Locus 1681

Sequence ID	X_DroMel_CAF1
Location	4,703,595 – 4,703,782
Length	187
Max. P	0.995910

overview

Window 3

Location	4,703,595 – 4,703,702
Length	107
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	74.69
Mean single sequence MFE	-29.31
Consensus MFE	-18.64
Energy contribution	-18.70
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-2.39
Structure conservation index	0.64
SVM decision value	2.63
SVM RNA-class probability	0.995910
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4703595 107 + 22224390
A-GCCACACAAAUUUG--UUUUUUAUUUUUUUUAACACACUUAUACGCCCCACUUUUCUCGCGGUGUGUCGUCUGAGCGCACAGUACGUGCUAAAAGUAUGUGCACAGGA
.-.((...........--...................(.((((.(((.(.((((........)))).).))).)))).)....((((((((.....))))))))...)). ( -20.50)
>DroSec_CAF1 56504 101 + 1
A-GCCGCACAUAUUUAACAUUUUUUUUUUUUUUUACACACUUAUAC-CCUCGCUUUUCUCUCGGUGUG-------CGCGCACAGUACGUGCUAAAAGUAUGUGCACAGGA
.-...((((((((((....................((((((.....-...............))))))-------...((((.....))))...))))))))))...... ( -22.55)
>DroEre_CAF1 57979 101 + 1
AUGCCACACAUCUGGCACAU------UGUUUUUUGCACACUUGA---CCCUUCUUUUCGCACUGUGUGUCGUCUGCGCGCACAGUACGUGCUAAAAGCAUGUGCACAGGA
..........((((((((((------.((((((.((((....((---....)).....(.((((((((.((....)))))))))).))))).)))))))))))).)))). ( -37.10)
>DroYak_CAF1 54776 101 + 1
AUGCCACACACUUUUCACAU------AGUUGGGUACACACUUGC---CCCUACUUUUCUCUCAGUGUGUGGCGAGCGCGCACAGUACGUGCUAAAAGUAUGUGCACAGGA
.(((((((((((........------(((.(((((......)))---))..)))........)))))))))))..........((((((((.....))))))))...... ( -37.09)
>consensus
A_GCCACACAUAUUUCACAU______UGUUUUUUACACACUUAU___CCCCACUUUUCUCUCGGUGUGUCGUCUGCGCGCACAGUACGUGCUAAAAGUAUGUGCACAGGA
...((..........................................................((((((.......)))))).((((((((.....))))))))...)). (-18.64 = -18.70 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	4,703,595 – 4,703,702
Length	107
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	74.69
Mean single sequence MFE	-30.82
Consensus MFE	-15.16
Energy contribution	-14.98
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.49
SVM decision value	0.48
SVM RNA-class probability	0.751528
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4703595 107 - 22224390
UCCUGUGCACAUACUUUUAGCACGUACUGUGCGCUCAGACGACACACCGCGAGAAAAGUGGGGCGUAUAAGUGUGUUAAAAAAAAUAAAAAA--CAAAUUUGUGUGGC-U
......((.(((((((((((((((...((((((((..(......).((((.......))))))))))))..)))))))))).((((......--...)))))))))))-. ( -26.50)
>DroSec_CAF1 56504 101 - 1
UCCUGUGCACAUACUUUUAGCACGUACUGUGCGCG-------CACACCGAGAGAAAAGCGAGG-GUAUAAGUGUGUAAAAAAAAAAAAAAAUGUUAAAUAUGUGCGGC-U
.....((((((((......((((.....))))(((-------(((..(....)....((....-))....))))))......................))))))))..-. ( -22.40)
>DroEre_CAF1 57979 101 - 1
UCCUGUGCACAUGCUUUUAGCACGUACUGUGCGCGCAGACGACACACAGUGCGAAAAGAAGGG---UCAAGUGUGCAAAAAACA------AUGUGCCAGAUGUGUGGCAU
...((..(((.(((((((....(((((((((.(((....)).).))))))))).....)))))---.)).)))..)).......------..((((((......)))))) ( -35.20)
>DroYak_CAF1 54776 101 - 1
UCCUGUGCACAUACUUUUAGCACGUACUGUGCGCGCUCGCCACACACUGAGAGAAAAGUAGGG---GCAAGUGUGUACCCAACU------AUGUGAAAAGUGUGUGGCAU
....(((((((((((((...((((((..(((((((((.(((.(..(((........)))..))---)).))))))))).....)------))))).))))))))).)))) ( -39.20)
>consensus
UCCUGUGCACAUACUUUUAGCACGUACUGUGCGCGCAGACGACACACCGAGAGAAAAGUAGGG___ACAAGUGUGUAAAAAAAA______AUGUGAAAUAUGUGUGGC_U
.((.((((((((((.........))).)))))))........(((((.......................)))))..............................))... (-15.16 = -14.98 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	4,703,665 – 4,703,782
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.47
Mean single sequence MFE	-33.20
Consensus MFE	-30.34
Energy contribution	-31.15
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-1.77
Structure conservation index	0.91
SVM decision value	1.50
SVM RNA-class probability	0.959069
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4703665 117 + 22224390
UGAGCGCACAGUACGUGCU-AAAAGUAUGUGCA--CAGGACUCGCAUAUAUAGAAAGCUUCGGCAUUAGUUUUUAGUUUUCGCAUCACAUGACGCUCGGGGGUGUCAUAUUGAAAAAAAA
(((((((((.....)))).-....((((((((.--........)))))))).(((((((..(((....)))...))))))))).))).((((((((....))))))))............ ( -33.20)
>DroPse_CAF1 16826 114 + 1
--UGUGCACAGUCCCUGCUGAAAAGCAUGUGCACACAGGCUCCGCAU--ACAGAACGCUUCGGCAUUAGUU-UUAGUUUUCACAUCACAUGACGCUCGGGGGUGUCAUAUUGAAA-AAAA
--((((((((.....((((....))))))))))))............--.......((....)).......-....((((((......((((((((....))))))))..)))))-)... ( -32.60)
>DroSec_CAF1 56570 115 + 1
--CGCGCACAGUACGUGCU-AAAAGUAUGUGCA--CAGGACUCGCAUAUAUAGAAAGCUUCGGCAUUAGUUUUUAGUUUUCGCAUCACAUGACGCUCGGGGGUGUCAUAUUGAAAAAAAA
--.((((((.....)))).-....((((((((.--........)))))))).(((((((..(((....)))...))))))))).(((.((((((((....))))))))..)))....... ( -33.30)
>DroEre_CAF1 58043 115 + 1
UGCGCGCACAGUACGUGCU-AAAAGCAUGUGCA--CAGGACUCGCAU--AUAGAAAGCUUCGGCAUUAGUUUUUAGUUUUCGCAUCACAUGACGCUCGGGGGUGUCAUAUUGAAAAAAAA
((((((..(.((((((((.-....)))))))).--...)...)))..--...(((((((..(((....)))...))))))))))(((.((((((((....))))))))..)))....... ( -34.90)
>DroYak_CAF1 54840 115 + 1
AGCGCGCACAGUACGUGCU-AAAAGUAUGUGCA--CAGGACUCGCAU--AUAGAAAGCUUCGGCAUUAGUUUUUAGUUUUCGCAUCACAUGACGCUCGGGGGUGUCAUAUUGAAAAAAAA
.(((((..(.((((((((.-....)))))))).--...)...)))..--...(((((((..(((....)))...))))))))).(((.((((((((....))))))))..)))....... ( -32.60)
>DroPer_CAF1 16185 114 + 1
--UGUGCACAGUCCCUGCUGAAAAGCAUGUGCACACAGGCUCCGCAU--ACAGAACGCUUCGGCAUUAGUU-UUAGUUUUCACAUCACAUGACGCUCGGGGGUGUCAUAUUGAAA-AAAA
--((((((((.....((((....))))))))))))............--.......((....)).......-....((((((......((((((((....))))))))..)))))-)... ( -32.60)
>consensus
__CGCGCACAGUACGUGCU_AAAAGCAUGUGCA__CAGGACUCGCAU__AUAGAAAGCUUCGGCAUUAGUUUUUAGUUUUCGCAUCACAUGACGCUCGGGGGUGUCAUAUUGAAAAAAAA
...((((...(((((((((....))))))))).....(....))).......(((((((..(((....)))...))))))))).(((.((((((((....))))))))..)))....... (-30.34 = -31.15 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:33 2006