consensus
UCAAUGUUGCUGU______UGCUGUUGCCAAUGCUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUU
.(((((((((((.......((((((((((..((((.........))))...)))))))))).........))))))))))).......... (-27.93 = -28.24 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	4,322,926 – 4,323,043
Length	117
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	93.35
Mean single sequence MFE	-39.28
Consensus MFE	-32.96
Energy contribution	-33.28
Covariance contribution	0.32
Combinations/Pair	1.06
Mean z-score	-1.49
Structure conservation index	0.84
SVM decision value	0.59
SVM RNA-class probability	0.791038
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4322926 117 + 22224390
UGCUGUUGCUGUUGCCAAUGC--UGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCAGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAU
.((((((((((((((((....--))))..........))))))))))))((((...((.((....)).))(((........)))..))))((((((.(.(........).).)))))). ( -39.20)
>DroSec_CAF1 109187 111 + 1
------UGCUGUUGCCAAUGC--UGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGUCGUAUUUUUUCGGGUUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAU
------.(((((((((..(((--......)))..(....))))))))))(..(((.((.((((...)))).))...)))..)..(((.(((((((((((....)))).))))))).))) ( -36.50)
>DroSim_CAF1 102524 111 + 1
------UGCUGUUGCCAAUGC--UGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAU
------.(((((((((..(((--......)))..(....))))))))))((((..(((.((((......))))........)))..))))((((((.(.(........).).)))))). ( -38.50)
>DroEre_CAF1 116175 110 + 1
------UGCUGUUGCCAUUGC--UGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUGGGCAAAUUUACGGUAAGGCA-A
------((((((((((.((((--......)))).(....)))))))(((((....))))))))).((((((((((..(((((.((((.....)))).)).)))..))))))..))))-. ( -39.30)
>DroYak_CAF1 110783 113 + 1
------UUCUGUUGCCAUUGCCGUGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUCACGGUAAGGUAAA
------.....(((((.(((((((((..(((...((((((((((((.((.((......)).))...))))))))........((....))))))....)))...)))))))))))))). ( -42.90)
>consensus
______UGCUGUUGCCAAUGC__UGGCGUGUAAAGUGAACGGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAU
.......(((((((((...((....))((.........)))))))))))(..(((....((((......))))...)))..)......(((((((((((....)))).))))))).... (-32.96 = -33.28 +   0.32)

alignment

secondary structure

dotplot

Window 1

Location	4,322,926 – 4,323,043
Length	117
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.35
Mean single sequence MFE	-29.83
Consensus MFE	-28.44
Energy contribution	-28.64
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.16
Structure conservation index	0.95
SVM decision value	0.51
SVM RNA-class probability	0.762584
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4322926 117 - 22224390
AUUACCUUACCGUAAAUUUGCCUAGGUAAGGGACCCCGAAAAAAUACGGCGACAUUGCUGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCA--GCAUUGGCAACAGCAACAGCA
....(((((((.............)))))))..............((((((((...((.(........).)).))))))))...........(((.--.....)))....((....)). ( -30.92)
>DroSec_CAF1 109187 111 - 1
AUUACCUUACCGUAAAUUUGCCUAGGUAAGGGAACCCGAAAAAAUACGACGACAUUGCCGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCA--GCAUUGGCAACAGCA------
....(((((((.............)))))))((((.((........))........(.(((((.........))))).))))).........(((.--.....))).......------ ( -24.22)
>DroSim_CAF1 102524 111 - 1
AUUACCUUACCGUAAAUUUGCCUAGGUAAGGGACCCCGAAAAAAUACGGCGACAUUGCCGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCA--GCAUUGGCAACAGCA------
....(((((((.............)))))))..............((((((((...((.(........).)).))))))))...........(((.--.....))).......------ ( -29.72)
>DroEre_CAF1 116175 110 - 1
U-UGCCUUACCGUAAAUUUGCCCAGGUAAGGGACCCCGAAAAAAUACGGCGACAUUGCCGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCA--GCAAUGGCAACAGCA------
.-..(((((((.............)))))))..............((((((((...((.(........).)).))))))))...........((((--....)))).......------ ( -32.12)
>DroYak_CAF1 110783 113 - 1
UUUACCUUACCGUGAAUUUGCCUAGGUAAGGGACCCCGAAAAAAUACGGCGACAUUGCCGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCACGGCAAUGGCAACAGAA------
....(((((((.............)))))))......((((.....(((((....)))))....))))..(((((.(((((..............))))).))))).......------ ( -32.16)
>consensus
AUUACCUUACCGUAAAUUUGCCUAGGUAAGGGACCCCGAAAAAAUACGGCGACAUUGCCGACGAUUUCCCGCCGUCGCCGUUCACUUUACACGCCA__GCAUUGGCAACAGCA______
....(((((((.............)))))))..............((((((((...((.(........).)).))))))))...........((((......))))............. (-28.44 = -28.64 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	4,322,964 – 4,323,068
Length	104
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	91.54
Mean single sequence MFE	-32.20
Consensus MFE	-26.22
Energy contribution	-26.86
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.81
SVM decision value	-0.02
SVM RNA-class probability	0.525056
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4322964 104 + 22224390
GGCGACGGCGGGAAAUCGUCAGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAUUUGCACAGAGAGAAAAACUAGAUA-A--
(((((((((((....)))))(....)))))))((.(((((((((....))....((..(((((((.((......)))))))))..)).)))))))))......-.-- ( -30.10)
>DroSec_CAF1 109219 105 + 1
GGCGACGGCGGGAAAUCGUCGGCAAUGUCGUCGUAUUUUUUCGGGUUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAUUUGCACAGAGAGAAAAACUAGGUAGG--
.((((((((((....)))))(((...))))))))........((....))(((((((((((((((.((......))))))))).(.....).....)))))))).-- ( -30.00)
>DroSim_CAF1 102556 104 + 1
GGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAUUUGCACAGAGAGAAAAACUAGGUA-A--
((.(((..((..(((....((((......))))...)))..))..))))).((((((((((((((.((......))))))))).(.....).....)))))))-.-- ( -33.10)
>DroEre_CAF1 116207 103 + 1
GGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUGGGCAAAUUUACGGUAAGGCA-AUUGCACUGAGCGAAAAUAUAGCCA-U--
(((..((((((....))))))((((((((((((((..(((((.((((.....)))).)).)))..))))))..))).-)))))................))).-.-- ( -36.20)
>DroYak_CAF1 110817 106 + 1
GGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUCACGGUAAGGUAAAUUGCACAGAGAGAAAAUAUAGCCA-CGC
(((..((((((....))))))((((((.(.(((........))).).)(((((((.............)))))))...)))))................))).-... ( -31.62)
>consensus
GGCGACGGCGGGAAAUCGUCGGCAAUGUCGCCGUAUUUUUUCGGGGUCCCUUACCUAGGCAAAUUUACGGUAAGGUAAUUUGCACAGAGAGAAAAACUAGCUA_A__
((((((.((.((......)).))...))))))...((((((((((........)))..(((((((..(.....)..)))))))...))))))).............. (-26.22 = -26.86 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:24 2006