Locus 7502

Sequence ID	2L_DroMel_CAF1
Location	20,803,583 – 20,803,739
Length	156
Max. P	0.777866

overview

Window 7

Location	20,803,583 – 20,803,703
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-37.16
Consensus MFE	-32.64
Energy contribution	-32.52
Covariance contribution	-0.12
Combinations/Pair	1.12
Mean z-score	-1.34
Structure conservation index	0.88
SVM decision value	0.55
SVM RNA-class probability	0.777866
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20803583 120 - 22407834
AAAAAGUACUCGCCCCAGGAGUACAGGGAGAAAAUUCUUAGCCUGUUUCCGCUUCCGCCGAGACCGGCAAAUAUGUGCCACGAUGCGUUCGUGAAGAAACUUCUGGAGCCCUAUGUCCUA
.....((((((.......))))))((((((((..(((((.(((.(((((.((....)).))))).)))..........(((((.....))))))))))..))))....))))........ ( -37.50)
>DroSec_CAF1 26845 120 - 1
AAAAAGUACUCGCCCCAGGAGUACAGGGAGAAAAUUCUUAGCCUGUUUCCGCUUCCGCCGAGACCGGCACAUAUGUGCCACGAUGCGUUCGUGAAGAAACUUCUGGAGCCCUAUGUCCUA
.....((((((.......))))))((((((((..(((((.(((.(((((.((....)).))))).)))..........(((((.....))))))))))..))))....))))........ ( -37.50)
>DroSim_CAF1 30428 120 - 1
AAAAAGUACUCGCCCCAGGAGUACAGGGAGAAAAUUCUUAGCCUGUUUCCGCUUCCGCCGAGACCGGCACAUAUGUGCCACGAUGCGUUCGUGAAGAAACUUCUGGAGCCCUAUGUCCUA
.....((((((.......))))))((((((((..(((((.(((.(((((.((....)).))))).)))..........(((((.....))))))))))..))))....))))........ ( -37.50)
>DroEre_CAF1 30243 120 - 1
AAGAAGUACUCACCACAGGAGUACAGGGAGAAAAUCCUUAGCCUGUUUCCGCUUCCGCCGAAACCGGAAAAUAUGUGCCACGAUGCGUUCGUGAAGGAGCUCCUGGAGCCAUAUGUCCUG
.....((((((.......)))))).(((((....(((((..((.(((((.((....)).))))).))...........(((((.....)))))))))).)))))(((........))).. ( -37.80)
>DroYak_CAF1 27741 120 - 1
AAAAAGUACUCACCUCAGGAGUACAGGGAGAAGAUCCUUAGUCUGUUUCCGCUUCCGCCGAGACCGGCAAAUAUGUGCCACGAUGCGUUCGUGAAGAAACUUCUCGAGCCAUAUGUCCUA
.....((((((.......)))))).((((.(((((.....))))(((((.((....)).))))).((((......))))...(((.(((((.((((...)))).)))))))).).)))). ( -35.50)
>consensus
AAAAAGUACUCGCCCCAGGAGUACAGGGAGAAAAUUCUUAGCCUGUUUCCGCUUCCGCCGAGACCGGCAAAUAUGUGCCACGAUGCGUUCGUGAAGAAACUUCUGGAGCCCUAUGUCCUA
.....((((((.......)))))).(((((....(((((.(((.(((((.((....)).))))).)))..........(((((.....)))))))))).)))))(((........))).. (-32.64 = -32.52 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	20,803,623 – 20,803,739
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.86
Mean single sequence MFE	-44.36
Consensus MFE	-32.36
Energy contribution	-33.16
Covariance contribution	0.80
Combinations/Pair	1.26
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.35
SVM RNA-class probability	0.700094
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20803623 116 + 22407834
UGGCACAUAUUUGCCGGUCUCGGCGGAAGCGGAAACAGGCUAAGAAUUUUCUCCCUGUACUCCUGGGGCGAGUACUUUUUGGGUUCCACCUUGAUACCGUGCAU----GUGGGACCCGCU
.(((...((((((((.......((....))(((.(((((...(((....))).)))))..)))...))))))))......(((((((((..((........)).----)))))))))))) ( -43.00)
>DroSec_CAF1 26885 116 + 1
UGGCACAUAUGUGCCGGUCUCGGCGGAAGCGGAAACAGGCUAAGAAUUUUCUCCCUGUACUCCUGGGGCGAGUACUUUUUGGGUUCCGCCUUGGUACCGUGACU----GUGGGACCCGAC
.(((((....)))))(((((((.(((..((((..(((((...(((....))).)))))....(..(((((.(.(((.....))).))))))..)..))))..))----)))))))).... ( -48.50)
>DroSim_CAF1 30468 116 + 1
UGGCACAUAUGUGCCGGUCUCGGCGGAAGCGGAAACAGGCUAAGAAUUUUCUCCCUGUACUCCUGGGGCGAGUACUUUUUGGGUUCCGCCUUGGUACCGUGACU----GUGGGACCCGAC
.(((((....)))))(((((((.(((..((((..(((((...(((....))).)))))....(..(((((.(.(((.....))).))))))..)..))))..))----)))))))).... ( -48.50)
>DroEre_CAF1 30283 120 + 1
UGGCACAUAUUUUCCGGUUUCGGCGGAAGCGGAAACAGGCUAAGGAUUUUCUCCCUGUACUCCUGUGGUGAGUACUUCUUGGGCUCCACCUUGUGGGAGUUCAUUUCAGGAGUUUCAGGC
.............((.(((((.((....)).))))).))..............((((.(((((((..((((..((((((.(((.....)))...))))))))))..)))))))..)))). ( -44.00)
>DroYak_CAF1 27781 116 + 1
UGGCACAUAUUUGCCGGUCUCGGCGGAAGCGGAAACAGACUAAGGAUCUUCUCCCUGUACUCCUGAGGUGAGUACUUUUUGGGUUCGAUCUUGUGAUUGUGCAU----GGCGCUACCGAG
..(((((...(..(.(((((..((....))(....)))))).((((((....(((.(((((((....).)))))).....)))...)))))))..).))))).(----((.....))).. ( -37.80)
>consensus
UGGCACAUAUUUGCCGGUCUCGGCGGAAGCGGAAACAGGCUAAGAAUUUUCUCCCUGUACUCCUGGGGCGAGUACUUUUUGGGUUCCACCUUGGUACCGUGCAU____GUGGGACCCGAC
.((((......))))(((((((((....))(((.(((((...(((....))).)))))..))).....)))).)))..(((((((((((...(((......)))....))))))))))). (-32.36 = -33.16 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:24 2006