Locus 1090

Sequence ID X_DroMel_CAF1
Location 3,208,578 – 3,208,704
Length 126
Max. P 0.999572
window1764 window1765 window1766

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

Postscript

secondary structure

Postscript

dotplot

Postscript

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

Postscript

secondary structure

Postscript

dotplot

Postscript

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

Postscript

secondary structure

Postscript

dotplot

Postscript


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