Locus 2204

Sequence ID	2R_DroMel_CAF1
Location	8,129,454 – 8,129,572
Length	118
Max. P	0.758602

overview

Window 5

Location	8,129,454 – 8,129,552
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.92
Mean single sequence MFE	-15.87
Consensus MFE	-9.31
Energy contribution	-9.03
Covariance contribution	-0.28
Combinations/Pair	1.20
Mean z-score	-1.85
Structure conservation index	0.59
SVM decision value	0.50
SVM RNA-class probability	0.758602
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8129454 98 + 20766785
CUC--------------------UCUUCUU-UA-CUUGCAGUUCCACUGCAUACAGAAAAAUAAACAAAUACAAGAAGCAUAAAAUAUGCAGAAAAUUAAAUACAAAAGGAGCCACUAAG
...--------------------.((((((-(.-..(((((.....)))))..........................(((((...)))))...............)))))))........ ( -15.10)
>DroVir_CAF1 24077 98 + 1
UUC--------------------UCUAUUU-UU-CUUGCAGUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGAAGCAUUUAAG
(((--------------------(.(((((-((-(.(((((.....)))))....))))))))..............(((((...)))))))))..((((((.(.......).)))))). ( -15.80)
>DroGri_CAF1 7191 99 + 1
UUC--------------------UCUUUUU-UUCAUUGCAGUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCGGAAAAUUAAAUACAAAAGGAGCAUUUAAG
..(--------------------(((((((-(((..(((((.....))))).....)))..................(((((...)))))..............))))))))........ ( -16.50)
>DroWil_CAF1 26687 87 + 1
UUU--------------------UCUUAUC--U-CUUGCAGUUCCAUUGCAUACAGAAAUAUAAACAAAUACAAGAAGUAUAAAGUAUGCAGAAAUUUAAAUACCA----------UAAG
...--------------------.......--.-............(((((((((....)........((((.....))))...))))))))..............----------.... (  -9.70)
>DroMoj_CAF1 7171 117 + 1
-UAAUGUAUAUGUAAAUGCAAAUGUUCUUU-UU-AUUGCAGUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGGAGCAUUUAAG
-....((((......))))(((((((((((-((-..(((((.....)))))..........................(((((...)))))..............)))))))))))))... ( -23.60)
>DroPer_CAF1 8195 99 + 1
CAC--------------------UCUUAUUCCA-CCUGCAGUUCCACUGCAUACAGAAAAAUAAACAAACACAAGAAGCAUAAAGUAUGCAGAAAAUUAAACACAAAAGGAGCCAUUAAG
..(--------------------((((.(((..-..(((((.....)))))....)))...................(((((...))))).................)))))........ ( -14.50)
>consensus
UUC____________________UCUUUUU_UU_CUUGCAGUUCCACUGCAUACAGAAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGGAGCAUUUAAG
....................................(((((.....)))))..........................(((((...))))).............................. ( -9.31 =  -9.03 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	8,129,472 – 8,129,572
Length	100
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	85.64
Mean single sequence MFE	-16.04
Consensus MFE	-13.42
Energy contribution	-13.23
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-1.71
Structure conservation index	0.84
SVM decision value	0.23
SVM RNA-class probability	0.642480
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8129472 100 + 20766785
GUUCCACUGCAUACAGAAAAAUAAACAAAUACAAGAAGCAUAAAAUAUGCAGAAAAUUAAAUACAAAAGGAGCCACUAAGUGUUUCGUGUGAAAUCAAU-U------------------
(((((.(((....))).....................(((((...)))))..................)))))(((...(.....)..)))........-.------------------ ( -12.90)
>DroVir_CAF1 24095 105 + 1
GUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGAAGCAUUUAAGUGUUGCGUGUGAGCGAA-AGUAAAAG-------------
......((((((((..............................)))))))).........((((...(.(((((....))))).).)))).((...-.)).....------------- ( -17.01)
>DroPse_CAF1 8113 102 + 1
GUUCCACUGCAUACAGAAAAAUAAACAAACACAAGAAGCAUAAAGUAUGCAGAAAAUUAAACACAAAAGGAGCCAUUAAGUGUUGCGUGUGAAAGAAAU-U-AA---------------
.(((..((((((((..............................)))))))).........((((...(.((((.....).))).).))))...)))..-.-..--------------- ( -16.21)
>DroGri_CAF1 7210 119 + 1
GUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCGGAAAAUUAAAUACAAAAGGAGCAUUUAAGUGUUGCGUGUGAAAGUAAAGCAAAAGCGAAGAGAAAAAG
.((((.((((((((..............................)))))))).........((((...(.(((((....))))).).))))........((....))...).))).... ( -17.21)
>DroMoj_CAF1 7208 106 + 1
GUUCCACUGCAUACCGGAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGGAGCAUUUAAGUGUUGCGUGUGAAAGAAAAGCAAAAA-------------
.(((..((((((((..............................)))))))).........((((...(.(((((....))))).).))))...))).........------------- ( -16.71)
>DroPer_CAF1 8214 102 + 1
GUUCCACUGCAUACAGAAAAAUAAACAAACACAAGAAGCAUAAAGUAUGCAGAAAAUUAAACACAAAAGGAGCCAUUAAGUGUUGCGUGUGAAAGAAAU-U-AA---------------
.(((..((((((((..............................)))))))).........((((...(.((((.....).))).).))))...)))..-.-..--------------- ( -16.21)
>consensus
GUUCCACUGCAUACAGAAAAAUAAACAAAUACAAGAAGCAUAAAGUAUGCAGAAAAUUAAAUACAAAAGGAGCAAUUAAGUGUUGCGUGUGAAAGAAAA_U_AA_______________
......((((((((..............................)))))))).........((((...(.(((........))).).))))............................ (-13.42 = -13.23 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:47 2006