Locus 4070

Sequence ID	X_DroMel_CAF1
Location	10,772,759 – 10,772,887
Length	128
Max. P	0.861219

overview

Window 4

Location	10,772,759 – 10,772,856
Length	97
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	85.77
Mean single sequence MFE	-35.69
Consensus MFE	-29.26
Energy contribution	-29.52
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.82
SVM decision value	0.53
SVM RNA-class probability	0.770781
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10772759 97 + 22224390
------------UGUACGCCAAGGCAAAGUGCUAAUAAAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGACUCUGGCCGGGCACUUUCAUU
------------.....((....))((((((((..........--((((((.(((((((((.......)).)))))))))))))(((.......)))..)))))))).... ( -30.90)
>DroSec_CAF1 22132 97 + 1
------------UGUACGCCAAGGCAAAGUGCUAAUAAAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUUUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUU
------------.....((((.((((..((((...........--.......))))))))))))..................(((((((((....)))))))))....... ( -35.37)
>DroSim_CAF1 20682 97 + 1
------------UGUACGCCAAGGCAAAGUGCUAAUAAAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUU
------------.....((((.((((..((((...........--.......)))))))))))).........((((.....(((((((((....)))))))))...)))) ( -36.17)
>DroEre_CAF1 19809 97 + 1
------------AGUACGUCAAGGCAAAGUGCUAAUAAAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUCGCCGGGCACUUUCAUU
------------(((((...........)))))........((--(((...((((((...........)))))).)))))..(((((((((....)))))))))....... ( -33.80)
>DroYak_CAF1 21672 97 + 1
------------AGUACGCCAAGGCAAAGUGCUAAUAAAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUGUGUGCCUGGCUCUUGCCGGCCACUUUCGUU
------------.....(((.(((((..((((...........--.......)))))))))((((..((((.(((.((......))))))))).))))))).......... ( -32.97)
>DroPer_CAF1 31655 111 + 1
AGUCCCAGCGAAAGUGUUCCAAGGCAAAGUGUUAAUAUACGGAGUGCGAAAUGCGUUACCUGGCAUUGAGUGCGCUCUUUGUGUGCCUGGCCCUCGCCGGGCACUGCCAAA
.......((....)).......((((..((((....))))((((((((.(((((........)))))...))))))))....(((((((((....)))))))))))))... ( -44.90)
>consensus
____________AGUACGCCAAGGCAAAGUGCUAAUAAAUCGA__GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUU
.................((((.(((..(((((....................))))))))))))..................(((((((((....)))))))))....... (-29.26 = -29.52 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	10,772,784 – 10,772,887
Length	103
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	82.98
Mean single sequence MFE	-41.52
Consensus MFE	-32.92
Energy contribution	-33.07
Covariance contribution	0.14
Combinations/Pair	1.16
Mean z-score	-2.30
Structure conservation index	0.79
SVM decision value	0.83
SVM RNA-class probability	0.861219
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10772784 103 + 22224390
AAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGACUCUGGCCGGGCACUUUCAUUUGUCAGGUAGGCGAAAUGGCUAAAC-----C-CAUGC-
.....(--((....(((.((((((((((.((((...((((((..((.(((.......)))))))))))))))..))))))))))))).....)))....-----.-.....- ( -34.60)
>DroSec_CAF1 22157 104 + 1
AAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUUUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUUUGUCAGGUAGGCGAAAUGGCGAAAC-----C-CAUGCG
......--((....(((.((((((((((.((((............(((((((((....))))))))).))))..)))))))))))))..((((......-----)-))))). ( -42.82)
>DroSim_CAF1 20707 104 + 1
AAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUUUGUCAGGUAGGCGAAAUGGCGAAAC-----C-CAUGCG
......--((....(((.((((((((((.(((((.....))....(((((((((....)))))))))..)))..)))))))))))))..((((......-----)-))))). ( -43.00)
>DroEre_CAF1 19834 110 + 1
AAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUCGCCGGGCACUUUCAUUUGUCAGGUAGGCGAAAUGGGGAAUUUUGGGCGAGUUUG
..(((.--.((((((.((((((((((((.(((((.....))....(((((((((....)))))))))..)))..))))))))).))).........))))))..)))..... ( -42.50)
>DroYak_CAF1 21697 105 + 1
AAUCGA--GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUGUGUGCCUGGCUCUUGCCGGCCACUUUCGUUUGUCAGGUAGGCGAAAUGGCGAAAAA----C-CAUUUG
......--......(((.((((((((((.(((((((((...))))))(((.(((....)))))).....)))..)))))))))))))((((((.......----)-))))). ( -37.80)
>DroPer_CAF1 31692 106 + 1
UACGGAGUGCGAAAUGCGUUACCUGGCAUUGAGUGCGCUCUUUGUGUGCCUGGCCCUCGCCGGGCACUGCCAAAUCGCAGGUAAGUGGAUAGGGUCAGG-----C-CAGACG
...((((((((.(((((........)))))...))))))))..((.(((((((((((..(((.((.((((......))))))...)))..)))))))))-----.-)).)). ( -48.40)
>consensus
AAUCGA__GCAAAAUGCGCUGCCUGGCAUUGAGCGCAGUGUUUUUGUGCCUGGCUCUGGCCGGGCACUUUCAUUUGUCAGGUAGGCGAAAUGGCGAAAC_____C_CAUGCG
..............(((.(((((((((((((....))))......(((((((((....)))))))))........))))))))))))......................... (-32.92 = -33.07 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:42 2006