Locus 1090

Sequence ID	X_DroMel_CAF1
Location	3,208,578 – 3,208,704
Length	126
Max. P	0.999572

overview

Window 4

Location	3,208,578 – 3,208,676
Length	98
Sequences	3
Columns	110
Reading direction	reverse
Mean pairwise identity	74.60
Mean single sequence MFE	-28.70
Consensus MFE	-18.90
Energy contribution	-18.90
Covariance contribution	0.00
Combinations/Pair	1.10
Mean z-score	-1.42
Structure conservation index	0.66
SVM decision value	0.29
SVM RNA-class probability	0.669691
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3208578 98 - 22224390
AUUUGAG-------UGAGUGAAGAUAUCACACACCGAUUCGCUUCACUCAAUGAAAUGUUACUGUCUUACUGGACAGCACUUCCGAUUUCGUUGGUUAUGUUUCU-----
.......-------(((((((((..(((.......)))...)))))))))..(((((((..((((((....)))))).(((..((....))..))).))))))).----- ( -27.90)
>DroSec_CAF1 17920 95 - 1
GUUUGAG-------GGAGUGGAGAUAUCACACACCGAUUAGCUCCACUCAAUGGGCUCCUACUGU---GGUGGACAGCACUUCCGAUCUCGCCGGUUAUGUUUCU-----
....(((-------(((((((((..(((.......)))...))))))))(((.(((.((......---))((((.......)))).....))).)))...)))).----- ( -26.70)
>DroEre_CAF1 19875 102 - 1
AUUUGAGCUAGAGUGGAGUGGAGAUAUCAC--AUCGCAUAGCUCCAUUCAAUGGGCUGUUACUGU------GGACAGCACUUCCGAGCUCGCUGGUUGUGUUUCUGUUCU
....(((((.(((((((((.(.(((.....--))).)...))))))))).....((((((.....------.)))))).......))))).................... ( -31.50)
>consensus
AUUUGAG_______GGAGUGGAGAUAUCACACACCGAUUAGCUCCACUCAAUGGGCUGUUACUGU_____UGGACAGCACUUCCGAUCUCGCUGGUUAUGUUUCU_____
...............((((((((..(((.......)))...))))))))......................(((((..(((..((....))..)))..)))))....... (-18.90 = -18.90 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	3,208,603 – 3,208,704
Length	101
Sequences	3
Columns	106
Reading direction	forward
Mean pairwise identity	72.31
Mean single sequence MFE	-28.77
Consensus MFE	-18.37
Energy contribution	-19.16
Covariance contribution	0.78
Combinations/Pair	1.12
Mean z-score	-1.61
Structure conservation index	0.64
SVM decision value	1.17
SVM RNA-class probability	0.925054
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3208603 101 + 22224390
GUGCUGUCCAGUAAGACAGUAACAUUUCAUUGAGUGAAGCGAAUCGGUGUGUGAUAUCUUCACUCACUCAAAUCAA-----AAUGGGCACUAUAUGCUAUCUAUAA
.(((((((......))))))).(((((..((((((((.(((......)))((((.....))))))))))))....)-----))))((((.....))))........ ( -26.20)
>DroSec_CAF1 17945 95 + 1
GUGCUGUCCACC---ACAGUAGGAGCCCAUUGAGUGGAGCUAAUCGGUGUGUGAUAUCUCCACUCCCUCAAACAGA-----AAUGGGCCUGCUGUGACGUC---AG
...(((.(...(---(((((((..(((((((((((((((...((((.....))))..))))))))..((.....))-----)))))))))))))))..).)---)) ( -36.80)
>DroYak_CAF1 22708 95 + 1
GUGCUGUCC------ACAGUAACAGCCCAUUGAAUGGAGCUAUGCGGU--GUGAUAUCUCCACUCCCUCAAAUGAAAUGAGAAUAGGCCUGAUGUGACGUC---AG
.(((((...------.)))))...(((.(((((.(((((.(((.....--...))).))))).)).((((.......))))))).)))((((((...))))---)) ( -23.30)
>consensus
GUGCUGUCCA_____ACAGUAACAGCCCAUUGAGUGGAGCUAAUCGGUGUGUGAUAUCUCCACUCCCUCAAAUAAA_____AAUGGGCCUGAUGUGACGUC___AG
.((((((........))))))...(((((((((((((((...((((.....))))..))))))))................))))))).................. (-18.37 = -19.16 +   0.78)

alignment

secondary structure

dotplot

Window 6

Location	3,208,603 – 3,208,704
Length	101
Sequences	3
Columns	106
Reading direction	reverse
Mean pairwise identity	72.31
Mean single sequence MFE	-31.65
Consensus MFE	-18.54
Energy contribution	-19.43
Covariance contribution	0.90
Combinations/Pair	1.16
Mean z-score	-2.67
Structure conservation index	0.59
SVM decision value	3.74
SVM RNA-class probability	0.999572
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3208603 101 - 22224390
UUAUAGAUAGCAUAUAGUGCCCAUU-----UUGAUUUGAGUGAGUGAAGAUAUCACACACCGAUUCGCUUCACUCAAUGAAAUGUUACUGUCUUACUGGACAGCAC
.........((((...)))).((((-----((...(((((((((((((...............))))).)))))))).))))))...((((((....))))))... ( -26.36)
>DroSec_CAF1 17945 95 - 1
CU---GACGUCACAGCAGGCCCAUU-----UCUGUUUGAGGGAGUGGAGAUAUCACACACCGAUUAGCUCCACUCAAUGGGCUCCUACUGU---GGUGGACAGCAC
((---(.(..(((((..((((((((-----((.....))..((((((((..(((.......)))...))))))))))))))))....))))---)..)..)))... ( -37.80)
>DroYak_CAF1 22708 95 - 1
CU---GACGUCACAUCAGGCCUAUUCUCAUUUCAUUUGAGGGAGUGGAGAUAUCAC--ACCGCAUAGCUCCAUUCAAUGGGCUGUUACUGU------GGACAGCAC
((---(...(((((...((((((((((((.......)))).((((((((.(((...--.....))).)))))))))))))))).....)))------)).)))... ( -30.80)
>consensus
CU___GACGUCACAUCAGGCCCAUU_____UUCAUUUGAGGGAGUGGAGAUAUCACACACCGAUUAGCUCCACUCAAUGGGCUGUUACUGU_____UGGACAGCAC
.................((((((((.....((.....))..((((((((..(((.......)))...))))))))))))))))....((((........))))... (-18.54 = -19.43 +   0.90)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:17 2006