Locus 1366

Sequence ID	3R_DroMel_CAF1
Location	4,003,521 – 4,003,734
Length	213
Max. P	0.959958

overview

Window 1

Location	4,003,521 – 4,003,626
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.01
Mean single sequence MFE	-23.42
Consensus MFE	-20.55
Energy contribution	-20.80
Covariance contribution	0.25
Combinations/Pair	1.04
Mean z-score	-2.18
Structure conservation index	0.88
SVM decision value	1.51
SVM RNA-class probability	0.959958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4003521 105 + 27905053
AAAC---------------CCAAAAUAUAUAUAAAACCAAAGCCCAAAAGCUGCAACAACAAUGGGCUUGGGCCAGGCUAAGUGCCAAGUGAAAAUGGUUUGGGGCAUCAACUGUCAAAA
...(---------------((((.............((((.(((((................)))))))))(((.(((.....)))..((....))))))))))................ ( -26.19)
>DroSec_CAF1 9122 119 + 1
AAACC-ACAAAAAAAAAAUCCAAAAUAUAUAUAAAACCAAAGCCCGAAAGCUGCAACAACAAUGGGCUUGGGCCAGGCUAAGUGCCAAGUGAAAAUGGUUUGGGGCAUCAACUGUCAAAA
.....-...........................((((((..(((((..((((.((.......)))))))))))..(((.....))).........))))))..((((.....)))).... ( -23.80)
>DroSim_CAF1 9700 116 + 1
AAACC-ACAAA---AAAAUCCAAAAUAUAUAUAAAACCAAAGCCCGAAAGCUGCAACAACAAUGGGCUUGGGCCAGGCUAAGUGCCAAGUGAAAAUGGUUUGGGGCAUCAACUGUCAAAA
.....-.....---...................((((((..(((((..((((.((.......)))))))))))..(((.....))).........))))))..((((.....)))).... ( -23.80)
>DroYak_CAF1 9096 119 + 1
AAACCAACAAA-AAAAUAAACAAAAUAUAUAUAAAACCAAAGACCAAAAGCUGCAACAACAAUGGGCUUGGGCCAGGCUAAGUGGCAAGUGAAAAUGGUUUGGGGCAUCAACUGUCAAAA
...........-........................(((..(((((...(((((....((....((((((...))))))..)).)).))).....))))))))((((.....)))).... ( -19.90)
>consensus
AAACC_ACAAA___AAAAUCCAAAAUAUAUAUAAAACCAAAGCCCAAAAGCUGCAACAACAAUGGGCUUGGGCCAGGCUAAGUGCCAAGUGAAAAUGGUUUGGGGCAUCAACUGUCAAAA
.................................((((((..(((((..((((.((.......)))))))))))..(((.....))).........))))))..((((.....)))).... (-20.55 = -20.80 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	4,003,546 – 4,003,666
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.06
Mean single sequence MFE	-40.45
Consensus MFE	-39.03
Energy contribution	-39.27
Covariance contribution	0.25
Combinations/Pair	1.02
Mean z-score	-1.93
Structure conservation index	0.96
SVM decision value	0.63
SVM RNA-class probability	0.804998
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4003546 120 - 27905053
GUUUUCUGGGCUGCGACGACGACUGUGACUGUGCUGUCACUUUUGACAGUUGAUGCCCCAAACCAUUUUCACUUGGCACUUAGCCUGGCCCAAGCCCAUUGUUGUUGCAGCUUUUGGGCU
((((...(((((((((((((((..((((..(((((((((....))))))(((......)))..)))..))))..(((.....))).(((....)))..)))))))))))))))..)))). ( -42.30)
>DroSec_CAF1 9161 120 - 1
GUUUUCUGGGCUGCGGCGACGACUGUGACUGUGCUGUCACUUUUGACAGUUGAUGCCCCAAACCAUUUUCACUUGGCACUUAGCCUGGCCCAAGCCCAUUGUUGUUGCAGCUUUCGGGCU
((((...(((((((((((((((..((((..(((((((((....))))))(((......)))..)))..))))..(((.....))).(((....)))..)))))))))))))))..)))). ( -41.10)
>DroSim_CAF1 9736 120 - 1
GUUUUCUGGGCUGCGGCGACGACUGUGACUGUGCUGUCACUUUUGACAGUUGAUGCCCCAAACCAUUUUCACUUGGCACUUAGCCUGGCCCAAGCCCAUUGUUGUUGCAGCUUUCGGGCU
((((...(((((((((((((((..((((..(((((((((....))))))(((......)))..)))..))))..(((.....))).(((....)))..)))))))))))))))..)))). ( -41.10)
>DroYak_CAF1 9135 120 - 1
GUUUUCUGGGCUGCGACGACGACUGUGACUGUGCUGUCACUUUUGACAGUUGAUGCCCCAAACCAUUUUCACUUGCCACUUAGCCUGGCCCAAGCCCAUUGUUGUUGCAGCUUUUGGUCU
.......(((((((((((((((..((((..(((((((((....))))))(((......)))..)))..))))..((((.......)))).........)))))))))))))))....... ( -37.30)
>consensus
GUUUUCUGGGCUGCGACGACGACUGUGACUGUGCUGUCACUUUUGACAGUUGAUGCCCCAAACCAUUUUCACUUGGCACUUAGCCUGGCCCAAGCCCAUUGUUGUUGCAGCUUUCGGGCU
((((...(((((((((((((((..((((..(((((((((....))))))(((......)))..)))..))))..(((.....))).(((....)))..)))))))))))))))..)))). (-39.03 = -39.27 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	4,003,626 – 4,003,734
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.96
Mean single sequence MFE	-26.70
Consensus MFE	-21.23
Energy contribution	-21.47
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.79
SVM decision value	0.25
SVM RNA-class probability	0.652048
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4003626 108 + 27905053
GUGACAGCACAGUCACAGUCGUCGUCGCAGCCCAGAAAACUGAAAACUGAGC------------GCCGAACACUGAAAACAGAAAGCAGAGCCAACGGUGGCUCAAAUUGAAAAUUAACU
(((((......)))))..(((.(((..(((..(((....)))....))).))------------).)))...(((....)))......((((((....))))))................ ( -26.20)
>DroSec_CAF1 9241 108 + 1
GUGACAGCACAGUCACAGUCGUCGCCGCAGCCCAGAAAACUGAAAACUGAGC------------GCCGAACACUGAAAACAGAAAGCAGAGCCAACGGUGGCUCAAAUUGAAAAUUAACU
(((((......)))))..(((.(((..(((..(((....)))....))).))------------).)))...(((....)))......((((((....))))))................ ( -27.90)
>DroSim_CAF1 9816 108 + 1
GUGACAGCACAGUCACAGUCGUCGCCGCAGCCCAGAAAACUGAAAACUGAGC------------GCCGAACACUGAAAACAGAAAGCAGAGCCAACGGUGGCUCAAAUUGAAAAUUAACU
(((((......)))))..(((.(((..(((..(((....)))....))).))------------).)))...(((....)))......((((((....))))))................ ( -27.90)
>DroYak_CAF1 9215 120 + 1
GUGACAGCACAGUCACAGUCGUCGUCGCAGCCCAGAAAACUGAAAACUGAACUGAACACUGAAAACAGAAAACUGAAAACAGAAAGCAGCGCCAACGGUGGCUCAAAUUGAAAAUUAACU
(((((......)))))((((..((((((.((.(((....)))................(((....(((....)))....)))...)).)))...)))..))))................. ( -24.80)
>consensus
GUGACAGCACAGUCACAGUCGUCGCCGCAGCCCAGAAAACUGAAAACUGAGC____________GCCGAACACUGAAAACAGAAAGCAGAGCCAACGGUGGCUCAAAUUGAAAAUUAACU
(((((......)))))(((..((...((....(((....)))..............................(((....)))...)).((((((....)))))).....))..))).... (-21.23 = -21.47 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:16 2006