Locus 3164

Sequence ID	3L_DroMel_CAF1
Location	9,200,620 – 9,200,713
Length	93
Max. P	0.993524

overview

Window 7

Location	9,200,620 – 9,200,713
Length	93
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	76.05
Mean single sequence MFE	-34.55
Consensus MFE	-21.62
Energy contribution	-23.62
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.83
Structure conservation index	0.63
SVM decision value	2.40
SVM RNA-class probability	0.993524
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9200620 93 + 23771897
GAAGUGC-----AGUGCACUGCAUGGGCCACGGCCACUUGAGAAGCUGGUGCAGCUGCACUUUUUCAUCGCGAGCCCGCG----UGAAAAAAGA---AAAAU--G---AA
...((((-----((((((((((...(((....))).(....)..)).)))))).))))))(((((((.((((....))))----)))))))...---.....--.---.. ( -36.30)
>DroPse_CAF1 63784 78 + 1
CAAGUGC-----AGU-----GCAUGGCCCGGAGAUGCUGCUGCUGCUAGUGCUGCUGCACUUUUUCAACGAAGG-CAACG--CAGGACCAA-------------------
..(((((-----(((-----((((.........)))).))))).))).((.(((((((.((((......)))))-))..)--))).))...------------------- ( -23.80)
>DroSec_CAF1 54542 87 + 1
GAAGUGC-----AGUGCACUGCAUGGGCCACGGCCACUUGAGAAGCUGGUGCAGCUGCACUUUUUCAUCGCGAGCCCGCG----UGAAAAAAAG---AA-----------
...((((-----((((((((((...(((....))).(....)..)).)))))).))))))(((((((.((((....))))----)))))))...---..----------- ( -36.30)
>DroSim_CAF1 55086 87 + 1
GAAGUGC-----AGUGCACUGCAUGGGCCACGGCCACUUGAGAAGCUGGUGCAGCUGCACUUUUUCAUCGCGAGCCCGCG----UGAAAAAAAG---AA-----------
...((((-----((((((((((...(((....))).(....)..)).)))))).))))))(((((((.((((....))))----)))))))...---..----------- ( -36.30)
>DroEre_CAF1 72185 96 + 1
GAAGUGC-----AGUGCACUGCAUGGGCCACGGCCACUUGAGAAGCUGGUGCAGCUGCACUUUUUCAUCGCGGGGCCGCG----UGAAAAAAAAUGAAAAAU--G---AA
...((((-----((((((((((...(((....))).(....)..)).)))))).))))))(((((((.((((....))))----)))))))...........--.---.. ( -37.70)
>DroYak_CAF1 71149 108 + 1
GAAGUGCAGUGCAGUGCACUGCAUGGGCCACGGCCACUUGAGAUGCUGGUGCAGCUGCACUUUUUCAUCGCAAGUCCGCGUG--UGAAAAAAGAUGAAAAAAGUGAAGAA
.....((.((((((((((((((((.(((....))).(....))))).)))))).))))))(((((((((((......))).)--)))))))...........))...... ( -36.90)
>consensus
GAAGUGC_____AGUGCACUGCAUGGGCCACGGCCACUUGAGAAGCUGGUGCAGCUGCACUUUUUCAUCGCGAGCCCGCG____UGAAAAAAAA___AA___________
.............(((((((((((.(((................))).)))))).)))))(((((((.((((....))))....)))))))................... (-21.62 = -23.62 +   2.00)

alignment

secondary structure

dotplot

Window 8

Location	9,200,620 – 9,200,713
Length	93
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	76.05
Mean single sequence MFE	-32.13
Consensus MFE	-21.08
Energy contribution	-22.45
Covariance contribution	1.37
Combinations/Pair	1.14
Mean z-score	-2.73
Structure conservation index	0.66
SVM decision value	2.32
SVM RNA-class probability	0.992259
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9200620 93 - 23771897
UU---C--AUUUU---UCUUUUUUCA----CGCGGGCUCGCGAUGAAAAAGUGCAGCUGCACCAGCUUCUCAAGUGGCCGUGGCCCAUGCAGUGCACU-----GCACUUC
..---.--.....---...(((((((----((((....)))).)))))))((((((.(((((..(((.....)))(((....)))......)))))))-----))))... ( -33.30)
>DroPse_CAF1 63784 78 - 1
-------------------UUGGUCCUG--CGUUG-CCUUCGUUGAAAAAGUGCAGCAGCACUAGCAGCAGCAGCAUCUCCGGGCCAUGC-----ACU-----GCACUUG
-------------------.((((((.(--.(.((-(....((((....(((((....)))))..))))....))).).).))))))(((-----...-----))).... ( -23.20)
>DroSec_CAF1 54542 87 - 1
-----------UU---CUUUUUUUCA----CGCGGGCUCGCGAUGAAAAAGUGCAGCUGCACCAGCUUCUCAAGUGGCCGUGGCCCAUGCAGUGCACU-----GCACUUC
-----------..---...(((((((----((((....)))).)))))))((((((.(((((..(((.....)))(((....)))......)))))))-----))))... ( -33.30)
>DroSim_CAF1 55086 87 - 1
-----------UU---CUUUUUUUCA----CGCGGGCUCGCGAUGAAAAAGUGCAGCUGCACCAGCUUCUCAAGUGGCCGUGGCCCAUGCAGUGCACU-----GCACUUC
-----------..---...(((((((----((((....)))).)))))))((((((.(((((..(((.....)))(((....)))......)))))))-----))))... ( -33.30)
>DroEre_CAF1 72185 96 - 1
UU---C--AUUUUUCAUUUUUUUUCA----CGCGGCCCCGCGAUGAAAAAGUGCAGCUGCACCAGCUUCUCAAGUGGCCGUGGCCCAUGCAGUGCACU-----GCACUUC
..---.--...........(((((((----((((....)))).)))))))((((((.(((((..(((.....)))(((....)))......)))))))-----))))... ( -35.00)
>DroYak_CAF1 71149 108 - 1
UUCUUCACUUUUUUCAUCUUUUUUCA--CACGCGGACUUGCGAUGAAAAAGUGCAGCUGCACCAGCAUCUCAAGUGGCCGUGGCCCAUGCAGUGCACUGCACUGCACUUC
..........................--..((((((((((.((((.....((((....))))...)))).)))))..))))).....((((((((...)))))))).... ( -34.70)
>consensus
___________UU___UUUUUUUUCA____CGCGGGCUCGCGAUGAAAAAGUGCAGCUGCACCAGCUUCUCAAGUGGCCGUGGCCCAUGCAGUGCACU_____GCACUUC
...................(((((((....((((....)))).)))))))(((((.(((((...((((...))))(((....)))..))))))))))............. (-21.08 = -22.45 +   1.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:10 2006