Locus 4985

Sequence ID	3R_DroMel_CAF1
Location	13,118,135 – 13,118,243
Length	108
Max. P	0.990257

overview

Window 1

Location	13,118,135 – 13,118,243
Length	108
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	76.11
Mean single sequence MFE	-39.68
Consensus MFE	-18.80
Energy contribution	-21.78
Covariance contribution	2.98
Combinations/Pair	1.29
Mean z-score	-2.84
Structure conservation index	0.47
SVM decision value	2.17
SVM RNA-class probability	0.989534
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13118135 108 + 27905053
AAAUGUCUGCCGGAGCAUCUGGAAGAC----U-CCCAGUCUCCGUUCCCUUACUCCGACUCACUCGAAGGCUGAGCUUCUGACUCCCUGGAUACUUUCCACGGAGUCAAGAGC
.....((.((((((((....(((.(((----.-....))))))))))).......(((.....)))..))).))(((..(((((((.((((.....)))).)))))))..))) ( -40.90)
>DroSec_CAF1 148512 108 + 1
AAAUGUUUGCCGGAGCAUCUGGAAUAC----U-CUCAAUCUCCGGUCCCUCACCAGGACUCACUCGAAGGAUGAGCUCCUGACUCCCUGGAUACUUUCCACGGAGUCAAGAGC
........(((((((.((..(((....----)-))..)))))))))..(((...((((((((.((....)))))).))))((((((.((((.....)))).))))))..))). ( -43.20)
>DroSim_CAF1 133260 108 + 1
AAAUGUCUGCCGGAGCAUCUGGAAGAC----U-CCCAAUCUCCGGUCCCUUACCAGGACUCACUCGAAGGCUGAGCUCUUGACUCCCUGGAUACUUUCCACGGAGUCAAGAGC
.....((.(((((((.((..(((....----)-))..))))))(((((.......)))))........))).))((((((((((((.((((.....)))).)))))))))))) ( -47.80)
>DroEre_CAF1 138611 106 + 1
AAAUGUCUGCCGCAGCAUCUGGAAGUC----U-CCCAAUCCCCGGUUCUUA-CUCCGACUCACUCGACGGCUGAGCCGCUGACUCCCUGGUUGC-UUCCACGGACUCAAGAGC
....(((((..(.((((((.((.((((----.-.........((((((...-(..(((.....)))..)...))))))..)))).)).)).)))-).)..)))))........ ( -26.40)
>DroYak_CAF1 145777 108 + 1
AAAUGUCUGCCGGAGCAUCUGGAAGUC----U-CCCAAUCUCCGGUCCUUAGCUCCGGCUCACUCGAAGGCUGAGCUCCUGACUCCCUGGACGCCUUCCACGGAGUCAAGAAC
....((((((((((((..(((((..(.----.-....)..)))))......))))))))((....)))))).....((.(((((((.((((.....)))).))))))).)).. ( -41.10)
>DroPer_CAF1 204791 102 + 1
AAGUGUCUGG-----AGUCUGGAGGCCGGAGUCCGGAGUCCGCGGUC---UGCCAUGUCCCAGUGCCAGUUCCAGCCACUG---CCGCGGAUACCUCAAGCGGAUUCAAGAGC
.....(((((-----(.(((((...))))).))).((((((((((..---..)).(((((..(((.((((.......))))---.))))))))......)))))))).))).. ( -38.70)
>consensus
AAAUGUCUGCCGGAGCAUCUGGAAGAC____U_CCCAAUCUCCGGUCCCUUACCACGACUCACUCGAAGGCUGAGCUCCUGACUCCCUGGAUACUUUCCACGGAGUCAAGAGC
.....((.(((((((....(((............)))..))))((((.........))))........))).))((((.(((((((.((((.....)))).))))))).)))) (-18.80 = -21.78 +   2.98)

alignment

secondary structure

dotplot

Window 2

Location	13,118,135 – 13,118,243
Length	108
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	76.11
Mean single sequence MFE	-44.47
Consensus MFE	-25.42
Energy contribution	-27.23
Covariance contribution	1.81
Combinations/Pair	1.29
Mean z-score	-2.66
Structure conservation index	0.57
SVM decision value	2.20
SVM RNA-class probability	0.990257
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13118135 108 - 27905053
GCUCUUGACUCCGUGGAAAGUAUCCAGGGAGUCAGAAGCUCAGCCUUCGAGUGAGUCGGAGUAAGGGAACGGAGACUGGG-A----GUCUUCCAGAUGCUCCGGCAGACAUUU
((((.(((((((.((((.....)))).)))))))((((......))))))))..(((((((((.(....)((((((....-.----))))))....)))))))))........ ( -47.70)
>DroSec_CAF1 148512 108 - 1
GCUCUUGACUCCGUGGAAAGUAUCCAGGGAGUCAGGAGCUCAUCCUUCGAGUGAGUCCUGGUGAGGGACCGGAGAUUGAG-A----GUAUUCCAGAUGCUCCGGCAAACAUUU
((((((((((((.((((.....)))).))))))))))))...(((((((...(....)...)))))))(((((((((..(-.----.....)..))).))))))......... ( -48.50)
>DroSim_CAF1 133260 108 - 1
GCUCUUGACUCCGUGGAAAGUAUCCAGGGAGUCAAGAGCUCAGCCUUCGAGUGAGUCCUGGUAAGGGACCGGAGAUUGGG-A----GUCUUCCAGAUGCUCCGGCAGACAUUU
((((((((((((.((((.....)))).))))))))))))...(((.......(.(((((.....))))))((((.(((((-(----...))))))...)))))))........ ( -52.10)
>DroEre_CAF1 138611 106 - 1
GCUCUUGAGUCCGUGGAA-GCAACCAGGGAGUCAGCGGCUCAGCCGUCGAGUGAGUCGGAG-UAAGAACCGGGGAUUGGG-A----GACUUCCAGAUGCUGCGGCAGACAUUU
((((.(((.(((.(((..-....))).))).)))(((((...))))).))))..((((.((-((........(((..((.-.----..)))))...)))).))))........ ( -37.10)
>DroYak_CAF1 145777 108 - 1
GUUCUUGACUCCGUGGAAGGCGUCCAGGGAGUCAGGAGCUCAGCCUUCGAGUGAGCCGGAGCUAAGGACCGGAGAUUGGG-A----GACUUCCAGAUGCUCCGGCAGACAUUU
((((((((((((.((((.....)))).))))))))))))...........((..((((((((...(((.........((.-.----..)))))....))))))))..)).... ( -50.20)
>DroPer_CAF1 204791 102 - 1
GCUCUUGAAUCCGCUUGAGGUAUCCGCGG---CAGUGGCUGGAACUGGCACUGGGACAUGGCA---GACCGCGGACUCCGGACUCCGGCCUCCAGACU-----CCAGACACUU
..(((.((.....((.(((((.(((((((---(((((.(.......).)))))...(......---).)))))))...(((...)))))))).))..)-----).)))..... ( -31.20)
>consensus
GCUCUUGACUCCGUGGAAAGUAUCCAGGGAGUCAGGAGCUCAGCCUUCGAGUGAGUCGGAGUAAGGGACCGGAGAUUGGG_A____GUCUUCCAGAUGCUCCGGCAGACAUUU
((((((((((((.((((.....)))).))))))))..((((.......))))))))............((((((.(((((..........)))))...))))))......... (-25.42 = -27.23 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:37 2006