Locus 7126

Sequence ID	3R_DroMel_CAF1
Location	18,770,103 – 18,770,193
Length	90
Max. P	0.880409

overview

Window 7

Location	18,770,103 – 18,770,193
Length	90
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	81.90
Mean single sequence MFE	-29.30
Consensus MFE	-14.63
Energy contribution	-15.71
Covariance contribution	1.08
Combinations/Pair	1.13
Mean z-score	-2.63
Structure conservation index	0.50
SVM decision value	0.91
SVM RNA-class probability	0.880409
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18770103 90 + 27905053
--ACAUAUAUCAAUCGCCGGUGACAGCAUUUUCCAGCGUUUUCCAACUGC--------------------UGUCUGCUCCUCAUUGUCAACCACAAUGUCGCUUGCCA-GCAG
--.............((.((((((((((...................)))--------------------)))).((....((((((.....))))))..))..))).-)).. ( -20.41)
>DroSec_CAF1 28351 97 + 1
--ACAUAUAUCAAUCGCCGGUGACAGCAUUUUCCAGCGUUUUCCAACUGC-------------UGGCUGCUGUCUGCUCCUCAUUGUCAACCACAAUGUCGCUUGCCA-GCAG
--.............((.((((((((((....((((((((....))).))-------------))).))))))).((....((((((.....))))))..))..))).-)).. ( -30.40)
>DroSim_CAF1 29048 97 + 1
--ACAUAUAUCAAUCGCCGGUGACAGCAUUUUCCAGCGUUUUCCCACUGC-------------UGGCUGCUGGCUGCUCCUCAUUGUCAACCACAAUGUCGCUUGCCG-GCAG
--.............(((((..((((((....(((((((......)).))-------------))).)))))...((....((((((.....))))))..)))..)))-)).. ( -32.90)
>DroEre_CAF1 28642 110 + 1
--ACAUAUAUCAAUCGCCGGUGACAGCGUUUUCCAGCGUUUUCCAACGUUUUCCAACGUUUUCCAGCUGCUGGCUGCUCCUCAUUGUCAACCACAAUGUCGACUGCCG-GCAC
--.............((((((....(((....((((((((....((((((....))))))....))).))))).)))((..((((((.....))))))..))..))))-)).. ( -32.40)
>DroYak_CAF1 23606 106 + 1
GUACAUAUAUCAAUCGCCGGUGACAGCGUUUUCCAGCAUUU-CCAGCUGC------UGGCUGCUGGUUGCUGGCUGCUCCUCAUUGACAACCACAAUGUCGCUUUCCAAACAC
...............(((((..((((((....((((((...-.....)))------))).)))).))..))))).((....(((((.......)))))..))........... ( -30.40)
>consensus
__ACAUAUAUCAAUCGCCGGUGACAGCAUUUUCCAGCGUUUUCCAACUGC_____________UGGCUGCUGGCUGCUCCUCAUUGUCAACCACAAUGUCGCUUGCCA_GCAG
...............((.((((((((((....((((((.............................)))))).))))....(((((.....))))))))))).))....... (-14.63 = -15.71 +   1.08)

alignment

secondary structure

dotplot

Window 8

Location	18,770,103 – 18,770,193
Length	90
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-34.37
Consensus MFE	-15.58
Energy contribution	-16.58
Covariance contribution	1.00
Combinations/Pair	1.09
Mean z-score	-2.46
Structure conservation index	0.45
SVM decision value	0.42
SVM RNA-class probability	0.731210
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18770103 90 - 27905053
CUGC-UGGCAAGCGACAUUGUGGUUGACAAUGAGGAGCAGACA--------------------GCAGUUGGAAAACGCUGGAAAAUGCUGUCACCGGCGAUUGAUAUAUGU--
.(((-(((...((..((((((.....))))))....)).((((--------------------(((.(..(......)..)....))))))).))))))............-- ( -28.30)
>DroSec_CAF1 28351 97 - 1
CUGC-UGGCAAGCGACAUUGUGGUUGACAAUGAGGAGCAGACAGCAGCCA-------------GCAGUUGGAAAACGCUGGAAAAUGCUGUCACCGGCGAUUGAUAUAUGU--
.(((-(((...((..((((((.....))))))....)).(((((((.(((-------------((.(((....))))))))....))))))).))))))............-- ( -39.50)
>DroSim_CAF1 29048 97 - 1
CUGC-CGGCAAGCGACAUUGUGGUUGACAAUGAGGAGCAGCCAGCAGCCA-------------GCAGUGGGAAAACGCUGGAAAAUGCUGUCACCGGCGAUUGAUAUAUGU--
.(((-(((...((..((((((.....))))))....)).(.(((((.(((-------------((.((......)))))))....))))).).))))))............-- ( -34.50)
>DroEre_CAF1 28642 110 - 1
GUGC-CGGCAGUCGACAUUGUGGUUGACAAUGAGGAGCAGCCAGCAGCUGGAAAACGUUGGAAAACGUUGGAAAACGCUGGAAAACGCUGUCACCGGCGAUUGAUAUAUGU--
.(((-(((..((((((......))))))..(((.(.((..(((((........((((((....)))))).......))))).....))).)))))))))............-- ( -36.06)
>DroYak_CAF1 23606 106 - 1
GUGUUUGGAAAGCGACAUUGUGGUUGUCAAUGAGGAGCAGCCAGCAACCAGCAGCCA------GCAGCUGG-AAAUGCUGGAAAACGCUGUCACCGGCGAUUGAUAUAUGUAC
.(((..(((.((((...(((((((((((......)).)))))).)))((((((.(((------(...))))-...))))))....)))).)).)..))).............. ( -33.50)
>consensus
CUGC_UGGCAAGCGACAUUGUGGUUGACAAUGAGGAGCAGCCAGCAGCCA_____________GCAGUUGGAAAACGCUGGAAAAUGCUGUCACCGGCGAUUGAUAUAUGU__
.(((.(((.......((((((.....)))))).((((((.(((((...............................)))))....)))).)).)))))).............. (-15.58 = -16.58 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:02 2006