Locus 810

Sequence ID 2R_DroMel_CAF1
Location 3,823,460 – 3,823,656
Length 196
Max. P 0.989972
window1416 window1417

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

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secondary structure

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dotplot

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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

Postscript

secondary structure

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dotplot

Postscript


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