Locus 5582

Sequence ID	3R_DroMel_CAF1
Location	14,756,412 – 14,756,560
Length	148
Max. P	0.981314

overview

Window 7

Location	14,756,412 – 14,756,503
Length	91
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-28.01
Consensus MFE	-18.94
Energy contribution	-19.80
Covariance contribution	0.86
Combinations/Pair	1.08
Mean z-score	-1.84
Structure conservation index	0.68
SVM decision value	0.33
SVM RNA-class probability	0.691985
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14756412 91 - 27905053
UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUU----UUGGGGACAUUUCGAAGAUGC----------------CAAGAUGCGCCACCAGGAGCGAGUA
.......(((((((.(((...((((.((((......))))(((((----((((...((((.....)))))----------------))))))))))))...)))))))))) ( -31.20)
>DroSec_CAF1 15371 91 - 1
UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUU----UUGGGGACAUUUCGAAGAUGC----------------CAAGAUGCGCCACCAGGAGCGAGUA
.......(((((((.(((...((((.((((......))))(((((----((((...((((.....)))))----------------))))))))))))...)))))))))) ( -31.20)
>DroSim_CAF1 16532 91 - 1
UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUU----UUGGGGACAUUUCGAAGAUGC----------------CAAGAUGCGCCACCAGGAGCGAGUA
.......(((((((.(((...((((.((((......))))(((((----((((...((((.....)))))----------------))))))))))))...)))))))))) ( -31.20)
>DroEre_CAF1 15545 99 - 1
UUUGAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCGUU----UUGGGGACAUUUCGAAGAUGCUAAGUUGCGA--------AGAUGCGCCACCAGGAGAGAGUA
.......(((((..((((...((((.((((......))))(((((----((.(.(((................))).).)--------))))))))))...)))).))))) ( -26.69)
>DroYak_CAF1 14914 107 - 1
UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCGUU----UUGUAGACAUUUCGAAGAUGCGAAGAUGUGAAGACGCCAAGAUGCGCCACCAGGAGCGAGUA
.......(((((((.(((...((((......((....))((((((----((....((((((((......)).)))))).)))))))).......))))...)))))))))) ( -31.10)
>DroAna_CAF1 18511 82 - 1
----AGCUAUUUGC-UCUAUUUGCCACUUAUUCAAUUGAGCCGUUACAUUUGGGGACACUUUU-----GC-------------------GCUGCACCACCAGGAGCGAGUA
----...(((((((-(((...(((..((((......)))).(((......((....)).....-----))-------------------)..)))......)))))))))) ( -16.70)
>consensus
UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUU____UUGGGGACAUUUCGAAGAUGC________________CAAGAUGCGCCACCAGGAGCGAGUA
.......(((((((.(((...((((.((((......))))(((((.....((....)).......)))))........................))))...)))))))))) (-18.94 = -19.80 +   0.86)

alignment

secondary structure

dotplot

Window 8

Location	14,756,437 – 14,756,537
Length	100
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	93.27
Mean single sequence MFE	-28.78
Consensus MFE	-25.56
Energy contribution	-25.60
Covariance contribution	0.04
Combinations/Pair	1.10
Mean z-score	-1.14
Structure conservation index	0.89
SVM decision value	-0.02
SVM RNA-class probability	0.525529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14756437 100 - 27905053
GAUUAGUGCGCUUAAGUGCGCUUAAGAGGAGCCU-UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUUUUGGGGACAUUUCGAAGAUGC----
.......((((....))))(((.(((((....))-))).)))....((((.......))))((((......))))(((((((.(((....))).)))))))---- ( -26.60)
>DroSec_CAF1 15396 99 - 1
GAUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUUUUGGGGACAUUUCGAAGAUGC----
.........(((.(((((((((.--...).)))))))).)))....((((.......))))((((......))))(((((((.(((....))).)))))))---- ( -27.70)
>DroSim_CAF1 16557 99 - 1
GAUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUUUUGGGGACAUUUCGAAGAUGC----
.........(((.(((((((((.--...).)))))))).)))....((((.......))))((((......))))(((((((.(((....))).)))))))---- ( -27.70)
>DroEre_CAF1 15574 103 - 1
GGUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUGAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCGUUUUGGGGACAUUUCGAAGAUGCUAAG
(((.((((.(((((((((((((.--...).)))))))))))))))).))).....((((((((((......)))).((...((....))...))....)))))). ( -34.70)
>DroYak_CAF1 14951 103 - 1
GGUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCGUUUUGUAGACAUUUCGAAGAUGCGAAG
(((.((((.(((.(((((((((.--...).)))))))).))))))).)))(((((((.((.((((......))))))(((.....))).......))))).)).. ( -27.20)
>consensus
GAUUAGUGCGCUUAAGUGGGCCU__GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCAAUUGAGGCAUUUUGGGGACAUUUCGAAGAUGC____
.........(((.((((((((((....)).)))))))).)))....((((.......))))((((......))))(((((((.(((....))).))))))).... (-25.56 = -25.60 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	14,756,469 – 14,756,560
Length	91
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	95.59
Mean single sequence MFE	-25.28
Consensus MFE	-22.26
Energy contribution	-22.14
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.84
Structure conservation index	0.88
SVM decision value	1.88
SVM RNA-class probability	0.981314
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14756469 91 + 27905053
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUAAAA-AGGCUCCUCUUAAGCGCACUUAAGCGCACUAAUCCAGUGCGACUGUGUACUCCGUAC
....(((((((.....(((((.....((((....-.))))))))).....)))))))((((((((.....)))))).))............. ( -27.10)
>DroSec_CAF1 15428 90 + 1
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUAAAAUAGGCUCCUC--AGGCCCACUUAAGCGCACUAAUCCAGUGCGACUGUGUGCUCCGUAC
.......((((......((((.....((((......))))))))--.((..(((...((((((((.....)))))).))..)))..)))))) ( -26.00)
>DroSim_CAF1 16589 90 + 1
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUAAAAUAGGCUCCUC--AGGCCCACUUAAGCGCACUAAUCCAGUGCGACUGUGUGCUCCGUAC
.......((((......((((.....((((......))))))))--.((..(((...((((((((.....)))))).))..)))..)))))) ( -26.00)
>DroEre_CAF1 15610 90 + 1
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUCAAAUAGGCUCCUC--AGGCCCACUUAAGCGCACUAACCCAGUGCGACUGUGUACUCCAUAC
..............((((((....((((.((.....((((....--.)))).........(((((.....)))))))))))...)))))).. ( -23.90)
>DroYak_CAF1 14987 90 + 1
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUAAAAUAGGCUCCUC--AGGCCCACUUAAGCGCACUAACCCAGUGCGACUGUGUACUCCGUAC
..............((((((((.....)).......((((....--.))))(((.....((((((.....))))))...)))..)))))).. ( -23.40)
>consensus
UGAAUAAGUGCCAAAUGGAGGCAAAUAGCUAAAAUAGGCUCCUC__AGGCCCACUUAAGCGCACUAAUCCAGUGCGACUGUGUACUCCGUAC
..............(((((((((....(((......((((.......))))......)))(((((.....))))).....))).)))))).. (-22.26 = -22.14 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	14,756,469 – 14,756,560
Length	91
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	95.59
Mean single sequence MFE	-28.14
Consensus MFE	-24.48
Energy contribution	-25.12
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	1.10
SVM RNA-class probability	0.915249
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14756469 91 - 27905053
GUACGGAGUACACAGUCGCACUGGAUUAGUGCGCUUAAGUGCGCUUAAGAGGAGCCU-UUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
....(((((((..((.(((((((...)))))))))...))))(((.(((((....))-))).)))....((((.......))))....))). ( -26.20)
>DroSec_CAF1 15428 90 - 1
GUACGGAGCACACAGUCGCACUGGAUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
....((((((.......((((((...))))))(((.(((((((((.--...).)))))))).)))....)).))))................ ( -27.30)
>DroSim_CAF1 16589 90 - 1
GUACGGAGCACACAGUCGCACUGGAUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
....((((((.......((((((...))))))(((.(((((((((.--...).)))))))).)))....)).))))................ ( -27.30)
>DroEre_CAF1 15610 90 - 1
GUAUGGAGUACACAGUCGCACUGGGUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUGAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
.....(((((.......((((((...))))))(((((((((((((.--...).))))))))))))....((((.......))))..))))). ( -32.00)
>DroYak_CAF1 14987 90 - 1
GUACGGAGUACACAGUCGCACUGGGUUAGUGCGCUUAAGUGGGCCU--GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
.....(((((.......((((((...))))))(((.(((((((((.--...).)))))))).)))....((((.......))))..))))). ( -27.90)
>consensus
GUACGGAGUACACAGUCGCACUGGAUUAGUGCGCUUAAGUGGGCCU__GAGGAGCCUAUUUUAGCUAUUUGCCUCCAUUUGGCACUUAUUCA
.....(((((.......((((((...))))))(((.((((((((((....)).)))))))).)))....((((.......))))..))))). (-24.48 = -25.12 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:40 2006