Locus 2159

Sequence ID	2R_DroMel_CAF1
Location	8,043,936 – 8,044,068
Length	132
Max. P	0.886516

overview

Window 9

Location	8,043,936 – 8,044,028
Length	92
Sequences	4
Columns	96
Reading direction	forward
Mean pairwise identity	90.28
Mean single sequence MFE	-20.79
Consensus MFE	-15.86
Energy contribution	-15.80
Covariance contribution	-0.06
Combinations/Pair	1.19
Mean z-score	-1.90
Structure conservation index	0.76
SVM decision value	0.46
SVM RNA-class probability	0.744353
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8043936 92 + 20766785
GGCCUGCCAGUCC--AAAAAAAAAUGCCUCCC--CCUUCUUUUUCACCCCGUCGUUUAUUUUUACGACGCUUUCGCUUAAGCGCUGGCAUUUAAUG
....(((((((..--.................--................(((((........)))))((((......)))))))))))....... ( -21.20)
>DroSec_CAF1 8845 94 + 1
GGCCUGCCAGUCCCAAAAAAAAAAUGCCUCCC--CCUUCUUUUUCACCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCGUUGGCAUUUAAUG
((....)).............(((((((....--................(((((........)))))((((......))))...))))))).... ( -20.80)
>DroEre_CAF1 7291 92 + 1
GGCCUGGCAGUCCCAA--AAAA--GGCCUCCCCUCCUUCUUUUUCAGCCCGUCGUUUAUUUUUACGAUGCUUUCGUUUAAGCGCUGGCAUUUAAUG
(((((...........--...)--))))..................(((.(.((((((.....((((.....)))).))))))).)))........ ( -21.84)
>DroYak_CAF1 7100 89 + 1
GGCCUGGCAGUCCCAA--AAAA--G-CCUCCC--CCUUCUUUUUCAGCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCACUGGCAUUUAAUG
((...(((........--....--)-))...)--)...........(((.(((((........)))))((((......))))...)))........ ( -19.30)
>consensus
GGCCUGCCAGUCCCAA__AAAA__GGCCUCCC__CCUUCUUUUUCACCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCGCUGGCAUUUAAUG
....(((((((.......................................(((((........)))))((((......)))))))))))....... (-15.86 = -15.80 +  -0.06)

alignment

secondary structure

dotplot

Window 0

Location	8,043,950 – 8,044,068
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.44
Mean single sequence MFE	-22.00
Consensus MFE	-14.70
Energy contribution	-14.94
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-2.21
Structure conservation index	0.67
SVM decision value	0.94
SVM RNA-class probability	0.886516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8043950 118 + 20766785
AAAAAAAAUGCCUCCC--CCUUCUUUUUCACCCCGUCGUUUAUUUUUACGACGCUUUCGCUUAAGCGCUGGCAUUUAAUGUGAAAUUUAUCAUUUCAACGCCACGCCCCCCACCCCACGC
.....(((((((....--................(((((........)))))((((......))))...)))))))....((((((.....))))))....................... ( -21.40)
>DroSec_CAF1 8861 118 + 1
AAAAAAAAUGCCUCCC--CCUUCUUUUUCACCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCGUUGGCAUUUAAUGUGAAAUUUAUCAUUUCAACGCCAUGCCCCCCGCCCCCCGC
.....(((((((....--................(((((........)))))((((......))))...)))))))....((((((.....))))))....................... ( -21.40)
>DroEre_CAF1 7307 109 + 1
--AAAA--GGCCUCCCCUCCUUCUUUUUCAGCCCGUCGUUUAUUUUUACGAUGCUUUCGUUUAAGCGCUGGCAUUUAAUGUGAAAUUUAUCAUUUCCACGC-----C--ACGCCCCCCGC
--....--(((...................(((.(.((((((.....((((.....)))).))))))).))).......(((((((.....)))).)))))-----)--........... ( -21.10)
>DroYak_CAF1 7116 111 + 1
--AAAA--G-CCUCCC--CCUUCUUUUUCAGCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCACUGGCAUUUAAUGUGAAAUUUAUCAUUUCCACGCCACGCC--ACGCCCCCCGC
--....--(-(.....--............(((.(((((........)))))((((......))))...))).......(((((((.....)))).)))))......--........... ( -17.90)
>DroAna_CAF1 10103 106 + 1
----------CCUCACAUCAUUGAUUGCCGGGCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCACUGGCAUUUAAUGUGAAAUUUAUCAUUUCGCUGCCACGCCCC-CACCCCU---
----------.........(((((.((((((...(((((........)))))((((......)))).)))))).)))))(((((((.....)))))))...........-.......--- ( -28.20)
>consensus
__AAAA__GGCCUCCC__CCUUCUUUUUCAGCCCGUCGUUUAUUUUUACGACGCUUUCGUUUAAGCGCUGGCAUUUAAUGUGAAAUUUAUCAUUUCAACGCCACGCCCCACGCCCCCCGC
..................................(((((........)))))((((......))))..((((.......((((......))))......))))................. (-14.70 = -14.94 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	8,043,950 – 8,044,068
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.44
Mean single sequence MFE	-29.82
Consensus MFE	-19.34
Energy contribution	-20.14
Covariance contribution	0.80
Combinations/Pair	1.13
Mean z-score	-1.94
Structure conservation index	0.65
SVM decision value	0.41
SVM RNA-class probability	0.726411
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8043950 118 - 20766785
GCGUGGGGUGGGGGGCGUGGCGUUGAAAUGAUAAAUUUCACAUUAAAUGCCAGCGCUUAAGCGAAAGCGUCGUAAAAAUAAACGACGGGGUGAAAAAGAAGG--GGGAGGCAUUUUUUUU
((((.(.((.....)).).))))((((((.....))))))....(((((((..(.(((..((....))(((((........))))).............)))--.)..)))))))..... ( -30.80)
>DroSec_CAF1 8861 118 - 1
GCGGGGGGCGGGGGGCAUGGCGUUGAAAUGAUAAAUUUCACAUUAAAUGCCAACGCUUAAACGAAAGCGUCGUAAAAAUAAACGACGGGGUGAAAAAGAAGG--GGGAGGCAUUUUUUUU
.((..(((((...(((((.....((((((.....))))))......)))))..)))))...))....((((((........)))))).....((((((((.(--......).)))))))) ( -30.10)
>DroEre_CAF1 7307 109 - 1
GCGGGGGGCGU--G-----GCGUGGAAAUGAUAAAUUUCACAUUAAAUGCCAGCGCUUAAACGAAAGCAUCGUAAAAAUAAACGACGGGCUGAAAAAGAAGGAGGGGAGGCC--UUUU--
.((..((((((--(-----((((.(((((.....))))).......)))))).)))))...))..(((.((((........))))...))).....((((((........))--))))-- ( -27.90)
>DroYak_CAF1 7116 111 - 1
GCGGGGGGCGU--GGCGUGGCGUGGAAAUGAUAAAUUUCACAUUAAAUGCCAGUGCUUAAACGAAAGCGUCGUAAAAAUAAACGACGGGCUGAAAAAGAAGG--GGGAGG-C--UUUU--
.((..((((((--(((((...((((((((.....))))).)))...)))))).)))))...))((((((((((........)))))...((........)).--.....)-)--))).-- ( -31.20)
>DroAna_CAF1 10103 106 - 1
---AGGGGUG-GGGGCGUGGCAGCGAAAUGAUAAAUUUCACAUUAAAUGCCAGUGCUUAAACGAAAGCGUCGUAAAAAUAAACGACGGCCCGGCAAUCAAUGAUGUGAGG----------
---.(((((.-.((((((((((......(((......))).......))))).)))))..)).....((((((........)))))).)))...................---------- ( -29.12)
>consensus
GCGGGGGGCGGGGGGCGUGGCGUGGAAAUGAUAAAUUUCACAUUAAAUGCCAGCGCUUAAACGAAAGCGUCGUAAAAAUAAACGACGGGCUGAAAAAGAAGG__GGGAGGCA__UUUU__
.((..(((((...(((((......(((((.....))))).......)))))..)))))...))....((((((........))))))................................. (-19.34 = -20.14 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:46 2006