Locus 810

Sequence ID	2R_DroMel_CAF1
Location	3,823,460 – 3,823,656
Length	196
Max. P	0.989972

overview

Window 6

Location	3,823,460 – 3,823,554
Length	94
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	96.10
Mean single sequence MFE	-17.68
Consensus MFE	-15.91
Energy contribution	-15.97
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.90
SVM decision value	2.19
SVM RNA-class probability	0.989972
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3823460 94 - 20766785
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..........(((((.(((((((..((((((....)((((((...................))))))..))))).))))))))))))....... ( -18.41)
>DroSec_CAF1 79905 94 - 1
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..........(((((.(((((((..((((((....)((((((...................))))))..))))).))))))))))))....... ( -18.41)
>DroSim_CAF1 96977 94 - 1
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..........(((((.(((((((..((((((....)((((((...................))))))..))))).))))))))))))....... ( -18.41)
>DroEre_CAF1 80675 94 - 1
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGGGAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..........(((((.(((((((..(((((.((((.((..((((.....))))......)).))))...))))).))))))))))))....... ( -19.70)
>DroYak_CAF1 77243 94 - 1
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..........(((((.(((((((..((((((....)((((((...................))))))..))))).))))))))))))....... ( -18.41)
>DroAna_CAF1 77905 93 - 1
UUACCUUCUGCUUUUUGUUCAAUUUGG-CAGGAAAAUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
..((((((((((..((....))...))-)))))(((((((((...................))))))))))))..................... ( -12.71)
>consensus
UUGCCCUCCAGUUUUUGUGCAAUUUAGCCAGGAAACUGAAAAAGCAAAACUUUAAUCAACAUUUUCAUUUGGUUUAUUGCAUAAAACAUUUCUC
............(((((((((((..(((((.((((.(((.((((.....))))..)))....))))...))))).)))))))))))........ (-15.91 = -15.97 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	3,823,554 – 3,823,656
Length	102
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	77.35
Mean single sequence MFE	-26.22
Consensus MFE	-10.70
Energy contribution	-10.62
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-2.34
Structure conservation index	0.41
SVM decision value	1.40
SVM RNA-class probability	0.950776
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3823554 102 + 20766785
UCGG-AGGGGAGAGCACGUG----UGUAUGGAGUGUGUGUUCUUAACAUAACACAUAAACACAAGUACAUACACA----A-----CUCUGGAGUACUUUUUAAAGGAAAACGAACU
((((-((..(.(....)(((----(((((.(..((((((((........))))))))..)....)))))))).).----.-----))))))(((.((((((....))))).).))) ( -23.40)
>DroSec_CAF1 79999 107 + 1
UCGAAAGGGGAAAGCACGUGUGUGUGUAUGGAGUGUGUGUUCUUAACAUAACACAUAAACACAAGUACAUACACA----A-----CUCUAGAGUAUUUUUUAAAGGAAAACGUACU
((....))....((.((((((((((((((.(..((((((((........))))))))..)....)))))))))).----.-----((.(((((....))))).))....)))).)) ( -27.60)
>DroSim_CAF1 97071 107 + 1
UCGAAAGGGGAAGGCACGUGUGUGUGUAUGGAGUGUGUGUUCUUAACAUAACACAUAAACACAAGUACAUACACA----U-----CUCUAGAGUAUUUUUUAGAGGAAAACGUACU
((....))....((.((((((((((((((.(..((((((((........))))))))..)....)))))))))).----(-----((((((((....)))))))))...)))).)) ( -34.10)
>DroEre_CAF1 80769 99 + 1
UCUG-AGGGGAAUC-ACGUG----UGUAUAGAGUGUGUGUUCUUAACAUAACACAUAAACAUAAGUACCUAUACAUACAACUCUUCUCUAGUUUAUUUUUUAAGG-----------
...(-((((((...-..(((----(((((((..((((((((........)))))))).((....))..))))))))))...))))))).................----------- ( -25.10)
>DroYak_CAF1 77337 96 + 1
UCUG-AGGGGAAUCGACGUG----UGUGUAGAGUGCGUGUUCUUAACAUAACAUAUAAACAUAAGUACAUACACA----UCUCGUCUCUAGUUUAUUUUUUAAAG-----------
....-.(((((..(((.(((----(((((...(((((((((..((........))..)))))..)))))))))))----).))))))))................----------- ( -20.90)
>consensus
UCGG_AGGGGAAAGCACGUG____UGUAUGGAGUGUGUGUUCUUAACAUAACACAUAAACACAAGUACAUACACA____A_____CUCUAGAGUAUUUUUUAAAGGAAAACG_ACU
.....(((((......)(((....(((((.(..((((((((........))))))))..)....)))))..)))...........))))........................... (-10.70 = -10.62 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:57 2006