Locus 4561

Sequence ID	3R_DroMel_CAF1
Location	12,065,477 – 12,065,716
Length	239
Max. P	0.999961

overview

Window 6

Location	12,065,477 – 12,065,597
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-37.10
Consensus MFE	-34.60
Energy contribution	-34.60
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-1.23
Structure conservation index	0.93
SVM decision value	0.33
SVM RNA-class probability	0.689764
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12065477 120 - 27905053
GCGACUGUGACGUUGAUGGUGCUGUUACAAUGCCGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUCGCCAACUGGUUUUAUUUUUAUUC
(((((.....(((..(((((((((((((......).))))))))))))..)))...(.(((((......))))).).)))))..((((((.......))))))................. ( -37.00)
>DroSec_CAF1 2066 120 - 1
GCGACAGUGACGUUGAUGGUGCUGUUACAAUGCCGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUCGCCAACUGGUUUUAUUUUUAUUC
((((((....(((..(((((((((((((......).))))))))))))..)))...(.(((((......))))).)))))))..((((((.......))))))................. ( -38.50)
>DroSim_CAF1 2535 120 - 1
GCGACAGUGACGUUGAUGGUGCUGUUACAAUGCCGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUCGCCAACUGGUUUUAUUUUUAUUC
((((((....(((..(((((((((((((......).))))))))))))..)))...(.(((((......))))).)))))))..((((((.......))))))................. ( -38.50)
>DroEre_CAF1 4043 120 - 1
GUGACUGUGACGUUGAUGUUGCUGUUACAAUGCUGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUAGCCAACUGGUUUUGUUUUUAUUC
(((((.(..(((....)))..).)))))...(((((..((((.((((...(((((.(.(((((......))))).).)))))....)))))))))))))..................... ( -35.30)
>DroYak_CAF1 4079 120 - 1
GUGACUGUGACGUUGAUGCCGCUGUUACAAUGCCGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUCGCCAACUGGUUUUAUUUUUAUUC
(((((.(((.((....)).))).)))))...((((.(((((((((.((..(((...((...((((((......))))))..)))))..))..)))))))))..))))............. ( -36.20)
>consensus
GCGACUGUGACGUUGAUGGUGCUGUUACAAUGCCGCUGGCGGCGCUGUUGGCGAUUUGAAUAUGUUAUGAUGUUGAUGUUGCAUGUUGGCCCGCGUCGCCAACUGGUUUUAUUUUUAUUC
(((((.....(((..(((((((((((((......).))))))))))))..)))...(.(((((......))))).).)))))..((((((.......))))))................. (-34.60 = -34.60 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	12,065,517 – 12,065,637
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.08
Mean single sequence MFE	-28.46
Consensus MFE	-24.62
Energy contribution	-26.06
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-1.30
Structure conservation index	0.87
SVM decision value	0.23
SVM RNA-class probability	0.642125
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12065517 120 + 27905053
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCGGCAUUGUAACAGCACCAUCAACGUCACAGUCGCCGUCGGCAGCGCAGCAUUCGAAUCCGGAGCUUUUACUCUC
...................................((((.(((.((((((((((.((............)).))))).))))).))).))))(((.((((....)))))))......... ( -32.60)
>DroSec_CAF1 2106 120 + 1
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCGGCAUUGUAACAGCACCAUCAACGUCACUGUCGCCGUCGGCAGCGCAGCAUUCGAAUCCGGAGCUUUUACUCUC
...................................((((.(((.(((((((.((.((............)).)).)).))))).))).))))(((.((((....)))))))......... ( -28.80)
>DroSim_CAF1 2575 120 + 1
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCGGCAUUGUAACAGCACCAUCAACGUCACUGUCGCCGUCGGCAGGGCAGCAUUCGAAUCCGGAGCUUUUACUCUC
............................(((.((((.((((....)))).))))...................((((((....)))))))))(((.((((....)))))))......... ( -28.10)
>DroEre_CAF1 4083 120 + 1
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCAGCAUUGUAACAGCAACAUCAACGUCACAGUCACCGUCGGCAGCGCAGCAUUCGGAACCGGAGCUUUUACUCUC
...................................((((.(((.((.(.(((((.((............)).)))))..).)).))).))))(((.((((....)))))))......... ( -23.20)
>DroYak_CAF1 4119 119 + 1
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCGGCAUUGUAACAGCGGCAUCAACGUCACAGUCACCGUCGGCAGCGCAGCAUUG-GGACCGGGGCUUUUACUCUC
............................(((....((((.(((.((((.(((((....(((.......))).)))))..)))).))).))))....(((-....)))))).......... ( -29.60)
>consensus
AACAUCAACAUCAUAACAUAUUCAAAUCGCCAACAGCGCCGCCAGCGGCAUUGUAACAGCACCAUCAACGUCACAGUCGCCGUCGGCAGCGCAGCAUUCGAAUCCGGAGCUUUUACUCUC
...................................((((.(((.((((((((((.((............)).))))).))))).))).))))(((.((((....)))))))......... (-24.62 = -26.06 +   1.44)

alignment

secondary structure

dotplot

Window 8

Location	12,065,597 – 12,065,716
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.82
Mean single sequence MFE	-41.54
Consensus MFE	-40.34
Energy contribution	-40.54
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.97
SVM decision value	4.91
SVM RNA-class probability	0.999961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12065597 119 - 27905053
GUUUAAUUCGUG-ACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCUCCGGAUUCGAAUGCUGCGCUGCCGACG
(((....(((..-...)))((((((((((((....((((......(((....((((((........)))))).....)))(.((((....))))).))))....))))))))))))))). ( -42.30)
>DroSec_CAF1 2186 119 - 1
GUUUAAUUCGUG-ACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCUCCGGAUUCGAAUGCUGCGCUGCCGACG
(((....(((..-...)))((((((((((((....((((......(((....((((((........)))))).....)))(.((((....))))).))))....))))))))))))))). ( -42.30)
>DroSim_CAF1 2655 119 - 1
GUUUAAUUCGUG-ACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCUCCGGAUUCGAAUGCUGCCCUGCCGACG
(((....(((..-...)))(((((.((((((....((((......(((....((((((........)))))).....)))(.((((....))))).))))....)))))).)))))))). ( -37.90)
>DroEre_CAF1 4163 120 - 1
GUUUAAUUCGUGGACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCUCCGGUUCCGAAUGCUGCGCUGCCGACG
(((....((((....))))((((((((((((....((((......(((....((((((........)))))).....)))(.((((....))))))))).....))))))))))))))). ( -42.90)
>DroYak_CAF1 4199 119 - 1
GUUAUACUCGUGGACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCCCCGGUCC-CAAUGCUGCGCUGCCGACG
(((....((((....))))((((((((((((................(((..((((((........)))))).....(....).......)))..(....-)..))))))))))))))). ( -42.30)
>consensus
GUUUAAUUCGUG_ACGCGAGGCAGUGCAGCAAAUAAAUCACAACAACGGCACGGCGGUGAUAAAAAAUCGCUUUUCACGUGAGAGUAAAAGCUCCGGAUUCGAAUGCUGCGCUGCCGACG
(((....((((....))))((((((((((((.....(((((..(........)...)))))........(((((((.(....).).))))))............))))))))))))))). (-40.34 = -40.54 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:31 2006