Locus 5702

Sequence ID	3R_DroMel_CAF1
Location	14,929,430 – 14,929,587
Length	157
Max. P	0.995861

overview

Window 7

Location	14,929,430 – 14,929,547
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.73
Mean single sequence MFE	-30.61
Consensus MFE	-26.08
Energy contribution	-25.80
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-1.99
Structure conservation index	0.85
SVM decision value	1.91
SVM RNA-class probability	0.982271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14929430 117 - 27905053
CGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAGU---CCAUCACCAUCACUCUCUCCUCGCGCGGCUCUCUUU
.((((.....))))(((.......(((.....((.....))...)))((((......((((....))))..((((......---.)))).................)))))))....... ( -29.80)
>DroSec_CAF1 59410 120 - 1
CGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAGCGAUGUCCAGUUCACCAUCACCAUCACUCUCUCCUCGCGCGGCUCUCUUU
.((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))....(((.((((.(...(((..............)))....).))))..)))....... ( -33.34)
>DroSim_CAF1 58109 120 - 1
CGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAGUUCACCAUCACCAUCACUCUCUCCUCGCGCGGCUCUCUUU
.((((.....))))(((.......(((.....((.....))...)))((((......((((....))))..((((..........)))).................)))))))....... ( -29.20)
>DroEre_CAF1 55968 111 - 1
CGGCAACAAUUGUUGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAGUG---------CAUCACUCUCUCCUCGGUCGGCUGUCUUU
.((((.........((((((.((((((((((.((.....))..))))).))))).))))))....((((((((.(...((((---------...))))....).))))).)))))))... ( -32.50)
>DroYak_CAF1 62769 111 - 1
CGGCUACAAUUGUUGCCAAUCGAAGCUGUUUUUCGAAUUGAUUAAGCGUGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAGUG---------CAUCACUCUCUCCUCGGUCGGCUCUCUUU
..............((((((.((((((((((.((.....))..))))).))))).))))))....((((((((.(...((((---------...))))....).))))).)))....... ( -28.20)
>consensus
CGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAGUG__CCAUCACCAUCACUCUCUCCUCGCGCGGCUCUCUUU
.((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))....(((..(((.(...(((..............)))....).)))...)))....... (-26.08 = -25.80 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	14,929,467 – 14,929,587
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-34.82
Consensus MFE	-29.72
Energy contribution	-30.00
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-1.78
Structure conservation index	0.85
SVM decision value	1.43
SVM RNA-class probability	0.952911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14929467 120 + 27905053
CUGGACAUCGAUGGCAAACGCCAAUAAAAGCGCGCUUAAUCAAUAAGAAAAACAGCUUCGAUUGGCGGCAAUUGUUGCCGCUCCAGAUCGCCAGAUCGACGAUUUAUGGUCCAUUGCAGA
.(((((((((..(((....((((((..((((...((((.....)))).......))))..))))))((((.....)))))))...((((....))))..)))).....)))))....... ( -35.80)
>DroSec_CAF1 59450 120 + 1
CUGGACAUCGCUGGCAAACGCCAAUAAAAGCGCGCUUAAUCAAUAAGAAAAACAGCUUCGAUUGGCGGCAAUUGUUGCCGCUCCAGAUCGCCAGAUCGACGAUUUAUGGUCCAUUGCAGA
.(((((...((.(((((.(((((((..((((...((((.....)))).......))))..))))))).......)))))))....((((....))))...........)))))....... ( -36.10)
>DroSim_CAF1 58149 120 + 1
CUGGACAUCGAUGGCAAACGCCAAUAAAAGCGCGCUUAAUCAAUAAGAAAAACAGCUUCGAUUGGCGGCAAUUGUUGCCGCUCCAGAUCGCCAGAUCGACGAUUUAUGGUCCAUUGCAGA
.(((((((((..(((....((((((..((((...((((.....)))).......))))..))))))((((.....)))))))...((((....))))..)))).....)))))....... ( -35.80)
>DroEre_CAF1 55999 119 + 1
CUGGACAUCGAUGGCAAACGCCAAUAAAAGCGCGCUUAAUCAAUAAGAAAAACAGCUUCGAUUGGCAACAAUUGUUGCCGCUCCAGAUCGC-AGAUCGACGAUUUAUGGUCCGUGGUAGA
(((((((((((((((....)))).....(((...((((.....)))).......)))))))).((((((....))))))).)))))(((((-.(((((........))))).)))))... ( -35.80)
>DroYak_CAF1 62800 119 + 1
CUGGACAUCGAUGGCAAACGCCAAUAAAAGCACGCUUAAUCAAUUCGAAAAACAGCUUCGAUUGGCAACAAUUGUAGCCGCUCCAGAUCGC-AGAUCGACGAUUUAUGGUGCAUGGUAGU
.......((((((((....))))....(((....))).......))))......(((.((((((....)))))).))).((.((((((((.-.......)))))..))).))........ ( -30.60)
>consensus
CUGGACAUCGAUGGCAAACGCCAAUAAAAGCGCGCUUAAUCAAUAAGAAAAACAGCUUCGAUUGGCGGCAAUUGUUGCCGCUCCAGAUCGCCAGAUCGACGAUUUAUGGUCCAUUGCAGA
.(((((((((..(((....((((((..((((...((((.....)))).......))))..))))))(((....))))))......((((....))))..)))).....)))))....... (-29.72 = -30.00 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	14,929,467 – 14,929,587
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-38.22
Consensus MFE	-33.90
Energy contribution	-34.02
Covariance contribution	0.12
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.89
SVM decision value	2.62
SVM RNA-class probability	0.995861
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14929467 120 - 27905053
UCUGCAAUGGACCAUAAAUCGUCGAUCUGGCGAUCUGGAGCGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAG
.......(((((........(((((..((((((.(......((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))).)))))))))))))))). ( -41.70)
>DroSec_CAF1 59450 120 - 1
UCUGCAAUGGACCAUAAAUCGUCGAUCUGGCGAUCUGGAGCGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAGCGAUGUCCAG
.......(((((........((((..(((((((.(......((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))).)))))))))))))))). ( -42.40)
>DroSim_CAF1 58149 120 - 1
UCUGCAAUGGACCAUAAAUCGUCGAUCUGGCGAUCUGGAGCGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAG
.......(((((........(((((..((((((.(......((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))).)))))))))))))))). ( -41.70)
>DroEre_CAF1 55999 119 - 1
UCUACCACGGACCAUAAAUCGUCGAUCU-GCGAUCUGGAGCGGCAACAAUUGUUGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAG
........((((........((((((..-((........))((((((....)))((((((.((((((((((.((.....))..))))).))))).))))))....))))))))))))).. ( -35.30)
>DroYak_CAF1 62800 119 - 1
ACUACCAUGCACCAUAAAUCGUCGAUCU-GCGAUCUGGAGCGGCUACAAUUGUUGCCAAUCGAAGCUGUUUUUCGAAUUGAUUAAGCGUGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAG
.....(((((.(((...(((((......-))))).))).))(((.((....)).((((((.((((((((((.((.....))..))))).))))).))))))....)))....)))..... ( -30.00)
>consensus
UCUGCAAUGGACCAUAAAUCGUCGAUCUGGCGAUCUGGAGCGGCAACAAUUGCCGCCAAUCGAAGCUGUUUUUCUUAUUGAUUAAGCGCGCUUUUAUUGGCGUUUGCCAUCGAUGUCCAG
.......(((((.....((((..((((....))))(((.((((((.....))))((((((.((((((((((.((.....))..))))).))))).))))))))...))).))))))))). (-33.90 = -34.02 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:16 2006