Locus 1563

Sequence ID	3L_DroMel_CAF1
Location	4,560,985 – 4,561,115
Length	130
Max. P	0.988651

overview

Window 2

Location	4,560,985 – 4,561,076
Length	91
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	80.07
Mean single sequence MFE	-33.80
Consensus MFE	-25.45
Energy contribution	-26.65
Covariance contribution	1.20
Combinations/Pair	1.22
Mean z-score	-2.53
Structure conservation index	0.75
SVM decision value	1.40
SVM RNA-class probability	0.950146
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4560985 91 + 23771897
UACGAUGUGCCACCGCAGGAGGUAAGUUCCGGUGGCAGUUCCGGUUCUGGUUGAUACCGAAAAAAAA--ACU-GUUGCAACCUGCAGUGGCAGC
.......((((((.(((((.((......)).(..((((((....(((.(((....)))))).....)--)))-))..)..))))).)))))).. ( -37.20)
>DroSec_CAF1 137976 89 + 1
UACGAUGUGCCACCGCAGGAGGUAAGUUCCGGUGGCAGUUCCGGUUCCGGUUGAUACCGAAAA--AA--GCA-GUUGCAACCUGCAGUGGCAGC
.......((((((.(((((..(((((..((((........))))..)((((....))))....--..--...-.))))..))))).)))))).. ( -35.30)
>DroSim_CAF1 138205 89 + 1
UACGAUGUGCCACCGCAGGAGGUAAGUUCCGGUGGCAGUUCCGGUUCCGGUUGAUACCGAAAA--AA--GCU-GUUGCAACCUGCAGUGGCAGU
.......((((((.(((((.((......)).(..((((((....((.((((....)))).)).--.)--)))-))..)..))))).)))))).. ( -37.40)
>DroEre_CAF1 146018 89 + 1
UACGACGUGCCACCGCAGGAGGUAAGUUCCGGUAACAGUUCCGGUUCCGGUUGGGACCGAAAA--AA--GCA-GUUGCAACCUGCAGUGGCAGC
.......((((((.(((((.((......)).(((((.(((.(((((((....)))))))....--.)--)).-)))))..))))).)))))).. ( -37.50)
>DroWil_CAF1 121563 85 + 1
UAUGAUGUGCCGCCGCAGGAGGUAAGUUUUUGGAGCAAGGCUACUUGCCGCUUGCAACAAAUU--CA--UAA-AUGACUACUUGUA----CAUC
...(((((((....(((((.((((((((((((...)))))..))))))).))))).......(--((--...-.)))......)))----)))) ( -23.80)
>DroYak_CAF1 142488 92 + 1
UACGACGUACCACCGCAGGAGGUAAGUUCCGGUAACAUUUCCGGUUCCGGUUGGGACCGAAAA--AAUAGCAGGUUGCAACCUGCAGUGGCAGC
.........((((.(((((..((((...((.((....(((.(((((((....))))))).)))--....)).))))))..))))).)))).... ( -31.60)
>consensus
UACGAUGUGCCACCGCAGGAGGUAAGUUCCGGUAGCAGUUCCGGUUCCGGUUGAUACCGAAAA__AA__GCA_GUUGCAACCUGCAGUGGCAGC
.......((((((.(((((..((((...((((........))))...((((....))))...............))))..))))).)))))).. (-25.45 = -26.65 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	4,560,985 – 4,561,076
Length	91
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	80.07
Mean single sequence MFE	-33.27
Consensus MFE	-26.25
Energy contribution	-27.75
Covariance contribution	1.50
Combinations/Pair	1.17
Mean z-score	-3.17
Structure conservation index	0.79
SVM decision value	1.60
SVM RNA-class probability	0.966969
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4560985 91 - 23771897
GCUGCCACUGCAGGUUGCAAC-AGU--UUUUUUUUCGGUAUCAACCAGAACCGGAACUGCCACCGGAACUUACCUCCUGCGGUGGCACAUCGUA
..((((((((((((......(-(((--(((..((..(((....)))..))..))))))).....((......)).))))))))))))....... ( -33.40)
>DroSec_CAF1 137976 89 - 1
GCUGCCACUGCAGGUUGCAAC-UGC--UU--UUUUCGGUAUCAACCGGAACCGGAACUGCCACCGGAACUUACCUCCUGCGGUGGCACAUCGUA
..((((((((((((..((...-.))--..--.(((((((....)))))))((((........)))).........))))))))))))....... ( -36.90)
>DroSim_CAF1 138205 89 - 1
ACUGCCACUGCAGGUUGCAAC-AGC--UU--UUUUCGGUAUCAACCGGAACCGGAACUGCCACCGGAACUUACCUCCUGCGGUGGCACAUCGUA
..((((((((((((..((...-.))--..--.(((((((....)))))))((((........)))).........))))))))))))....... ( -36.60)
>DroEre_CAF1 146018 89 - 1
GCUGCCACUGCAGGUUGCAAC-UGC--UU--UUUUCGGUCCCAACCGGAACCGGAACUGUUACCGGAACUUACCUCCUGCGGUGGCACGUCGUA
((((((((((((((..((...-.))--..--.(((((((..((.(((....)))...))..))))))).......)))))))))))).)).... ( -37.70)
>DroWil_CAF1 121563 85 - 1
GAUG----UACAAGUAGUCAU-UUA--UG--AAUUUGUUGCAAGCGGCAAGUAGCCUUGCUCCAAAAACUUACCUCCUGCGGCGGCACAUCAUA
((((----(.(..(((((((.-...--))--).((((..((((..(((.....)))))))..))))..........))))....).)))))... ( -19.30)
>DroYak_CAF1 142488 92 - 1
GCUGCCACUGCAGGUUGCAACCUGCUAUU--UUUUCGGUCCCAACCGGAACCGGAAAUGUUACCGGAACUUACCUCCUGCGGUGGUACGUCGUA
((((((((((((((..((.....))....--.(((((((..((.(((....)))...))..))))))).......)))))))))))).)).... ( -35.70)
>consensus
GCUGCCACUGCAGGUUGCAAC_UGC__UU__UUUUCGGUACCAACCGGAACCGGAACUGCCACCGGAACUUACCUCCUGCGGUGGCACAUCGUA
..((((((((((((..(...............(((((((....)))))))((((........))))......)..))))))))))))....... (-26.25 = -27.75 +   1.50)

alignment

secondary structure

dotplot

Window 4

Location	4,561,025 – 4,561,115
Length	90
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	93.56
Mean single sequence MFE	-27.22
Consensus MFE	-23.04
Energy contribution	-23.24
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.85
SVM decision value	2.13
SVM RNA-class probability	0.988651
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4561025 90 - 23771897
CAACAACAACAACAUCGAAGAAGGCAGCAUAUGUUUGUGGCUGCCACUGCAGGUUGCAAC-AGU--UUUUUUUUCGGUAUCAACCAGAACCGG
.............((((((((((((((((((....))).))))))..(((.....)))..-...--...)))))))))............... ( -22.30)
>DroSec_CAF1 138016 88 - 1
CAACAACAACAACAUCGAAGACGGCAGCAUAUGUUUGUGGCUGCCACUGCAGGUUGCAAC-UGC--UU--UUUUCGGUAUCAACCGGAACCGG
.............((((((((.(((((((((....))).))))))...((((.......)-)))--..--)))))))).....(((....))) ( -27.90)
>DroSim_CAF1 138245 88 - 1
CAACAACAACAACAUCGAAGAAGGCAGCAUAUGUUUGUGACUGCCACUGCAGGUUGCAAC-AGC--UU--UUUUCGGUAUCAACCGGAACCGG
.............((((((((((((((((((....)))).)))))..(((.....)))..-...--.)--)))))))).....(((....))) ( -25.80)
>DroEre_CAF1 146058 88 - 1
CAACAACAACAACAUCGAAGAAGGCAGCAUAUGUCUGUGGCUGCCACUGCAGGUUGCAAC-UGC--UU--UUUUCGGUCCCAACCGGAACCGG
.............((((((((((((((((((....))))((.(((......))).))..)-)))--))--)))))))).....(((....))) ( -28.00)
>DroYak_CAF1 142528 91 - 1
CAACAACAACAACAUCGAAGAAGGCAGCAUAUGUUUGUGGCUGCCACUGCAGGUUGCAACCUGCUAUU--UUUUCGGUCCCAACCGGAACCGG
.............((((((((((((((((((....))).))))))...((((((....))))))...)--)))))))).....(((....))) ( -32.10)
>consensus
CAACAACAACAACAUCGAAGAAGGCAGCAUAUGUUUGUGGCUGCCACUGCAGGUUGCAAC_UGC__UU__UUUUCGGUAUCAACCGGAACCGG
.............((((((((.(((((((((....)))).)))))..(((.....)))............)))))))).....(((....))) (-23.04 = -23.24 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:43 2006