Locus 1533

Sequence ID	2R_DroMel_CAF1
Location	5,793,633 – 5,793,728
Length	95
Max. P	0.969450

overview

Window 6

Location	5,793,633 – 5,793,728
Length	95
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.88
Mean single sequence MFE	-31.52
Consensus MFE	-23.46
Energy contribution	-24.68
Covariance contribution	1.22
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.74
SVM decision value	1.64
SVM RNA-class probability	0.969450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5793633 95 + 20766785
---------AGCU-------------UCCUUGCAGCUGAAGCGGCAGGAGUCGAACGACUCCCACUGCUCUGACAGCACCACCCACAGCCAAUGCACGGCCAUCAACCUGGCCAGUC
---------.((.-------------.....)).((((.(((((..((((((....))))))..)))))....))))..........((....))..(((((......))))).... ( -33.70)
>DroVir_CAF1 124054 108 + 1
---------AGCAUCCAAUCCUUAACCCCUUGUUGCUCAAUCGACAAGAGUCGAACGAUUCGCACUGCUCGGACAGCACACAGCACAGCCAAUGCACUGCCAUACAUCUGGCCUCGC
---------.((((....(((.......(((((((......)))))))((((((.....))).)))....)))..((.....)).......))))...((((......))))..... ( -21.90)
>DroSim_CAF1 85251 95 + 1
---------AGCU-------------UCCUUGCAGCUGAAGCGGCAGGAGUCUAACGACUCCCACUGCUCCGACAGCACCACCCACAGCCAAUGCACGGCCAUCAACCUGGCCAGUC
---------.((.-------------.....)).((((.(((((..((((((....))))))..)))))....))))..........((....))..(((((......))))).... ( -35.10)
>DroEre_CAF1 87125 95 + 1
---------AGCU-------------UCCUUGCAGCUGAAGCGGCAGGAGUCGAACGACUCCCACUGCUCCGACAGCACCACCCACAGCCAAUGCACGGCCAUCAACCUGGCCAGUC
---------.((.-------------.....)).((((.(((((..((((((....))))))..)))))....))))..........((....))..(((((......))))).... ( -33.70)
>DroYak_CAF1 85540 95 + 1
---------AGCU-------------UCCUUGCAGCUGAAGCGGCAGGAGUCGAACGACUCCCACUGCUCCGACAGCACCACCCACAGCCAAUGCACGGCCAUCAACCUGGCCAGUC
---------.((.-------------.....)).((((.(((((..((((((....))))))..)))))....))))..........((....))..(((((......))))).... ( -33.70)
>DroMoj_CAF1 125470 117 + 1
AAUUUGAUUUGCAUGCCAAAGUGAAUCCCUUGUUGCUCUCGCGGCAAGAGUCGAACGAUUCGCACUGCUCGGACAGCACACAGCACAGCCAAUGCACCGCCAUUAACAUGGCCUCAC
....(((..(((((......(((((((.((((((((....)))))))).(.....)))))))).......((...((.....))....)).)))))..(((((....))))).))). ( -31.00)
>consensus
_________AGCU_____________UCCUUGCAGCUGAAGCGGCAGGAGUCGAACGACUCCCACUGCUCCGACAGCACCACCCACAGCCAAUGCACGGCCAUCAACCUGGCCAGUC
..............................((((((....))(((.((((((....))))))...((((.....)))).........)))..)))).(((((......))))).... (-23.46 = -24.68 +   1.22)

alignment

secondary structure

dotplot

Window 7

Location	5,793,633 – 5,793,728
Length	95
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.88
Mean single sequence MFE	-41.33
Consensus MFE	-28.16
Energy contribution	-29.13
Covariance contribution	0.97
Combinations/Pair	1.11
Mean z-score	-1.86
Structure conservation index	0.68
SVM decision value	1.19
SVM RNA-class probability	0.928558
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5793633 95 - 20766785
GACUGGCCAGGUUGAUGGCCGUGCAUUGGCUGUGGGUGGUGCUGUCAGAGCAGUGGGAGUCGUUCGACUCCUGCCGCUUCAGCUGCAAGGA-------------AGCU---------
....(((((......))))).((((...((((.((((((((((((....)))))(((((((....))))))))))))))))))))))....-------------....--------- ( -42.80)
>DroVir_CAF1 124054 108 - 1
GCGAGGCCAGAUGUAUGGCAGUGCAUUGGCUGUGCUGUGUGCUGUCCGAGCAGUGCGAAUCGUUCGACUCUUGUCGAUUGAGCAACAAGGGGUUAAGGAUUGGAUGCU---------
(((.((((((.(((((....))))))))))).))).((((.(.((((((((.((....)).))))..(((((((.(......).))))))).....)))).).)))).--------- ( -35.80)
>DroSim_CAF1 85251 95 - 1
GACUGGCCAGGUUGAUGGCCGUGCAUUGGCUGUGGGUGGUGCUGUCGGAGCAGUGGGAGUCGUUAGACUCCUGCCGCUUCAGCUGCAAGGA-------------AGCU---------
(((.(((((......)))))..((((((.(....).)))))).)))(((((.(..((((((....))))))..).)))))((((.......-------------))))--------- ( -44.10)
>DroEre_CAF1 87125 95 - 1
GACUGGCCAGGUUGAUGGCCGUGCAUUGGCUGUGGGUGGUGCUGUCGGAGCAGUGGGAGUCGUUCGACUCCUGCCGCUUCAGCUGCAAGGA-------------AGCU---------
(((.(((((......)))))..((((((.(....).)))))).)))(((((.(..((((((....))))))..).)))))((((.......-------------))))--------- ( -43.90)
>DroYak_CAF1 85540 95 - 1
GACUGGCCAGGUUGAUGGCCGUGCAUUGGCUGUGGGUGGUGCUGUCGGAGCAGUGGGAGUCGUUCGACUCCUGCCGCUUCAGCUGCAAGGA-------------AGCU---------
(((.(((((......)))))..((((((.(....).)))))).)))(((((.(..((((((....))))))..).)))))((((.......-------------))))--------- ( -43.90)
>DroMoj_CAF1 125470 117 - 1
GUGAGGCCAUGUUAAUGGCGGUGCAUUGGCUGUGCUGUGUGCUGUCCGAGCAGUGCGAAUCGUUCGACUCUUGCCGCGAGAGCAACAAGGGAUUCACUUUGGCAUGCAAAUCAAAUU
.(((.((.(((((((.(((((..(((.(((...))))))..)))))(((((.((....)).))))).((((((..((....))..)))))).......)))))))))...))).... ( -37.50)
>consensus
GACUGGCCAGGUUGAUGGCCGUGCAUUGGCUGUGGGUGGUGCUGUCGGAGCAGUGGGAGUCGUUCGACUCCUGCCGCUUCAGCUGCAAGGA_____________AGCU_________
....(((((......)))))((((...(((.((.......)).)))(((((.(((((((((....))))))))).))))).)).))............................... (-28.16 = -29.13 +   0.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:00 2006